WARNING: PMID '30599920 referencing id but no author overlap' malformed and ignored WARNING: PMID '29654922 id not listed in paper but many others, title diff' malformed and ignored WARNING: PMID 'doublecheck supp 29687628' malformed and ignored ProteomeXchange Datasets

Home | Datasets | USI | Quetzal | PROXI

Last refresh: Wed Jun 10 14:00:03 PDT 2026

Articles in PubMed that reference a PXD that has not been announced

PXD074042 (from PRIDE)
Dataset title:
Possible reference: Basirattalab, A. et al. (2026) LC-MS profiling of prmt-1 and prmt-5 knockout C. elegans reveals PRMT-1 substrates and global proteome remodeling., bioRxiv, PMID 41756837

PXD073693 (from PRIDE)
Dataset title:
Possible reference: Tobias, F. et al. (2026) Global Proteomic Analysis of Colorectal Cancers Stratified by Microsatellite Instability Subtype Reveals Protein Differences., bioRxiv, PMID 41727057

PXD070795 (from PRIDE)
Dataset title:
Possible reference: Giuliano, A. et al. (2026) Integrated data-independent acquisition and thermal proteome profiling for proteomic characterization of lamotrigine-treated MCF-7 cells., Anal Bioanal Chem, PMID 42159682

PXD063599 (from PRIDE)
Dataset title:
Possible reference: Sharma, Y. et al. (2026) Multi-Omics Assessment of Primed Tissue-Specific MSCs-sEV to Unveil Their Regenerative Potential., Proteomics, PMID 41121583

PXD055114 (from MassIVE)
Dataset title:
Possible reference: Marchese, M. et al. (2025) CLN5 deficiency impairs glucose uptake and uncovers PHGDH as a potential biomarker in Batten disease., Mol Psychiatry, PMID 40346285

PXD053169 (from PRIDE)
Dataset title:
Possible reference: Kolokotronis, T. et al. (2024) Differential miRNA and Protein Expression Reveals miR-1285, Its Targets TGM2 and CDH-1, as Well as CD166 and S100A13 as Potential New Biomarkers in Patients with Diabetes Mellitus and Pancreatic Adenocarcinoma., Cancers (Basel), PMID 39123454

PXD052127 (from iProX)
Dataset title:
Possible reference: Zhao, W. et al. (2025) The Antioxidant Ergothioneine Alleviates Cisplatin-Induced Hearing Loss Through the Nrf2 Pathway., Antioxid Redox Signal, PMID 38770822

PXD051468 (from iProX)
Dataset title:
Possible reference: Weng, L. et al. (2024) Picoliter Single-Cell Reactor for Proteome Profiling by In Situ Cell Lysis, Protein Immobilization, Digestion, and Droplet Transfer., J Proteome Res, PMID 38833655

PXD044896 (from iProX)
Dataset title:
Possible reference: Chang, Q. et al. (2024) Comprehensive Urinary Proteome Profiling Analysis Identifies Diagnosis and Relapse Surveillance Biomarkers for Bladder Cancer., J Proteome Res, PMID 38787199

PXD043800 (from MassIVE)
Dataset title:
Possible reference: Abad, P. et al. (2024) Shotgun Characterization of the Circulating IgM Antigenome of an Infectious Pathogen by Immunocapture-LC-MS/MS from Dried Serum Spots., J Proteome Res, PMID 38183416

PXD041422 (from PRIDE)
Dataset title:
Possible reference: Paula, GM. et al. (2024) Profiling the neuroproteomics of honeybee brain: A clue for understanding the role of neuropeptides in the modulation of aggressivity., J Proteomics, PMID 38246419

PXD041026 (from MassIVE)
Dataset title:
Possible reference: Helbing, DL. et al. (2023) Proteomic analysis of peripheral nerve myelin during murine aging., Front Cell Neurosci, PMID 37964793

PXD040368 (from iProX)
Dataset title:
Possible reference: Gong, Z. et al. (2023) Label-free quantitative detection and comparative analysis of lysine acetylation during the different life stages of Eimeria tenella., J Proteome Res, PMID 37562054

PXD038173 (from iProX)
Dataset title:
Possible reference: Xiao, D. et al. (2023) Protein Biomarkers for the Identification of Forensically Relevant Human Hair from Different Body Parts in Intimate Contact Cases., J Proteome Res, PMID 37314855

PXD037541 (from iProX)
Dataset title:
Possible reference: Zhou, J. et al. (2023) Intra-Individual Variation in Disease-Specific IgG Fc Glycoform Ratios to Monitor the Disease Progression of Lung Cancer., J Proteome Res, PMID 36503223

PXD029768 (from PRIDE)
Dataset title:
Possible reference: Mirza, MR. et al. (2022) Label-free quantitation of the changes in salivary proteome associated with the chronic consumption of the betel nut (Areca catechu)., Mol Omics, PMID 34851339

PXD021573 (from MassIVE)
Dataset title:
Possible reference: Na, K. et al. (2020) Potential Regulatory Role of Human-Carboxylesterase-1 Glycosylation in Liver Cancer Cell Growth., J Proteome Res, PMID 33206527

PXD012244 (from PRIDE)
Dataset title:
Possible reference: Mulcahy, MJ. et al. (2020) Brain Region-Specific nAChR and Associated Protein Abundance Alterations Following Chronic Nicotine and/or Menthol Exposure., J Proteome Res, PMID 31657575

Summary of results:
18 Datasets of status 'ID requested' with a possible article found
26108 Datasets of status 'ID requested' with no articles found

Last refresh: Wed Jun 10 22:55:22 PDT 2026

Articles in PubMed that reference a PXD that has not been announced

PXD041026 (from MassIVE)
Dataset title:
Possible reference: Helbing, DL. et al. (2023) Proteomic analysis of peripheral nerve myelin during murine aging., Front Cell Neurosci, PMID 37964793

PXD037274 (from PRIDE)
Dataset title:
Possible reference: Wong, TL. et al. (2023) Glycoproteomic Analyses of Influenza A Viruses Using timsTOF Pro MS., J Proteome Res, PMID 36480915

PXD034407 (from PanoramaPublic)
Dataset title:
Possible reference: Husain, AA. et al. (2023) Development of multiple reaction monitoring (MRM) assays to identify Brucella abortus proteins in the serum of humans and livestock., Proteomics Clin Appl, PMID 35925648

Summary of results:
18 Datasets of status 'ID requested' with a possible article found
26108 Datasets of status 'ID requested' with no articles found

Announced datasets with no listed publication but with a title that brings up a hit in PubMed

RPXD056882 no publication (from jPOST)
Dataset title: An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes [Reanalysis: PXD004452]
Possible reference: Bekker-Jensen, DB. et al. (2017) An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes., Cell Syst, PMID 28601559

RPXD055697 no publication (from jPOST)
Dataset title: Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice [Reanalysis: JPST002136]
Possible reference: Ohira, T. et al. (2024) Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice., J Appl Physiol (1985), PMID 38328826

RPXD055696 no publication (from jPOST)
Dataset title: Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice [Reanalysis: JPST002136]
Possible reference: Ohira, T. et al. (2024) Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice., J Appl Physiol (1985), PMID 38328826

RPXD055695 no publication (from jPOST)
Dataset title: Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice [Reanalysis: JPST002136]
Possible reference: Ohira, T. et al. (2024) Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice., J Appl Physiol (1985), PMID 38328826

RPXD055694 no publication (from jPOST)
Dataset title: Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice [Reanalysis: JPST002136]
Possible reference: Ohira, T. et al. (2024) Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice., J Appl Physiol (1985), PMID 38328826

RPXD055693 no publication (from jPOST)
Dataset title: Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice [Reanalysis: JPST002136]
Possible reference: Ohira, T. et al. (2024) Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice., J Appl Physiol (1985), PMID 38328826

RPXD055692 no publication (from jPOST)
Dataset title: Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice [Reanalysis: JPST002136]
Possible reference: Ohira, T. et al. (2024) Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice., J Appl Physiol (1985), PMID 38328826

RPXD055691 no publication (from jPOST)
Dataset title: Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice [Reanalysis: JPST002136]
Possible reference: Ohira, T. et al. (2024) Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice., J Appl Physiol (1985), PMID 38328826

RPXD055690 no publication (from jPOST)
Dataset title: Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice [Reanalysis: JPST002136]
Possible reference: Ohira, T. et al. (2024) Plasminogen deficiency exacerbates skeletal muscle loss during mechanical unloading in developing mice., J Appl Physiol (1985), PMID 38328826

RPXD055685 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055684 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055683 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055682 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055681 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055680 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055679 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055678 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055677 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055676 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055675 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD055674 no publication (from jPOST)
Dataset title: Identification of gravity-responsive proteins in mouse soleus muscle using proteomic analysis [Reanalysis: JPST002107]
Possible reference: Kimura, Y. et al. (2024) Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry., Proteomics, PMID 38475964

RPXD034764 no publication (from jPOST)
Dataset title: JPST000090-2 Extended Coverage of Singly and Multiply Phosphorylated Peptides from a Single Titanium Dioxide Microcolumn [Reanalysis: JPST000090]
Possible reference: Wakabayashi, M. et al. (2015) Extended Coverage of Singly and Multiply Phosphorylated Peptides from a Single Titanium Dioxide Microcolumn., Anal Chem, PMID 26402220

RPXD034763 no publication (from jPOST)
Dataset title: JPST000090-1 Extended Coverage of Singly and Multiply Phosphorylated Peptides from a Single Titanium Dioxide Microcolumn [Reanalysis: JPST000090]
Possible reference: Wakabayashi, M. et al. (2015) Extended Coverage of Singly and Multiply Phosphorylated Peptides from a Single Titanium Dioxide Microcolumn., Anal Chem, PMID 26402220

RPXD034758 no publication (from jPOST)
Dataset title: JPST000589-6 Mass Spectrometry-compatible Subcellular Fractionation [Reanalysis: JPST000589]
Possible reference: Grote, E. et al. (2013) Using pure protein to build a multiple reaction monitoring mass spectrometry assay for targeted detection and quantitation., Methods Mol Biol, PMID 23606259

RPXD034757 no publication (from jPOST)
Dataset title: JPST000589-3 Mass Spectrometry-compatible Subcellular Fractionation [Reanalysis: JPST000589]
Possible reference: Grote, E. et al. (2013) Using pure protein to build a multiple reaction monitoring mass spectrometry assay for targeted detection and quantitation., Methods Mol Biol, PMID 23606259

RPXD034692 no publication (from jPOST)
Dataset title: PXD019423-1 MS analysis of SARS-CoV2 proteins from patient samples [Reanalysis: PXD019423]
Possible reference: Iles, RK. et al. (2022) Direct Detection of Glycated Human Serum Albumin and Hyperglycosylated IgG3 in Serum, by MALDI-ToF Mass Spectrometry, as a Predictor of COVID-19 Severity., Diagnostics (Basel), PMID 36292212

RPXD034691 no publication (from jPOST)
Dataset title: PXD019645-7 Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing [Reanalysis: PXD019645]
Possible reference: Zecha, J. et al. (2020) Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing., Mol Cell Proteomics, PMID 32591346

RPXD034690 no publication (from jPOST)
Dataset title: PXD019645-6 Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing [Reanalysis: PXD019645]
Possible reference: Zecha, J. et al. (2020) Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing., Mol Cell Proteomics, PMID 32591346

RPXD034689 no publication (from jPOST)
Dataset title: PXD019645-5 Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing [Reanalysis: PXD019645]
Possible reference: Zecha, J. et al. (2020) Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing., Mol Cell Proteomics, PMID 32591346

RPXD034688 no publication (from jPOST)
Dataset title: PXD019645-4 Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing [Reanalysis: PXD019645]
Possible reference: Zecha, J. et al. (2020) Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing., Mol Cell Proteomics, PMID 32591346

RPXD034687 no publication (from jPOST)
Dataset title: PXD019645-3 Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing [Reanalysis: PXD019645]
Possible reference: Zecha, J. et al. (2020) Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing., Mol Cell Proteomics, PMID 32591346

RPXD034686 no publication (from jPOST)
Dataset title: PXD019645-2 Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing [Reanalysis: PXD019645]
Possible reference: Zecha, J. et al. (2020) Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing., Mol Cell Proteomics, PMID 32591346

RPXD034685 no publication (from jPOST)
Dataset title: PXD019645-1 Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing [Reanalysis: PXD019645]
Possible reference: Zecha, J. et al. (2020) Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing., Mol Cell Proteomics, PMID 32591346

RPXD034670 no publication (from jPOST)
Dataset title: JPST000589-8 Mass Spectrometry-compatible Subcellular Fractionation [Reanalysis: JPST000589]
Possible reference: Grote, E. et al. (2013) Using pure protein to build a multiple reaction monitoring mass spectrometry assay for targeted detection and quantitation., Methods Mol Biol, PMID 23606259

RPXD034669 no publication (from jPOST)
Dataset title: JPST000589-7 Mass Spectrometry-compatible Subcellular Fractionation [Reanalysis: JPST000589]
Possible reference: Grote, E. et al. (2013) Using pure protein to build a multiple reaction monitoring mass spectrometry assay for targeted detection and quantitation., Methods Mol Biol, PMID 23606259

RPXD034667 no publication (from jPOST)
Dataset title: JPST000589-4 Mass Spectrometry-compatible Subcellular Fractionation [Reanalysis: JPST000589]
Possible reference: Grote, E. et al. (2013) Using pure protein to build a multiple reaction monitoring mass spectrometry assay for targeted detection and quantitation., Methods Mol Biol, PMID 23606259

RPXD034666 no publication (from jPOST)
Dataset title: JPST000589-2 Mass Spectrometry-compatible Subcellular Fractionation [Reanalysis: JPST000589]
Possible reference: Grote, E. et al. (2013) Using pure protein to build a multiple reaction monitoring mass spectrometry assay for targeted detection and quantitation., Methods Mol Biol, PMID 23606259

RPXD034665 no publication (from jPOST)
Dataset title: JPST000589-1 Mass Spectrometry-compatible Subcellular Fractionation [Reanalysis: JPST000589]
Possible reference: Grote, E. et al. (2013) Using pure protein to build a multiple reaction monitoring mass spectrometry assay for targeted detection and quantitation., Methods Mol Biol, PMID 23606259

RPXD034664 no publication (from jPOST)
Dataset title: JPST000115-1 Identification of ubiquitylation sites by K0-Ub [Reanalysis: JPST000115]
Possible reference: Oshikawa, K. et al. (2012) Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin., J Proteome Res, PMID 22053931

RPXD034321 no publication (from jPOST)
Dataset title: JPST000362 HeLa, Orbitrap Fusion Lumos, Parameter optimization [Reanalysis: JPST000362]
Possible reference: Greguš, M. et al. (2024) Improved Data Acquisition Settings on Q Exactive HF-X and Fusion Lumos Tribrid Orbitrap-Based Mass Spectrometers for Proteomic Analysis of Limited Samples., J Proteome Res, PMID 38690845

RPXD034300 no publication (from jPOST)
Dataset title: JPST000067 PC12, NF1 disease model, iTRAQ analysis [Reanalysis: JPST000067]
Possible reference: Hirayama, M. et al. (2013) Integrated proteomics identified novel activation of dynein IC2-GR-COX-1 signaling in neurofibromatosis type I (NF1) disease model cells., Mol Cell Proteomics, PMID 23358504

PXD079577 Dataset with its publication pending (from PRIDE)
Dataset title: A STRUBBELIG-NHL3 cell surface receptor complex mediates the response to cellulose deficiency in Arabidopsis
Possible reference: Chaudhary, A. et al. (2020) The Arabidopsis receptor kinase STRUBBELIG regulates the response to cellulose deficiency., PLoS Genet, PMID 31961852

PXD079457 Dataset with its publication pending (from PRIDE)
Dataset title: Diverse bacterial pattern recognition receptors sense the core phage proteome
Possible reference: Lee, H. et al. (2026) Diverse bacterial pattern recognition receptors sense the conserved phage proteome., bioRxiv, PMID 41542633

PXD079381 Dataset with its publication pending (from iProX)
Dataset title: Proteomic profiling of exosomes derived from gastric cancer-associated fibroblasts
Possible reference: Fan, Y. et al. (2025) Exosomal Galectin-3 promotes peritoneal metastases in gastric adenocarcinoma via microenvironment alterations., iScience, PMID 39811647

PXD079111 Dataset with its publication pending (from iProX)
Dataset title: Homoharringtonine (HHT) treatment on 4T1 cells
Possible reference: Zhang, X. et al. (2024) Homoharringtonine induces apoptosis of mammary carcinoma cells by inhibiting the AKT/mTOR signaling pathway., Vet Comp Oncol, PMID 38081660

PXD078834 Dataset with its publication pending (from iProX)
Dataset title: Anti-Toxoplasma effect of Panobinostat
Possible reference: Zhang, Y. et al. (2022) In vitro and in vivo anti-Toxoplasma activities of HDAC inhibitor Panobinostat on experimental acute ocular toxoplasmosis., Front Cell Infect Microbiol, PMID 36171756

PXD078716 Dataset with its publication pending (from iProX)
Dataset title: Proteins identified by TurboID-based proximity labeling of TgCoq4 in Toxoplasma gondii
Possible reference: Br�hlmann, F. et al. (2024) TurboID mapping reveals the exportome of secreted intrinsically disordered proteins in the transforming parasite Theileria annulata., mBio, PMID 38747635

PXD078700 Dataset with its publication pending (from iProX)
Dataset title: Untargeted Metabolomics of Plasma From Coronavirus Disease 2019 Patients One Year After Recover
Possible reference: Zhang, XT. et al. (2025) Untargeted Metabolomics of Plasma From Coronavirus Disease 2019 Patients One Year After Recovery., Zhongguo Yi Xue Ke Xue Yuan Xue Bao, PMID 40948255

PXD078636 Dataset with its publication pending (from jPOST)
Dataset title: Proteomics reveal serum biomarkers for early diagnosis in premature ovarian insufficiency
Possible reference: Liu, Z. et al. (2024) Identification of energy metabolism anomalies and serum biomarkers in the progression of premature ovarian failure via extracellular vesicles' proteomic and metabolomic profiles., Reprod Biol Endocrinol, PMID 39160560

PXD078567 no publication (from MassIVE)
Dataset title: Targeted extracellular degradation of LRP8 promotes ferroptosis in cancer cells
Possible reference: Zhao, F. et al. (2026) Targeted extracellular degradation of LRP8 promotes ferroptosis in cancer cells., bioRxiv, PMID 42239248

PXD078474 Dataset with its publication pending (from iProX)
Dataset title: KAT8-mediated PCBP1 acetylation drives neutrophil recruitment in papain-induced airway inflammation
Possible reference: Huang, R. et al. (2026) KAT8-mediated PCBP1 acetylation drives neutrophil recruitment in papain-induced airway inflammation., Am J Respir Cell Mol Biol, PMID 42244110

PXD078467 Dataset with its publication pending (from iProX)
Dataset title: Plasma Proteomic Analysis in Extremely Premature Infants with Brain Injury
Possible reference: Pereira-Fantini, PM. et al. (2024) Plasma Proteome Profiles Associated with Early Development of Lung Injury in Extremely Preterm Infants., Am J Respir Cell Mol Biol, PMID 39051934

PXD078456 Dataset with its publication pending (from iProX)
Dataset title: Phosphoproteomics and glycoproteomics of small cell lung cancer
Possible reference: Chen, YJ. et al. (2025) Metal Ion-Enhanced ZIC-cHILIC StageTip for N-Glycoproteomic and Phosphoproteomic Profiling in EGFR-Mutated Lung Cancer Cells., Mol Cell Proteomics, PMID 40154885

PXD078423 Zelter A, Riffle M, Merrihew GE, Mutawe B, Shulman N, Sanders JA, Noble WS, Johnson Erickson DP, Morimoto A, Shaver BA, Steins TN, Cao N, Ford EC, Rudnick PA, Chelsky D, Wan KH, Inman JL, Chang H, Snijders AM, Mao JH, Celniker SE, De Chant J, Obst-Huebl L (from PanoramaPublic)
Dataset title: A quantitative proteomics dataset for assessment and prediction of low dose X-ray radiation exposure in mice
Possible reference: Zelter, A. et al. (2026) A quantitative proteomics dataset for assessment and prediction of low dose X-ray radiation exposure in mice., bioRxiv, PMID 42239236

PXD078247 Dataset with its publication pending (from jPOST)
Dataset title: Serum proteome profiling of patients with non-small cell lung cancer treated with immune checkpoint blockade monotherapy
Possible reference: Mouri, A. et al. (2026) Analysis of Peripheral T Cell Profiling and Plasma Proteomics in Advanced NSCLC Patients Treated With Atezolizumab., Cancer Sci, PMID 41627979

PXD078239 no publication (from MassIVE)
Dataset title: Engineering lipid nanoparticle surface hydrophobicity to modulate nano-bio interface and enable tissue-selective mRNA delivery
Possible reference: Xu, Z. et al. (2026) Engineering lipid nanoparticle surface hydrophobicity to modulate nano-bio interface and enable tissue-selective mRNA delivery., Biomaterials, PMID 42085855

PXD078220 Dataset with its publication pending (from iProX)
Dataset title: Proteomics reveal serum biomarkers for early diagnosis in premature ovarian insufficiency
Possible reference: Liu, Z. et al. (2024) Identification of energy metabolism anomalies and serum biomarkers in the progression of premature ovarian failure via extracellular vesicles' proteomic and metabolomic profiles., Reprod Biol Endocrinol, PMID 39160560

PXD078180 Dataset with its publication pending (from iProX)
Dataset title: Proteomic study of NXDA on TGF-β-induced activation of rat cardiac fibroblasts
Possible reference: Edmunds, KJ. et al. (2025) Identification and characterization of a Fibrillin-1 derived matrikine for cardiac regeneration and repair., bioRxiv, PMID 41383782

PXD078149 no publication (from MassIVE)
Dataset title: Visual exoproteomics of Clostridium thermocellum during anaerobic biomass-degradation identifies functional spirosomes
Possible reference: Agdanowski, MP. et al. (2026) Visual exoproteomics of Clostridium thermocellum during anaerobic biomass-degradation identifies functional spirosomes., bioRxiv, PMID 42239438

PXD077909 Dataset with its publication pending (from PRIDE)
Dataset title: Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways
Possible reference: Olwal, CO. et al. (2025) Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways., bioRxiv, PMID 40661570

PXD077596 no publication (from MassIVE)
Dataset title: Targeted Proteomics for Quantitation of Pseudomonas aeruginosa Podovirus LUZ19
Possible reference: Nguyen, TD. et al. (2026) Translational Quantitative Proteomic Assay for Bacteriophages: A New Frontier in Phage Pharmaceutical Development., bioRxiv, PMID 42244767

PXD077545 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated top-down and bottom-up mass spectrometry enables precise characterization of proteoforms and their post-translational modifications within the protein corona
Possible reference: Mahmoudi, M. et al. (2025) Integrated top-down and bottom-up mass spectrometry enables precise characterization of proteoforms and their post-translational modifications within the protein corona., Res Sq, PMID 41001529

PXD077488 Dataset with its publication pending (from PRIDE)
Dataset title: Metaproteomics on biological phosphorus removal microbes
Possible reference: Elahinik, A. et al. (2022) Glycerol conversion by aerobic granular sludge., Water Res, PMID 36395566

PXD077396 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial surveillance activates the primary UPRmt
Possible reference: Deng, P. et al. (2019) Mitochondrial UPR repression during Pseudomonas aeruginosa infection requires the bZIP protein ZIP-3., Proc Natl Acad Sci U S A, PMID 30850535

PXD077365 Dataset with its publication pending (from iProX)
Dataset title: Molecular Glue Degraders of HuR to Treat BRAF-Mutant Colorectal Cancer
Possible reference: Lu, X. et al. (2026) Molecular glue degraders of HuR suppress BRAF-mutant colorectal cancer., Nature, PMID 42271059

PXD077337 no publication (from PanoramaPublic)
Dataset title: Multimodal analysis of molecular remodeling in aging spleen identified global and cell type specific changes
Possible reference: Vlajic, K. et al. (2026) Multimodal analysis of molecular remodeling in aging spleen identified global and cell type specific changes., bioRxiv, PMID 42079143

PXD077305 Dataset with its publication pending (from PRIDE)
Dataset title: Plasmodium falciparum PfMyoF with a Rab-like tail domain associates with perinuclear membranes and trafficking proteins
Possible reference: Holmes, AJ. et al. (2026) Plasmodium falciparum PfMyoF contains a Rab-like tail domain and associates with perinuclear membrane trafficking proteins., Commun Biol, PMID 42141018

PXD077246 Dataset with its publication pending (from PRIDE)
Dataset title: LC-MS on porcine pancreatic remodeling
Possible reference: Zhang, Q. et al. (2025) Agathis dammara Extract and its Monomer Araucarone Attenuate Abdominal Aortic Aneurysm in Mice., Cardiovasc Drugs Ther, PMID 37979015

PXD077187 Dataset with its publication pending (from PRIDE)
Dataset title: Establishment and application of a vesicle extraction method for clinical strains of Pseudomonas aeruginosa
Possible reference: Henriquez, T. et al. (2026) Establishment and application of a vesicle extraction method for clinical strains of Pseudomonas aeruginosa., Microbiol Spectr, PMID 42117715

PXD077140 Dataset with its publication pending (from PRIDE)
Dataset title: RNA-based full length immunoglobulin light chain sequencing reveals lambda constant domain mutations with potential implications for thermodynamic stability in light chain amyloidosis
Possible reference: Naser, E. et al. (2026) RNA-based full length immunoglobulin light chain sequencing reveals lambda constant domain mutations with potential implications for thermodynamic stability in light chain amyloidosis., Amyloid, PMID 42241304

PXD076840 Dataset with its publication pending (from iProX)
Dataset title: Comprehensive O-Phosphoproteomic Landscape of Corynebacterium glutamicum
Possible reference: Kim, D. et al. (2018) Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories., Appl Microbiol Biotechnol, PMID 30238140

PXD076837 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteomics of tau from tau knockout mice expressing tau or phospho-deficient tauT205A in active hippocampal cells upon fear conditioning
Possible reference: Hoos, MD. et al. (2013) Longitudinal study of differential protein expression in an Alzheimer's mouse model lacking inducible nitric oxide synthase., J Proteome Res, PMID 24006891

PXD076832 Dataset with its publication pending (from jPOST)
Dataset title: Proteome of stress granule during bacterial infection
Possible reference: Xian, W. et al. (2024) An Emerging Way for Bacteria to Engage with Host Cells via Protein ADP-riboxanation., Toxins (Basel), PMID 39591223

PXD076659 Dataset with its publication pending (from iProX)
Dataset title: Stearoyl-CoA desaturase is regulated upon viral infection and influences the activation of innate immune responses
Possible reference: Qin, D. et al. (2026) SCD1 licenses STING signaling through fatty acid desaturation-mediated membrane remodeling., Proc Natl Acad Sci U S A, PMID 41973923

PXD076520 Dataset with its publication pending (from PRIDE)
Dataset title: qChIP-MS reveals the local chromatin composition by label-free quantitative proteomics
Possible reference: Yong, WK. et al. (2026) qChIP-MS reveals the local chromatin composition by label-free quantitative proteomics., Nat Commun, PMID 42191725

PXD076496 Dataset with its publication pending (from PRIDE)
Dataset title: Statistical crystallography reveals an allosteric network in SARS-CoV-2 Mpro
Possible reference: Creon, A. et al. (2026) Statistical crystallography reveals an allosteric network in SARS-CoV-2 Mpro., Commun Biol, PMID 42069849

PXD076341 Dataset with its publication pending (from iProX)
Dataset title: The protein of adventitious root formation in Platycladus orientalis
Possible reference: Liao, T. et al. (2024) Uncovering protein regulation during adventitious root formation in Platycladus orientalis cuttings., Tree Physiol, PMID 39566084

PXD076334 no publication (from PanoramaPublic)
Dataset title: Sperm, egg and embryo proteins critical for genetic adaptation of herring to low salinity in the Baltic Sea
Possible reference: Ma, C. et al. (2026) Sperm, egg, and embryo proteins critical for genetic adaptation of herring to low salinity in the Baltic Sea., Proc Natl Acad Sci U S A, PMID 42113979

PXD076321 no publication (from MassIVE)
Dataset title: Sirtuin 1 Activation Mitigates Murine Vasculitis Severity by Promoting Mitophagy
Possible reference: Atici, AE. et al. (2025) Sirtuin 1 Activation Mitigates Murine Vasculitis Severity by Promoting Autophagy and Mitophagy., bioRxiv, PMID 40950042

PXD076268 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphorylation of rhizobial effector NopZ by soybean NORK promotes association with NENA and enhances nodulation
Possible reference: Lei, Y. et al. (2026) Phosphorylation of rhizobial effector NopZ by soybean NORK promotes association with NENA and enhances nodulation., Nat Commun, PMID 42014410

PXD076219 no publication (from PanoramaPublic)
Dataset title: Serum proteomics reveals distinct phenotypic signatures to IL-6 blockade between two immunotherapies
Possible reference: Sniezek, C. et al. (2026) Serum proteomics reveals distinct phenotypic signatures to IL-6 blockade between two immunotherapies., bioRxiv, PMID 41959136

PXD076218 Dataset with its publication pending (from jPOST)
Dataset title: Proteomics on the effect of cannabidiol on C6 rat glioma cell
Possible reference: Viwatpinyo, K. et al. (2026) Acute anti-proliferative and anti-migratory effects of cannabidiol on C6 rat glioma, SH-SY5Y human neuroblastoma, and HT22 mouse hippocampal neuronal cell cultures., Front Toxicol, PMID 42088408

PXD076189 Dataset with its publication pending (from PRIDE)
Dataset title: Structural Basis of Membrane Potential Coupled Vectorial COâ Hydration by the DAB2 Complex in Chemolithoautotrophs
Possible reference: Lo, YK. et al. (2026) Structural basis of membrane potential coupled vectorial CO₂ hydration by the DAB2 complex in chemolithoautotrophs., Nat Commun, PMID 42086541

PXD076033 no publication (from MassIVE)
Dataset title: Stage- and stress-specific phosphorylation of ribosomal protein Rps5 (uS7) by Smk1 and Kns1 kinases in Saccharomyces cerevisiae.
Possible reference: Resch, G. et al. (2026) Stage- and stress-specific phosphorylation of ribosomal protein Rps5 (uS7) by Smk1 and Kns1 kinases in Saccharomyces cerevisiae., Mol Biol Cell, PMID 42054203

PXD076006 Dataset with its publication pending (from iProX)
Dataset title: Quantitative analysis of mycelial protein in six samples
Possible reference: Kurt-Kızıldoğan, A. et al. (2023) In-depth comparative transcriptome analysis of Purpureocillium sp. CB1 under cadmium stress., Appl Microbiol Biotechnol, PMID 37436480

PXD075986 Dataset with its publication pending (from PRIDE)
Dataset title: Activated T cell extracellular vesicle DNA transfer enhances antigen presentation and anti-tumor immunity
Possible reference: Hu, M. et al. (2026) Activated T cell extracellular vesicle DNA transfer enhances antigen presentation and anti-tumor immunity., Cancer Cell, PMID 42066762

PXD075951 Dataset with its publication pending (from PRIDE)
Dataset title: Sucrose-Activated TOR and phyA Signaling Alleviates Shade-Mediated Inhibition of Leaf Development in Arabidopsis
Possible reference: Wang, J. et al. (2026) Sucrose-activated TOR and phyA signaling alleviates shade-mediated inhibition of leaf development in Arabidopsis., Nat Commun, PMID 42014725

PXD075939 Dataset with its publication pending (from jPOST)
Dataset title: Enhanced Proteolytic Stability and Distinct Mechanisms of a D-Amino Acid-Modified Antimicrobial Peptide Against Pseudomonas aeruginosa
Possible reference: Khlaychinda, S. et al. (2026) Enhanced proteolytic stability and distinct mechanisms of a D-amino acid-modified antimicrobial peptide against Pseudomonas aeruginosa., Sci Rep, PMID 42168333

PXD075925 Dataset with its publication pending (from iProX)
Dataset title: GL261 Affinity purification mass spectrometry
Possible reference: Chen, H. et al. (2022) [18F]BIBD-239: 18F-Labeled ER176, a Positron Emission Tomography Tracer Specific for the Translocator Protein., Mol Pharm, PMID 35671264

PXD075774 Dataset with its publication pending (from PRIDE)
Dataset title: Cupriavidus necator, an alternative source for isotopic enrichment of proteins expressed in insect cells for NMR
Possible reference: Gande, SL. et al. (2026) Cupriavidus necator, an alternative source for isotopic enrichment of proteins expressed in insect cells for NMR investigations., J Biomol NMR, PMID 41739268

PXD075756 Dataset with its publication pending (from PRIDE)
Dataset title: An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infection
Possible reference: Lebon, S. et al. (2026) An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infection., Nat Immunol, PMID 42120792

PXD075752 Dataset with its publication pending (from jPOST)
Dataset title: Cytoplasmic RNase III Drosha controls lipogenesis by noncanonical regulation of SREBP1
Possible reference: Nie, T. et al. (2026) Cytoplasmic RNase III Drosha controls lipogenesis by noncanonical regulation of SREBP1., Mol Cell, PMID 41997157

PXD075747 Dataset with its publication pending (from PRIDE)
Dataset title: Small Molecule Guided Small Molecule Guided Photocatalytic Proteomics Profiling of Amyloid Deposits in Hippocampal and Cortical Alzheimer’s Disease TissuesPhotocatalytic Proteomics Profiling of Amyloid Deposits in Hippocampal and Cortical Alzheimer’s
Possible reference: Yan, J. et al. (2026) Small Molecule Guided Photocatalytic Proteomics Profiling of Amyloid Deposits in Hippocampal and Cortical Alzheimer's Disease Tissues., Anal Chem, PMID 42080913

PXD075635 Dataset with its publication pending (from PRIDE)
Dataset title: A Fkh1/2 binding site array in the WHI5 promoter drives sub-scaling transcription
Possible reference: Kim, J. et al. (2025) A Fkh1/2 binding site array in the WHI5 promoter drives sub-scaling transcription., bioRxiv, PMID 41279126

PXD075554 Dataset with its publication pending (from PRIDE)
Dataset title: HIV-1 infection induces Vif-mediated SUMOylation of host RNA splicing factors important for proper viral RNA splicing
Possible reference: Kelenis, DP. et al. (2026) HIV-1 infection induces Vif-mediated SUMOylation of host RNA splicing factors important for proper viral RNA splicing., Proc Natl Acad Sci U S A, PMID 42048450

PXD075539 Dataset with its publication pending (from PRIDE)
Dataset title: Cell type-specific proximity labeling of organ secretomes reveals energy balance-dependent proteomic remodeling.
Possible reference: Plucińska, K. et al. (2026) Cell type-specific proximity labeling of organ secretomes reveals energy balance-dependent proteomic remodeling., bioRxiv, PMID 41648385

PXD075518 Dataset with its publication pending (from PRIDE)
Dataset title: Light-Controlled Disruption of Cancer Cell Dormancy via Photoswitchable Stress Hormone Receptor Degraders
Possible reference: Freitag, KM. et al. (2026) Light-controlled disruption of cancer cell dormancy via photoswitchable stress hormone receptor degraders., Proc Natl Acad Sci U S A, PMID 42166243

PXD075514 Dataset with its publication pending (from PRIDE)
Dataset title: Glycan-based Biological Degraders Targeting the Cytokine Immune Axis
Possible reference: Seifert, M. et al. (2026) Glycan-based biological degraders targeting the cytokine immune axis., Commun Biol, PMID 41965429

PXD075507 Dataset with its publication pending (from PRIDE)
Dataset title: Unveiling Alternate Pathways for SARS-CoV-2 Infection via Extracellular Vesicle-Mediated Transfer of ACE2 and TMPRSS2
Possible reference: Rea-Moreno, M. et al. (2026) Unveiling alternate pathways for SARS-CoV-2 infection via extracellular vesicle-mediated transfer of ACE2 and TMPRSS2., Nat Commun, PMID 41963354

PXD075504 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of lymphoma EV and serum samples
Possible reference: Lucien, F. et al. (2023) MIBlood-EV: Minimal information to enhance the quality and reproducibility of blood extracellular vesicle research., J Extracell Vesicles, PMID 38063210

PXD075483 Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics. Bo Wen, J. Sebastian Paez, Chris Hsu, Daniele Canzani, Alexis Taylor Chang, Nicholas Shulman, Brendan X. MacLean, Matthew D. Berg, Judi (from PanoramaPublic)
Dataset title: Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics
Possible reference: Wen, B. et al. (2026) Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics., bioRxiv, PMID 41959400

PXD075449 Dataset with its publication pending (from jPOST)
Dataset title: Gauging Lipid Vulnerabilities in mRNA-LNPs Under Various Environmental Stressors Through TIMS-TOF Analysis
Possible reference: Girgis, M. et al. (2026) Gauging lipid vulnerabilities in mRNA-LNPs under various environmental stressors through TIMS-TOF analysis., RSC Adv, PMID 41969377

PXD075386 Dataset with its publication pending (from iProX)
Dataset title: Targets identification of Biotin-Orf9b probe in HEK293T lysates
Possible reference: Huang, SQ. et al. (2015) Sensitive detection of point mutation using exponential strand displacement amplification-based surface enhanced Raman spectroscopy., Biosens Bioelectron, PMID 25461157

PXD075383 Dataset with its publication pending (from iProX)
Dataset title: Studies on the Development and Function of the Spines in Quasipaa spinosa
Possible reference: Wan, G. et al. (2024) Integrated Morphological, Comparative Transcriptomic, and Metabolomic Analyses Reveal Mechanisms Underlying Seasonal Patterns of Variation in Spines of the Giant Spiny Frog (Quasipaa spinosa)., Int J Mol Sci, PMID 39201815

PXD075364 no publication (from MassIVE)
Dataset title: Plasma Extracellular-Vesicle Proteomics Nominates Candidate Biomarkers of 177Lu-PSMA-617 Outcomes in Metastatic Prostate Cancer Patients
Possible reference: Arafa, AT. et al. (2026) Plasma extracellular vesicle proteomics nominates candidate biomarkers of 177Lu-PSMA-617 outcomes in metastatic prostate cancer patients., Cell Rep Med, PMID 42013849

PXD075361 Dataset with its publication pending (from jPOST)
Dataset title: A distinct tau oligomer strain defines the molecular and proteomic landscape of rapidly progressive Alzheimer’s disease
Possible reference: Saleem, T. et al. (2026) A distinct tau oligomer strain defines the molecular and proteomic landscape of rapidly progressive Alzheimer's disease., Acta Neuropathol, PMID 41851356

PXD075335 Dataset with its publication pending (from PRIDE)
Dataset title: The environmental stress response regulates biophysics of the cytoplasm and survival in quiescence
Possible reference: Kronig, L. et al. (2026) The environmental stress response regulates biophysics of the cytoplasm and survival in quiescence., J Cell Biol, PMID 42059870

PXD075265 Dataset with its publication pending (from PRIDE)
Dataset title: Uridine restores oocyte quality and mitigates female reproductive aging by inhibition of ferroptosis in mice
Possible reference: Chen, J. et al. (2026) Uridine restores oocyte quality and mitigates female reproductive aging by inhibition of ferroptosis in mice., Nat Commun, PMID 42056098

PXD075237 Dataset with its publication pending (from iProX)
Dataset title: A proteomic analysis in febrile seizures to identify diagnostic biomarkers and therapeutic targets
Possible reference: Fan, C. et al. (2026) Integrating plasma proteomics and cytokine profiles identifies immunopathogenic biomarkers for early acute-stage ANE in children., Transl Res, PMID 41655631

PXD075217 Dataset with its publication pending (from jPOST)
Dataset title: Siglec-7 inhibits TLR3-induced pro-inflammatory cytokine production from human monocytes and macrophages
Possible reference: Keeney, JN. et al. (2026) Siglec-7 inhibits TLR3-induced pro-inflammatory cytokine production from human monocytes and macrophages., Front Immunol, PMID 41924269

PXD075197 Dataset with its publication pending (from PRIDE)
Dataset title: Salmonella-derived heme inhibits macrophage phagocytosis and promotes infection in mice
Possible reference: Wang, Z. et al. (2026) Salmonella-derived haem inhibits macrophage phagocytosis and promotes infection in mice., Nat Microbiol, PMID 42009756

PXD075140 Dataset with its publication pending (from PRIDE)
Dataset title: Human Angiotensin-Converting Enzyme 2-Specific Benzothiazole Allosteric Inhibitor against Pan-Sarbecoviruses
Possible reference: Liu, L. et al. (2026) Human angiotensin‑converting enzyme 2‑specific benzothiazole-based allosteric inhibitor against pan‑sarbecoviruses., Nat Commun, PMID 42248906

PXD075090 no publication (from MassIVE)
Dataset title: Endurance exercise drives temporal and sexual dimorphic multi-omic adaptations in liver metabolism-Findings from MoTrPAC
Possible reference: Kelty, TJ. et al. (2025) Endurance exercise drives temporal and sexual dimorphic multi-omic adaptations in liver metabolism-Findings from MoTrPAC., bioRxiv, PMID 40475656

PXD075088 Dataset with its publication pending (from jPOST)
Dataset title: Plasma Proteomics Reveals Persistent and Surgery-Responsive Molecular Signatures in Osteoarthritis Patients
Possible reference: Sari-Ak, D. et al. (2026) Plasma Proteomics Reveals Persistent and Surgery-Responsive Molecular Signatures in Osteoarthritis Patients., Int J Mol Sci, PMID 41898721

PXD075065 no publication (from MassIVE)
Dataset title: An orally active dual CBP/p300 degrader targets core dependencies of multiple myeloma
Possible reference: Tiwari, PK. et al. (2026) An orally active dual CBP/p300 degrader targets core dependencies of multiple myeloma., Cell Rep, PMID 42228563

PXD074954 Dataset with its publication pending (from PRIDE)
Dataset title: A human iPSC-derived sensory neuron platform for high-throughput discovery of neuroprotectants against chemotherapy-induced peripheral neuropathy
Possible reference: Petrova, V. et al. (2026) A human iPSC-derived sensory neuron platform for high-throughput discovery of neuroprotectants against chemotherapy-induced peripheral neuropathy., Cell Rep Med, PMID 42097147

PXD074952 no publication (from MassIVE)
Dataset title: Endurance exercise drives temporal and sexual dimorphic multi-omic adaptations in liver metabolism-Findings from MoTrPAC
Possible reference: Kelty, TJ. et al. (2025) Endurance exercise drives temporal and sexual dimorphic multi-omic adaptations in liver metabolism-Findings from MoTrPAC., bioRxiv, PMID 40475656

PXD074949 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of P-body components by proximity labeling and IP-MSMS
Possible reference: Yu, H. et al. (2024) Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in Drosophila mushroom body contributing to olfactory learning., Elife, PMID 38619103

PXD074830 Dataset with its publication pending (from PRIDE)
Dataset title: dia-PASEF Enables Rapid Profiling of the Human Secretome for Deeper Insights into Cellular Dynamics and Inflammatory Mechanisms
Possible reference: Tayler, CL. et al. (2026) dia-PASEF Enables Rapid Profiling of the Human Secretome for Deeper Insights into Cellular Dynamics and Inflammatory Mechanisms., Mol Cell Proteomics, PMID 42214753

PXD074663 Dataset with its publication pending (from jPOST)
Dataset title: Cross-Linking and Covalent Labeling Mass Spectrometry Reveal Proteoform-Driven Conformational Changes in Alpha Synuclein
Possible reference: Dollar, AN. et al. (2026) Cross-Linking and Covalent Labeling Mass Spectrometry Reveal Proteoform-Driven Conformational Changes in Alpha Synuclein., Anal Chem, PMID 41574935

PXD074647 no publication (from MassIVE)
Dataset title: KRAS4A Promotes Oligomerization of Hexokinase 1 on Mitochondria
Possible reference: Nuevo-Tapioles, C. et al. (2026) KRAS4A promotes oligomerization of hexokinase 1 on mitochondria., Cell Rep, PMID 42241281

PXD074624 Dataset with its publication pending (from PRIDE)
Dataset title: Sex-specific KDM6A-HNF4A-CREBH network controls lipoprotein cholesterol metabolism and atherosclerosis via epigenetic reprograming of hepatocytes.
Possible reference: Chen, L. et al. (2026) Sex-specific KDM6A-HNF4A-CREBH network controls lipoprotein cholesterol metabolism and atherosclerosis via epigenetic reprograming of hepatocytes., Nat Commun, PMID 41872164

PXD074602 no publication (from MassIVE)
Dataset title: Identification of a component of the Tubulin Poly-glutamylase Complex required for phosphoinositide homeostasis and cilium assembly and maintenance
Possible reference: Badarudeen, B. et al. (2026) Identification of a component of the tubulin poly-glutamylase complex required for phosphoinositide homeostasis and cilium assembly and maintenance., Nat Commun, PMID 42140944

PXD074586 Dataset with its publication pending (from jPOST)
Dataset title: Organ-Specific Proteomic Responses to Tetrodotoxin Administration in the Liver and Skin of Takifugu rubripes
Possible reference: Ono, N. et al. (2026) Organ-specific proteomic responses to tetrodotoxin administration in the liver and skin of Takifugu rubripes., Toxicon, PMID 41895378

PXD074523 Dataset with its publication pending (from PRIDE)
Dataset title: Stress-induced ribosome degradation in Bacillus subtilis is mediated by the RNase Y-specificity complex
Possible reference: Cornejo, FA. et al. (2026) Stress-induced ribosome degradation in Bacillus subtilis is mediated by the RNase Y-specificity complex., Nat Commun, PMID 42230597

PXD074503 Dataset with its publication pending (from PRIDE)
Dataset title: High-risk EBV promotes immune evasion in nasopharyngeal carcinoma by upregulating HLA-DP via the encoded BALF2-HR variant
Possible reference: Meng, Y. et al. (2026) High-risk EBV promotes immune evasion in nasopharyngeal carcinoma by upregulating HLA-DP via the encoded BALF2-HR variant., Nat Commun, PMID 41896559

PXD074485 Dataset with its publication pending (from PRIDE)
Dataset title: Identical Tumor Antigen Peptides by Canine and Human MHC Class I
Possible reference: Kaabinejadian, S. et al. (2026) Presentation of identical tumor antigen peptides by canine and human MHC class I., iScience, PMID 42199926

PXD074452 Dataset with its publication pending (from PRIDE)
Dataset title: proteomics conducted in control and KIF11-depleted HRECs
Possible reference: Saddala, MS. et al. (2020) Placental growth factor regulates the pentose phosphate pathway and antioxidant defense systems in human retinal endothelial cells., J Proteomics, PMID 32058040

PXD074420 no publication (from MassIVE)
Dataset title: Soil microbiome pH perturbation proteomics
Possible reference: Priya, P. et al. (2021) Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health., J Microbiol Methods, PMID 33839214

PXD074388 Dataset with its publication pending (from PRIDE)
Dataset title: Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8
Possible reference: G�zquez-Guti�rrez, A. et al. (2026) Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8., Nucleic Acids Res, PMID 41784265

PXD074386 no publication (from MassIVE)
Dataset title: Preclinical evaluation of waste-derived pomegranate extract (PWE) as potential preventing and therapeutic for benign prostatic hyperplasia
Possible reference: Consoli, V. et al. (2026) Preclinical evaluation of waste-derived pomegranate extract (PWE) as a potential preventing and therapeutic agent for benign prostatic hyperplasia., Front Mol Biosci, PMID 41797990

PXD074382 Dataset with its publication pending (from PRIDE)
Dataset title: SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis
Possible reference: Liu, S. et al. (2026) SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis., bioRxiv, PMID 41676593

PXD074379 Dataset with its publication pending (from jPOST)
Dataset title: Phosphoproteomic of fibroblast from celiac disease patients compared to controls
Possible reference: Montefusco, A. et al. (2026) Proteomic Analysis Highlights Peculiar Protein and Phosphoprotein Profiles in Dermal Fibroblasts from Celiac Disease Patients., Int J Mol Sci, PMID 42123523

PXD074341 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis highlights peculiar protein and phosphoprotein profiles in dermal fibroblasts from celiac disease patients
Possible reference: Montefusco, A. et al. (2026) Proteomic Analysis Highlights Peculiar Protein and Phosphoprotein Profiles in Dermal Fibroblasts from Celiac Disease Patients., Int J Mol Sci, PMID 42123523

PXD074306 no publication (from MassIVE)
Dataset title: CryAB-driven amyloidogenesis in Drosophila muscle engages extracellular vesicle pathways for cellular release
Possible reference: Zhao, Z. et al. (2026) CryAB-driven amyloidogenesis in Drosophila muscle engages extracellular vesicle pathways for cellular release., iScience, PMID 42006321

PXD074256 no publication (from MassIVE)
Dataset title: Pilot Study on Cannabis-Induced Alterations in Platelet Function: Implications for Transfusion Medicine
Possible reference: Laflamme, G. et al. (2026) Pilot study on cannabis-induced alterations in platelet function: implications for transfusion medicine., Platelets, PMID 41870043

PXD074179 Dataset with its publication pending (from PRIDE)
Dataset title: CDK1-dependent N-terminal NuMA phosphorylation promotes dynein-dynactin-NuMA assembly for accurate chromosome segregation
Possible reference: van Toorn, M. et al. (2026) CDK1-dependent N-terminal NuMA phosphorylation promotes dynein-dynactin-NuMA assembly for accurate chromosome segregation., Cell Rep, PMID 41880324

PXD074112 no publication (from MassIVE)
Dataset title: Epigenetic and transcriptomic impacts of ethanol vary by brain region and extent of exposure
Possible reference: Periandri, EM. et al. (2026) Epigenetic and Transcriptomic Impacts of Ethanol Vary by Brain Region and Extent of Exposure., eNeuro, PMID 41912333

PXD074101 no publication (from MassIVE)
Dataset title: Developmental Reprogramming Underlies Chemotherapy Resistance in Favorable-Histology Wilms Tumor
Possible reference: Fleming, AM. et al. (2026) Developmental reprogramming underlies chemotherapy resistance in favorable-histology Wilms tumor., Cell Rep, PMID 41850280

PXD074049 Dataset with its publication pending (from PRIDE)
Dataset title: Recombinant dimeric PICK1 protein inhibitors for long-term relief of chronic pain by AAV therapeutics
Possible reference: Noes-Holt, G. et al. (2026) Recombinant dimeric PICK1 peptide inhibitors for long-term relief of chronic pain by AAV therapeutics., Cell Rep Med, PMID 42134332

PXD074043 Dataset with its publication pending (from iProX)
Dataset title: Proteomic for influenza A virus infected airway ciliated cell
Possible reference: Thomas, SN. et al. (2023) Down syndrome is associated with altered frequency and functioning of tracheal multiciliated cells, and response to influenza virus infection., iScience, PMID 37554445

PXD074027 Dataset with its publication pending (from PRIDE)
Dataset title: Exercise beneficially reshapes fasted rat skeletal muscle involving the combined action of beta-hydroxybutyrate and palmitoleic acid
Possible reference: Lara Castillo, NA. et al. (2026) Exercise beneficially reshapes fasted rat skeletal muscle involving the combined action of β-hydroxybutyrate and palmitoleic acid., Am J Physiol Cell Physiol, PMID 41740633

PXD074014 Dataset with its publication pending (from PRIDE)
Dataset title: HR3/RORÎ±-mediated cholesterol sensing regulates TOR signaling
Possible reference: Lassen, M. et al. (2026) HR3/RORα-mediated cholesterol sensing regulates TOR signaling., Nat Commun, PMID 41912517

PXD074004 no publication (from MassIVE)
Dataset title: Reliable Identification of Cardiac Maturation Markers Using Robust and Flexible Label-Free Proteomic Quantitation by Spectral Counting of Relatively Abundant Proteins
Possible reference: Chang, G. et al. (2026) Reliable Identification of Cardiac Maturation Markers Using Robust and Flexible Label-Free Proteomic Quantitation by Spectral Counting on Relatively Abundant Proteins., J Proteome Res, PMID 41770908

PXD073925 Dataset with its publication pending (from PRIDE)
Dataset title: Recombinant dimeric PICK1 protein inhibitors for long-term relief of chronic pain by AAV therapeutics
Possible reference: Noes-Holt, G. et al. (2026) Recombinant dimeric PICK1 peptide inhibitors for long-term relief of chronic pain by AAV therapeutics., Cell Rep Med, PMID 42134332

PXD073881 no publication (from MassIVE)
Dataset title: Single-Cell Proteomics of Human Peripheral Blood Mononuclear Cells Exceeding 600 Cells per Day
Possible reference: Fulcher, JM. et al. (2026) Single-Cell Proteomics of Human Peripheral Blood Mononuclear Cells Exceeding 600 Cells per Day., bioRxiv, PMID 41676720

PXD073797 no publication (from MassIVE)
Dataset title: Development of PolyHis-Targeting PROTAC Degraders
Possible reference: Chen, H. et al. (2026) Development of PolyHis-Targeting PROTAC Degraders., Angew Chem Int Ed Engl, PMID 41630184

PXD073733 no publication (from MassIVE)
Dataset title: Characterization and Amelioration of Filtration Difficulties Encountered in Metabolomic Studies of Clostridium thermocellum at Elevated Sugar Concentrations
Possible reference: Sharma, BD. et al. (2023) Characterization and Amelioration of Filtration Difficulties Encountered in Metabolomic Studies of Clostridium thermocellum at Elevated Sugar Concentrations., Appl Environ Microbiol, PMID 37039651

PXD073717 no publication (from MassIVE)
Dataset title: Loss of function variants in SAXO6, encoding a microtubule inner protein of photoreceptor cilia, causes a late-onset retinal dystrophy
Possible reference: Moye, AR. et al. (2026) Loss-of-function variants in SAXO6, encoding a microtubule inner protein of photoreceptor cilia, cause a late-onset retinal dystrophy., Am J Hum Genet, PMID 41742423

PXD073702 Dataset with its publication pending (from PRIDE)
Dataset title: 5âtRNA-derived fragments modulate beta-cell homeostasis and islet macrophage activation in type 2 diabetes
Possible reference: Cosentino, C. et al. (2026) 5'tRNA-derived fragments modulate β-cell homeostasis and islet macrophage activation in type 2 diabetes., Nat Commun, PMID 42082525

PXD073685 Dataset with its publication pending (from PRIDE)
Dataset title: Synaptic vesicles that store monoamines and glutamate differ in protein composition
Possible reference: Asmerian, H. et al. (2025) Synaptic vesicles that store monoamines and glutamate differ in protein composition., bioRxiv, PMID 40661501

PXD073656 no publication (from MassIVE)
Dataset title: Single-Cell Proteomics Reveals Cytoplasmic Defects in Patl2-Deficient Oocytes Rescued by Spindle Transfer
Possible reference: Cardona Barber�n, A. et al. (2026) Single-cell proteomics reveals cytoplasmic defects in Patl2-deficient oocytes rescued by spindle transfer., Hum Reprod, PMID 42062216

PXD073650 Dataset with its publication pending (from PRIDE)
Dataset title: Macrophage SH3GLB1 is required for Rab7-1 mediated mitophagy in inflammation during acute lung injury
Possible reference: Ning, H. et al. (2026) Macrophage SH3 domain‑containing GRB2‑like protein B1 is required for Rab7‑mediated mitophagy in inflammation during sea water drowning acute lung injury., Int J Mol Med, PMID 41891976

PXD073617 no publication (from MassIVE)
Dataset title: Metabolic plasticity and optimal redox homeostasis are essential for efficient metastatic colonization
Possible reference: Grace, E. et al. (2026) Metabolic plasticity and optimal redox homeostasis are essential for efficient metastatic colonization., Mol Metab, PMID 42155637

PXD073579 no publication (from MassIVE)
Dataset title: A non-canonical histidine kinase (Rv1127c, VadK) from Mycobacterium tuberculosis.
Possible reference: Pascoe, J. et al. (2025) VadK, a Non-Canonical Kinase that Regulates the Methylcitrate Cycle and is Essential for Mycobacterium tuberculosis Virulence., bioRxiv, PMID 41279192

PXD073497 no publication (from PanoramaPublic)
Dataset title: Identification and characterization of a novel aldehyde metabolite of WIN18,446 and associated WIN18,446-ALDH1A2 protein adducts using mass spectrometry
Possible reference: Zelter, A. et al. (2026) Identification and characterization of a novel aldehyde metabolite of WIN18,446 and associated WIN18,446-ALDH1A2 protein adducts using mass spectrometry., Drug Metab Rev, PMID 42124481

PXD073487 no publication (from MassIVE)
Dataset title: Native yeast kinetochore structures identify an essential inner kinetochore interaction.
Possible reference: Jiang, M. et al. (2026) Native yeast kinetochore structures identify an essential inner kinetochore interaction., bioRxiv, PMID 41659542

PXD073462 Dataset with its publication pending (from PRIDE)
Dataset title: Outer Membrane Vesicles Secreted by Bacteroides fragilis Inhibit CFTR Chloride Secretion by Human Colon Organoids
Possible reference: Barnaby, R. et al. (2025) Outer Membrane Vesicles Secreted by Bacteroides fragilis Inhibit CFTR Chloride Secretion by Human Colon Organoids., bioRxiv, PMID 40894535

PXD073451 Dataset with its publication pending (from PRIDE)
Dataset title: Cytoplasmic lattices are megadalton storage complexes for tubulin and ubiquitination factors in mammalian oocytes
Possible reference: Kılıç, ZI. et al. (2026) Cytoplasmic lattices are megadalton storage complexes in mammalian oocytes., Nature, PMID 41986725

PXD073327 Dataset with its publication pending (from iProX)
Dataset title: Simultaneous profiling of phosphorylation and S-nitrosylation during maize seed germination
Possible reference: Zhang, W. et al. (2026) Temporal dynamics of protein phosphorylation and S-nitrosylation direct maize seed germination programs., Plant J, PMID 41911598

PXD073314 Dataset with its publication pending (from iProX)
Dataset title: Multi-omics Analysis Reveals Molecular Regulation of Ovarian ageing in Chickens
Possible reference: Wei, S. et al. (2024) Quercetin mitigates iron-induced cell death in chicken granulosa cell., J Anim Sci Biotechnol, PMID 39645563

PXD073312 Dataset with its publication pending (from iProX)
Dataset title: Bacillus subtilis-derived extracellular vesicles_extracellular vesicles
Possible reference: Chen, J. et al. (2026) Bacillus subtilis-derived extracellular vesicles displaying superoxide dismutase exhibit superior antioxidant ability in ameliorating skin damage., Int J Biol Macromol, PMID 41483878

PXD073308 no publication (from MassIVE)
Dataset title: The Desmoglein 2 interactome in primary neonatal cardiomyocytes
Possible reference: Li, Y. et al. (2025) The Desmoglein 2 interactome in primary neonatal cardiomyocytes., bioRxiv, PMID 40661579

PXD073277 no publication (from MassIVE)
Dataset title: Integrative nuclear and total proteomics of compound leaves in semi-leafless and leafed pea cultivars reveal regulatory cues in leaf development
Possible reference: Tripathi, RK. et al. (2026) Integrative nuclear and total proteomics of compound leaves in semi-leafless and leafed pea cultivars reveal regulatory cues in leaf development., BMC Plant Biol, PMID 41781886

PXD073248 Dataset with its publication pending (from PRIDE)
Dataset title: Degradation of G-Quadruplex Binding Proteins in Chromatin Using G4-Ligand-Based PROTACs
Possible reference: Wang, Z. et al. (2026) Degradation of G-quadruplex-binding proteins in chromatin using G4-ligand-based proteolysis-targeting chimeras., Nat Chem, PMID 41857122

PXD073224 Dataset with its publication pending (from iProX)
Dataset title: Transgenic hookworm secretes anti-tetrodotoxin human single chain antibody
Possible reference: Singh, KS. et al. (2026) Transgenic hookworm secretes anti-tetrodotoxin human single chain antibody., Nat Commun, PMID 42236698

PXD073158 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of extracellular vesicles from engineered Lactobacillus plantarum
Possible reference: Bajic, SS. et al. (2020) Proteomic profile of extracellular vesicles released by Lactiplantibacillus plantarum BGAN8 and their internalization by non-polarized HT29 cell line., Sci Rep, PMID 33311536

PXD073085 Dataset with its publication pending (from iProX)
Dataset title: VdEGe1, a Cell Wall-Degrading Enzyme Gene from Verticillium dahliae Required for Cotton Pathogenesis
Possible reference: Li, Y. et al. (2026) VdEGe1, a cell wall-degrading enzyme gene from Verticillium dahliae required for cotton pathogenesis., BMC Microbiol, PMID 41923196

PXD073056 no publication (from MassIVE)
Dataset title: Lipoproteome of Parageobacillus thermoglucosidasius
Possible reference: Jackson, M. et al. (2026) Exploring the lipoproteome of Parageobacillus thermoglucosidasius., Access Microbiol, PMID 41971188

PXD073041 Dataset with its publication pending (from iProX)
Dataset title: Proteomics and acetylated proteomics of cartilage degeneration in osteoarthritis
Possible reference: Yu, J. et al. (2025) Stress causes lipid droplet accumulation in chondrocytes by impairing microtubules., Osteoarthritis Cartilage, PMID 39730095

PXD073004 no publication (from MassIVE)
Dataset title: Tissue-layer resolved proteome landscape of Crohns disease strictures highlights potential drivers of fibrosis progression
Possible reference: Alfredsson, J. et al. (2026) Tissue-layer-resolved proteome landscape of Crohn's disease strictures highlights potential drivers of fibrosis progression., JCI Insight, PMID 41665933

PXD073001 no publication (from MassIVE)
Dataset title: RHOA Controls Oncogenic B-Cell Receptor Signaling in Aggressive Lymphoma
Possible reference: Jacobs, AN. et al. (2026) RHOA controls oncogenic B cell receptor signaling in aggressive lymphoma., Proc Natl Acad Sci U S A, PMID 41591906

PXD072930 Dataset with its publication pending (from iProX)
Dataset title: Exosome-Mediated Bidirectional Immune Dysregulation in Tuberculosis: Proteomic Profiling Reveals Strain-Specific Strategies of Virulent H37Rv and Attenuated H37Ra
Possible reference: Zhang, X. et al. (2025) Exosome-mediated bidirectional immune dysregulation in tuberculosis: proteomic profiling reveals strain-specific strategies of virulent H37Rv and attenuated H37Ra., Front Immunol, PMID 41660623

PXD072897 Dataset with its publication pending (from iProX)
Dataset title: A Plasma Proteomic Signature of the Actin-Coagulation Axis Accurately Predicts Progression to Active Tuberculosis
Possible reference: Lu, P. et al. (2025) A plasma proteomic signature of the actin-coagulation axis accurately predicts progression to active tuberculosis., Front Microbiol, PMID 41669692

PXD072889 no publication (from MassIVE)
Dataset title: Nuclear proteome map of mouse heart chamber
Possible reference: Eslami, SS. et al. (2026) Nuclear Proteome Map of Mouse Heart Chambers., Mol Cell Proteomics, PMID 42140427

PXD072864 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of the parasitic nematode Ascaridia galli
Possible reference: Feix, AS. et al. (2026) Proteomic profiling of Ascaridia galli reveals sex- and stage-specific protein signatures., Vet Parasitol, PMID 41581493

PXD072811 no publication (from MassIVE)
Dataset title: Characterization of large extracellular vesicles released by apoptotic and pyroptotic cells
Possible reference: Khamari, D. et al. (2026) Characterization of Large Extracellular Vesicles Released by Apoptotic and Pyroptotic Cells., Int J Mol Sci, PMID 41596620

PXD072807 no publication (from MassIVE)
Dataset title: Oxidative stress causes a reversible decrease of deubiquitylases activity in old vertebrate brains - DUB
Possible reference: Sahu, AK. et al. (2026) Oxidative stress causes a reversible decrease of deubiquitylases activity in old vertebrate brains., Nat Commun, PMID 42014687

PXD072785 Dataset with its publication pending (from iProX)
Dataset title: Mammalian M�ller glia Fate Determination between Gliosis and Reprogramming
Possible reference: Yin, Z. et al. (2024) Identifying Hmga2 preserving visual function by promoting a shift of M�ller glia cell fate in mice with acute retinal injury., Stem Cell Res Ther, PMID 38414051

PXD072756 Dataset with its publication pending (from PRIDE)
Dataset title: ACSL4-Associated Lipid Metabolism is a Distinct Therapeutic Vulnerability in KMT2A-Rearranged Acute Myeloid Leukemia
Possible reference: Sch�fer, S. et al. (2026) ACSL4-associated lipid metabolism is a distinct therapeutic vulnerability in KMT2A-rearranged acute myeloid leukemia., Cell Rep, PMID 41712378

PXD072748 Dataset with its publication pending (from PRIDE)
Dataset title: IQGAP3 bridges matrix stiffness with glioma stem cell maintenance and radioresistance by stabilizing SOX2
Possible reference: Zhang, P. et al. (2026) IQGAP3 bridges matrix stiffness with glioma stem cell maintenance and radioresistance by stabilizing SOX2., Nat Commun, PMID 42251046

PXD072740 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of neuron-derived exosomes from a cohort of familial Alzheimer's disease patients
Possible reference: Eitan, E. et al. (2023) Synaptic proteins in neuron-derived extracellular vesicles as biomarkers for Alzheimer's disease: novel methodology and clinical proof of concept., Extracell Vesicles Circ Nucl Acids, PMID 37842184

PXD072725 Dataset with its publication pending (from PRIDE)
Dataset title: IQGAP3 bridges matrix stiffness with glioma stem cell maintenance and radioresistance by stabilizing SOX2
Possible reference: Zhang, P. et al. (2026) IQGAP3 bridges matrix stiffness with glioma stem cell maintenance and radioresistance by stabilizing SOX2., Nat Commun, PMID 42251046

PXD072715 Dataset with its publication pending (from PRIDE)
Dataset title: Chaperone-mediated autophagy is required for regulatory T cell function
Possible reference: Harrison, R. et al. (2026) Chaperone-mediated autophagy is required for regulatory T cell function., Nat Commun, PMID 42173902

PXD072710 Dataset with its publication pending (from PRIDE)
Dataset title: Effects of human immunoglobulins on Cryptococcus neoformans morphology and proteome
Possible reference: Souza, TN. et al. (2026) Effects of human immunoglobulins on Cryptococcus neoformans morphology and proteome., mBio, PMID 41660986

PXD072694 no publication (from MassIVE)
Dataset title: Targeting CD4 + T cell epitopes conserved across bacterial species for broadly acting bacterial vaccines
Possible reference: Braverman, J. et al. (2026) Conserved CD4+ T cell staphylococcal and streptococcal epitopes enable broad-acting vaccines in mice., Nat Microbiol, PMID 41714815

PXD072679 Dataset with its publication pending (from iProX)
Dataset title: Cryo-EM Structures of ALECT2 Filaments from Human Renal Biopsies
Possible reference: Zheng, JL. et al. (2026) Cryo-EM structures of ALECT2 filaments from human renal biopsies., Nat Commun, PMID 42173881

PXD072640 Dataset with its publication pending (from iProX)
Dataset title: CRL4AMBRA1 mediated progesterone receptor degradation drives progestin resistance and represents a therapeutic vulnerability in endometrial cancer
Possible reference: Sheng, Y. et al. (2026) CRL4AMBRA1-mediated progesterone receptor degradation drives progestin resistance and represents a therapeutic vulnerability in endometrial cancer., Int J Biol Sci, PMID 42157930

PXD072638 Dataset with its publication pending (from iProX)
Dataset title: Fusobacterium nucleatum Promotes PD-L1 Expression in Macrophages by Inducing Exosomal lncRNA MANCR from Colorectal Cancer Cells
Possible reference: Han, S. et al. (2026) Fusobacterium nucleatum Promotes Exosomal LncRNA MANCR Secretion from Colorectal Cancer Cells to Induce PD-L1 Expression in Macrophages., Cancer Res, PMID 42202059

PXD072588 Dataset with its publication pending (from PRIDE)
Dataset title: Composite SMG5-1 SMG6 PIN domain formation is essential for NMD
Possible reference: Kurscheidt, K. et al. (2026) Composite SMG5-SMG6 PIN domain formation is essential for NMD., Nat Commun, PMID 41714610

PXD072555 Dataset with its publication pending (from iProX)
Dataset title: Identify the Therapeutic Role and Potential Mechanism of Î±-Cyperone in diminished ovarian reserve Based on Network Pharmacology, Molecular docking, Lip-MS and Experimental Validation
Possible reference: Guo, J. et al. (2025) Identify the therapeutic role and potential mechanism of α-cyperone in diminished ovarian reserve based on network pharmacology, molecular docking, Lip-MS and experimental validation., Front Pharmacol, PMID 41625331

PXD072553 Dataset with its publication pending (from iProX)
Dataset title: Endoplasmic Reticulum Stress-induced Histone Lactylation Mediating Immune Escape of Gastric Cancer via PDIA6 Overexpression in Dendritic Cells
Possible reference: Tu, C. et al. (2026) Endoplasmic reticulum stress-induced histone lactylation mediating immune escape of gastric cancer via PDIA6 overexpression in dendritic cells., Cell Death Dis, PMID 41896533

PXD072536 Dataset with its publication pending (from iProX)
Dataset title: MetaSpaR-DIA: Enabling Accurate Metaproteomic DIA Analysis Independent of Spectral Libraries and Metagenomic Sequencing
Possible reference: Wu, E. et al. (2024) High-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics., Anal Chem, PMID 38180447

PXD072514 no publication (from MassIVE)
Dataset title: Hydrogen-deuterium exchange mass spectrometry reveals an antibody-induced allosteric pathway driving SARS-CoV-2 spike trimer disassembly
Possible reference: Luo, Y. et al. (2026) Hydrogen-Deuterium Exchange Mass Spectrometry Reveals an Antibody-Induced Allosteric Pathway Driving SARS-CoV-2 Spike Trimer Disassembly., J Am Chem Soc, PMID 41784932

PXD072506 Dataset with its publication pending (from iProX)
Dataset title: rhTPO promotes liver regeneration in rats with acute liver failure
Possible reference: Shen, Y. et al. (2025) Recombinant human thrombopoietin as a novel platelet-driven regulator accelerating hepatic regeneration in acute liver failure., Front Pharmacol, PMID 41601961

PXD072496 no publication (from MassIVE)
Dataset title: Cellular consequences, citrullination substrates, and antigenicity resulting from wild-type and targeted PAD4 on cell surfaces
Possible reference: Kong, S. et al. (2026) Cellular consequences, citrullination substrates, and antigenicity resulting from wild-type and targeted PAD4 on cell surfaces., bioRxiv, PMID 41542531

PXD072480 no publication (from MassIVE)
Dataset title: Single Cell-Type Spatial Proteomics Uncovers Regional Heterogeneity of Astrocytes
Possible reference: Kim, Y. et al. (2023) Highly Multiplexed Spatially Resolved Proteomic and Transcriptional Profiling of the Glioblastoma Microenvironment Using Archived Formalin-Fixed Paraffin-Embedded Specimens., Mod Pathol, PMID 36788070

PXD072476 Dataset with its publication pending (from iProX)
Dataset title: BES system degrades polystyrene
Possible reference: Zhang, S. et al. (2026) Mechanism of chemical-biological coupling in an electric field-driven bioelectrochemical system for enhanced polystyrene (PS) degradation., J Hazard Mater, PMID 42184536

PXD072418 Dataset with its publication pending (from PRIDE)
Dataset title: The ULK1-NCOA3 axis restrains de novo lipogenesis and prevents progression of MASLD
Possible reference: Koo, YD. et al. (2026) The ULK1-NCOA3 axis restrains de novo lipogenesis and prevents diet-induced steatohepatitis and fibrosis in mice., J Clin Invest, PMID 41926189

PXD072392 Dataset with its publication pending (from iProX)
Dataset title: Intradermal Delivery of Catalase via Extracellular Vesicles for Targeted Photoaging Therapy
Possible reference: Zhang, P. et al. (2026) Intradermal Delivery of Catalase via Extracellular Vesicles for Targeted Photoaging Therapy., Biomater Res, PMID 41859756

PXD072386 Dataset with its publication pending (from PRIDE)
Dataset title: Early-activated extracellular matrix proteins shape metabolic and spatial dynamics of the kidney fibrotic microenvironment
Possible reference: Gui, Y. et al. (2026) Early-activated extracellular matrix proteins shape the metabolic and spatial dynamics of the kidney fibrotic microenvironment., Nat Metab, PMID 41776110

PXD072349 no publication (from MassIVE)
Dataset title: MARCO promotes cholangiocarcinogenesis by inducing immunosuppression and its targeting reduces tumour growth
Possible reference: Agirre-Lizaso, A. et al. (2026) MARCO promotes cholangiocarcinogenesis by inducing immunosuppression and its targeting reduces tumor growth., Signal Transduct Target Ther, PMID 42049706

PXD072344 Dataset with its publication pending (from iProX)
Dataset title: Bacterial extracellular vesicles from Streptococcus mutans drive OSCC progression through Î²-catenin signaling
Possible reference: Cao, G. et al. (2026) Bacterial extracellular vesicles from Streptococcus mutans drive OSCC progression through β-catenin signaling., Sci Rep, PMID 41991997

PXD072322 Dataset with its publication pending (from iProX)
Dataset title: Prenylated flavonoids from Sophora flavescens (Kushen) inhibit hepatocellular carcinoma growth by suppressing the Akt/MDM2/p53 pathway to activate mitochondrial apoptosis
Possible reference: Kong, S. et al. (2026) Prenylated flavonoids from Sophora flavescens (Kushen) inhibit hepatocellular carcinoma growth by suppressing the Akt/MDM2/p53 pathway to activate mitochondrial apoptosis., Phytomedicine, PMID 42214227

PXD072313 Dataset with its publication pending (from PRIDE)
Dataset title: Organic di-selenide hydrogel microspheres for multimodal treatment of osteoarthritis.
Possible reference: Liu, Y. et al. (2026) Organic di-selenide hydrogel microspheres for multimodal treatment of osteoarthritis., Nat Commun, PMID 41634043

PXD072311 no publication (from MassIVE)
Dataset title: Age-related Delays in Osteochondral Remodeling of Fracture Healing Illustrated by Mass Spectrometry Imaging
Possible reference: Schurman, CA. et al. (2026) Age-related Delays in Osteochondral Remodeling of Fracture Healing Illustrated by Mass Spectrometry Imaging., bioRxiv, PMID 41756952

PXD072281 Dataset with its publication pending (from iProX)
Dataset title: Molecular Glue Degraders of the RNA Binding Protein HuR to Treat BRAF-Mutant Colorectal Cancer
Possible reference: Lu, X. et al. (2026) Molecular glue degraders of HuR suppress BRAF-mutant colorectal cancer., Nature, PMID 42271059

PXD072246 no publication (from MassIVE)
Dataset title: Mass Spectrometry-Based Peptidomics for Discovery and Profiling of Antimicrobial and Neuropeptide in Crustacean Hemolymph
Possible reference: Dang, TC. et al. (2026) Mass Spectrometry-Based Peptidomics for the Discovery and Profiling of Endogenous Peptides in Crustacean Hemolymph., ACS Omega, PMID 42179631

PXD072235 Dataset with its publication pending (from PRIDE)
Dataset title: Epitranscriptomic editing screening identifies functional m6A Sites
Possible reference: Zhang, X. et al. (2026) FOCAS: Transcriptome-wide screening of individual m6A sites functionally dissects epitranscriptomic control of gene expression in cancer., Cell, PMID 41478283

PXD072187 Dataset with its publication pending (from iProX)
Dataset title: Ovarian proteomics and ubiquitin-proteomics of Drosophila
Possible reference: Zhang, HB. et al. (2026) Wolbachia-induced proteostasis remodeling in ovaries supports cytoplasmic incompatibility rescue in Drosophila., J Insect Physiol, PMID 42155847

PXD072179 Dataset with its publication pending (from iProX)
Dataset title: Acupuncture for acute ischemic infraction
Possible reference: Feng, B. et al. (2023) Transcutaneous Electrical Acupuncture Point Stimulation Is Cardioprotective for Patients With Stable Ischemic Heart Disease., Am J Cardiol, PMID 37708752

PXD072146 Dataset with its publication pending (from PRIDE)
Dataset title: The seminal proteome of a monandrous fly, Drosophila subobscura
Possible reference: Dean, R. et al. (2026) The seminal proteome of a monandrous fly, Drosophila subobscura., Proc Biol Sci, PMID 42264492

PXD072077 Dataset with its publication pending (from PRIDE)
Dataset title: CDK9 interacts with a RanGTP-NEMP1-Importin-β complex to regulate erythroid enucleation
Possible reference: Chen, Y. et al. (2025) BRD4 acts as a transcriptional repressor of RhoB to inhibit terminal erythropoiesis., J Hematol Oncol, PMID 40598222

PXD072063 Dataset with its publication pending (from PRIDE)
Dataset title: Association of tear fluid glutathione synthetase and glutathione levels with amyloid positivity
Possible reference: van de Sande, N. et al. (2026) Association of tear fluid glutathione synthetase and glutathione levels with amyloid positivity., Sci Rep, PMID 41927845

PXD072061 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of circulating extracellular vesicles from COVID-19 patients and their impact on innate Vdelta2 T-cell response.
Possible reference: Montaldo, C. et al. (2026) Proteomic profiling of circulating extracellular vesicles from COVID-19 patients and their impact on innate Vdelta2 T-cell response., Front Immunol, PMID 41756302

PXD072057 Dataset with its publication pending (from PRIDE)
Dataset title: Crosstalk between and developmental dynamics of C. elegans Argonaute proteins
Possible reference: Seistrup, AS. et al. (2026) Crosstalk between and developmental dynamics of Caenorhabditis elegans Argonaute proteins., Genetics, PMID 41870199

PXD072045 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of Pseudomonas sp. M1 and evolved lineages
Possible reference: Soares, F. et al. (2026) Multi-omics characterization of β-myrcene-evolved Pseudomonas sp. M1 reveals convergent FleQ mutations and altered catabolic efficiency., Front Mol Biosci, PMID 42052151

PXD072017 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamic regulatory grammar of human promoters uncovered by MPRA-trained deep learning
Possible reference: Barbadilla-Mart�nez, L. et al. (2026) Regulatory grammar in human promoters uncovered by MPRA-based deep learning., Nature, PMID 41639451

PXD071971 no publication (from MassIVE)
Dataset title: Drugging the intrinsically disordered transactivation domain of androgen receptor
Possible reference: Obst, JK. et al. (2026) Drugging the intrinsically disordered transactivation domain of androgen receptor., Signal Transduct Target Ther, PMID 42045150

PXD071969 Dataset with its publication pending (from PRIDE)
Dataset title: ccRCC cells treated with DMSO or UNC8209
Possible reference: Liao, C. et al. (2026) Selective degradation of TBK1 uncovers mechanistic insights into blocking ccRCC progression., Cell Chem Biol, PMID 41950925

PXD071938 Dataset with its publication pending (from PRIDE)
Dataset title: Origins and consequences of kinetoplast loss in trypanosomes
Possible reference: Carnes, J. et al. (2015) Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty., PLoS Negl Trop Dis, PMID 25568942

PXD071925 no publication (from MassIVE)
Dataset title: Proteome-based identification and validation of NXPE3 in childhood acute lymphoblastic leukaemia
Possible reference: Tabassum, N. et al. (2026) Proteome-based identification and validation of NXPE3 in childhood acute lymphoblastic leukaemia., Pak J Pharm Sci, PMID 42001290

PXD071885 Dataset with its publication pending (from PRIDE)
Dataset title: P69B+EPI1 purification in WT and ppo
Possible reference: Dmitrenko, M. et al. (2022) Novel PDMS-b-PPO Membranes Modified with Graphene Oxide for Efficient Pervaporation Ethanol Dehydration., Membranes (Basel), PMID 36135851

PXD071838 Dataset with its publication pending (from PRIDE)
Dataset title: Community context reshapes microbial proteomes and reduces functional overlap
Possible reference: Mora�s, S. et al. (2026) Community context reshapes microbial proteomes and reduces functional overlap., Nat Microbiol, PMID 42032280

PXD071705 Dataset with its publication pending (from jPOST)
Dataset title: Screening pertactin-specific antibodies and evaluating competitive epitope recognition by native mass spectrometry
Possible reference: Gadallah, MI. et al. (2026) Screening pertactin-specific antibodies and evaluating competitive epitope recognition by native mass spectrometry., Chem Sci, PMID 41853578

PXD071700 Dataset with its publication pending (from iProX)
Dataset title: Coro1a promotes the multivesicular body and plasma membrane fusion by facilitating PKM2-mediated SNAP-23 phosphorylation
Possible reference: Cai, Z. et al. (2026) Coro1a promotes the multivesicular body and plasma membrane fusion by facilitating PKM2-mediated SNAP-23 phosphorylation., Commun Biol, PMID 42265296

PXD071690 . The molecular basis for nuclear pore destruction by a proximity-inducing molecular glue. https://doi.org/10.1016/j.chembiol.2026.04.016. (from MassIVE)
Dataset title: The molecular basis for nuclear pore destruction by a proximity-inducing molecular glue
Possible reference: Hinshaw, SM. et al. (2026) The molecular basis for nuclear pore destruction by a proximity-inducing molecular glue., Cell Chem Biol, PMID 42202785

PXD071667 Dataset with its publication pending (from PRIDE)
Dataset title: A multi-omics atlas of the plant nuclear envelope
Possible reference: Nam, H. et al. (2026) A multiomics atlas of the Arabidopsis nuclear envelope., Sci Adv, PMID 42102208

PXD071661 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-Omics and Machine Learning-Based Profiling of Severity Signatures in Mycoplasma Pneumoniae Infection in Children
Possible reference: Li, G. et al. (2026) Multi-omics and machine learning-based profiling of severity signatures in Mycoplasma pneumoniae infection in children., iScience, PMID 41732270

PXD071655 no publication (from MassIVE)
Dataset title: CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis
Possible reference: Samelson, AJ. et al. (2024) CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis., bioRxiv, PMID 37398204

PXD071647 no publication (from MassIVE)
Dataset title: Proteomics reveals extensive phosphoregulation of outer kinetochore protein KNL1
Possible reference: Jurasin, AC. et al. (2026) Proteomics reveals extensive phosphoregulation of outer kinetochore protein KNL1., bioRxiv, PMID 41959482

PXD071582 Dataset with its publication pending (from PRIDE)
Dataset title: Robust Neurogenesis in Chronic Stroke Monkeys Following Mesenchymal Stem Cell Transplantation Plus Intermittent Theta-burst Stimulation
Possible reference: Ma, YH. et al. (2026) Robust neurogenesis in chronic stroke monkeys following mesenchymal stem cell transplantation plus intermittent theta-burst stimulation., Signal Transduct Target Ther, PMID 42031725

PXD071580 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial energetic failure underlies FLVCR1-related sensory neuropathy
Possible reference: Bertino, F. et al. (2026) Mitochondrial energetic failure underlies FLVCR1-related sensory neuropathy., Commun Biol, PMID 41691085

PXD071531 Dataset with its publication pending (from PRIDE)
Dataset title: Methionine Restriction Alleviates Kidney Fibrosis through Epigenetic Repression of the TGF-Î²-Smad3-Hoxc8/P-TEFb axis
Possible reference: Liu, Y. et al. (2025) Methionine restriction alleviates kidney fibrosis through epigenetic repression of the TGF-β-Smad3-Hoxc8/P-TEFb axis., Nat Commun, PMID 41476080

PXD071487 Dataset with its publication pending (from PRIDE)
Dataset title: SIRT1 mediates brain metabolic and developmental consequences of methionine synthase deficiency in inborn errors of cobalamin metabolism
Possible reference: Matmat, K. et al. (2026) SIRT1 mediates brain metabolic and developmental consequences of methionine synthase deficiency in inborn errors of cobalamin metabolism., Cell Rep Med, PMID 41747718

PXD071468 Dataset with its publication pending (from PRIDE)
Dataset title: Urine proteomics as a source of biological information and outcome predictor in living kidney transplantation - Validation cohort
Possible reference: Hoyer-Allo, KJR. et al. (2026) Urine Proteomics as a Source of Biological Information and Outcome Predictor in Living Kidney Transplantation., Mol Cell Proteomics, PMID 41825594

PXD071466 Dataset with its publication pending (from PRIDE)
Dataset title: A multi-omics atlas of the plant nuclear envelope
Possible reference: Nam, H. et al. (2026) A multiomics atlas of the Arabidopsis nuclear envelope., Sci Adv, PMID 42102208

PXD071457 no publication (from MassIVE)
Dataset title: RBM10 modulation of circRNAs in lung cancer
Possible reference: Utrilla-Maestre, A. et al. (2026) RBM10 modulation of circRNA biogenesis contributes to its tumor suppressor role in lung adenocarcinoma., Biomark Res, PMID 41673707

PXD071415 Dataset with its publication pending (from iProX)
Dataset title: Label-free phosphoproteomic analysis for Adcy7-knockout BMDMs
Possible reference: Wu, L. et al. (2025) Integrated proteomics and phosphoproteomics profiling dynamic signaling networks underlying two distinct types of macrophage activation., Cell Immunol, PMID 40398355

PXD071411 Dataset with its publication pending (from iProX)
Dataset title: Assessing the Suitability of Deubiquitylases As Substrates For Targeted Protein Degradation
Possible reference: Tong, J. et al. (2025) Assessing the Suitability of Deubiquitylases As Substrates For Targeted Protein Degradation., bioRxiv, PMID 40661558

PXD071408 Dataset with its publication pending (from iProX)
Dataset title: SLC6A6 imports taurine into mitochondria to sustain mitochondrial translation and tumour growth
Possible reference: Li, L. et al. (2026) SLC6A6 imports taurine into mitochondria to sustain mitochondrial translation and tumour growth., Nat Metab, PMID 41652173

PXD071400 no publication (from MassIVE)
Dataset title: A self-organizing single-cell morphology circuit optimizes Podophrya collini predatory trap structure
Possible reference: Xu, Z. et al. (2025) A self-organizing single-cell morphology circuit optimizes Podophrya collini predatory trap structure., bioRxiv, PMID 41292725

PXD071389 Dataset with its publication pending (from PRIDE)
Dataset title: Nucleophagy removes cytotoxic trapped PARP1
Possible reference: Hoslett, G. et al. (2026) Nucleophagy removes cytotoxic trapped PARP1., Nat Cell Biol, PMID 42230924

PXD071381 no publication (from MassIVE)
Dataset title: ASNA1 Is Essential for Cardiac Development and Function by Regulating Tail-Anchored Protein Stability and Vesicular Transport in Cardiomyocytes
Possible reference: Feng, W. et al. (2025) ASNA1 is essential for cardiac development and function by regulating tail-anchored protein stability and vesicular transport in cardiomyocytes., PLoS Genet, PMID 41370295

PXD071366 Dataset with its publication pending (from PRIDE)
Dataset title: CD47 stabilizes ROBO2 to regulate glioblastoma progression by preventing ITCH mediated ubiquitination
Possible reference: Polara, R. et al. (2026) CD47 stabilizes ROBO2 to regulate glioblastoma progression by preventing ITCH-mediated ubiquitination., Proc Natl Acad Sci U S A, PMID 41871254

PXD071328 Dataset with its publication pending (from PRIDE)
Dataset title: Adherens junction protein expression is associated with poor response to neoadjuvant FLOT chemotherapy and pro-inflammatory tumor microenvironment in esophageal adenocarcinoma
Possible reference: Grothey, B. et al. (2026) Adherens junction protein expression is associated with poor response to neoadjuvant FLOT chemotherapy and pro-inflammatory tumor microenvironment in esophageal adenocarcinoma., Int J Cancer, PMID 41784062

PXD071289 Dataset with its publication pending (from iProX)
Dataset title: Optimization of methods for the quantitative analysis of global cell surface proteome and cell surface polarization
Possible reference: Kuffa, K. et al. (2025) Optimization of Methods for the Quantitative Analysis of Global Cell Surface Proteome and Cell Surface Polarization., Int J Mol Sci, PMID 41373727

PXD071272 Dataset with its publication pending (from jPOST)
Dataset title: Optimization of methods for the quantitative analysis of global cell surface proteome and cell surface polarization
Possible reference: Kuffa, K. et al. (2025) Optimization of Methods for the Quantitative Analysis of Global Cell Surface Proteome and Cell Surface Polarization., Int J Mol Sci, PMID 41373727

PXD071261 Dataset with its publication pending (from PRIDE)
Dataset title: A fold switch regulates conformation of an alphavirus virus RNA-dependent RNA polymerase
Possible reference: Arnold, JJ. et al. (2025) A fold switch regulates conformation of an alphavirus virus RNA-dependent RNA polymerase., bioRxiv, PMID 41000967

PXD071200 Dataset with its publication pending (from PRIDE)
Dataset title: Differentially Expressed Proteins in Plasma-Derived Extracellular Vesicles from Chronic Myeloid Leukemia Patients
Possible reference: Kusma Wosniaki, D. et al. (2026) Differentially expressed proteins in plasma-derived extracellular vesicles from chronic myeloid leukemia patients., Front Genet, PMID 41773228

PXD071164 Dataset with its publication pending (from iProX)
Dataset title: Plasma Proteomic Characterization of Adolescent Idiopathic Scoliosis
Possible reference: Makino, H. et al. (2019) Differential proteome analysis in adolescent idiopathic scoliosis patients with thoracolumbar/lumbar curvatures., BMC Musculoskelet Disord, PMID 31122237

PXD071153 no publication (from MassIVE)
Dataset title: The E3 ubiquitin ligase MGRN1 targets melanocortin receptors MC1R and MC4R via interactions with transmembrane adapters
Possible reference: Parashara, P. et al. (2025) The E3 ubiquitin ligase MGRN1 targets melanocortin receptors MC1R and MC4R via interactions with transmembrane adapters., bioRxiv, PMID 40196599

PXD071138 Dataset with its publication pending (from PRIDE)
Dataset title: Insights into the proteome of Next-Generation Probiotic Faecalibacterium duncaniae A2-165 through label-free proteomics approach
Possible reference: Ferrary Am�rico, M. et al. (2026) Insights into the proteome of next-generation probiotic Faecalibacterium duncaniae A2-165 through label-free proteomics approach., BMC Microbiol, PMID 41709136

PXD071118 Dataset with its publication pending (from iProX)
Dataset title: Jasmine( Jasminum sambac) Proteomics
Possible reference: Wang, H. et al. (2021) An integrated transcriptomic and proteomic approach to dynamically study the mechanism of pollen-pistil interactions during jasmine crossing., J Proteomics, PMID 34517123

PXD071103 Dataset with its publication pending (from iProX)
Dataset title: Proteome analysis of spermathecal fluid and seminal plasma reveals the mechanism of sperm storage in Amphioctopus fangsiao
Possible reference: Sun, X. et al. (2025) Proteome Analysis of Spermathecal Fluid and Seminal Plasma Reveals the Mechanism of Sperm Storage in Amphioctopus Fangsiao., Animals (Basel), PMID 41375555

PXD071084 Dataset with its publication pending (from PRIDE)
Dataset title: proteomics of adhesive and semi-buoyant eggs from northern and southern populations of Culter alburnus
Possible reference: Chen, H. et al. (2026) Comparison of transcriptomics and proteomics revealed distinct molecular mechanisms underlying egg development of Culter alburnus between northern and southern China., Comp Biochem Physiol Part D Genomics Proteomics, PMID 41687135

PXD071044 no publication (from MassIVE)
Dataset title: Proteomics Analysis of Cerebrospinal Fluid in Survivors of Childhood Acute Lymphoblastic Leukemia
Possible reference: Niu, M. et al. (2026) Longitudinal Proteomics Analysis of Cerebrospinal Fluid in Survivors of Childhood Acute Lymphoblastic Leukemia., Sci Data, PMID 42056117

PXD071008 Dataset with its publication pending (from PRIDE)
Dataset title: Lipid metabolism drives osimertinib resistance in non-small cell lung cancer
Possible reference: Ma, L. et al. (2026) PKC-iota drives EGFR-TKI resistance in EGFR-mutated NSCLC by phosphorylating FASN to reprogram lipid metabolism., Transl Lung Cancer Res, PMID 41808706

PXD070982 Dataset with its publication pending (from iProX)
Dataset title: Staphylococcus aureus Aggravates Atopic Dermatitis through Enhanced Bacterial Colonization
Possible reference: Malhotra, N. et al. (2016) IL-22 derived from γδ T cells restricts Staphylococcus aureus infection of mechanically injured skin., J Allergy Clin Immunol, PMID 27543072

PXD070972 Dataset with its publication pending (from iProX)
Dataset title: Purification and structural characterization of Ampelopsis grossedentata polysaccharide and its activities
Possible reference: Liu, CY. et al. (2021) Effect of steam explosion pretreatment on the structure and bioactivity of Ampelopsis grossedentata polysaccharides., Int J Biol Macromol, PMID 34166690

PXD070949 Dataset with its publication pending (from PRIDE)
Dataset title: DNA-intercalating antiphage molecules trigger abortive infection through ‘mutual destruction’ and synergize with bacterial immunity
Possible reference: Ernst, L. et al. (2026) DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity., Proc Natl Acad Sci U S A, PMID 42234519

PXD070940 Dataset with its publication pending (from PRIDE)
Dataset title: MAP4K2 promotes Treg differentiation and suppresses antitumor immunity
Possible reference: Chuang, HC. et al. (2026) MAP4K2 suppresses antitumor immunity in a pancreatic cancer model by promoting Treg differentiation., J Clin Invest, PMID 41615953

PXD070899 Dataset with its publication pending (from PRIDE)
Dataset title: Capture and functional conversion of mitochondrial protein translocase by lipid metabolism enzyme
Possible reference: Heinen, S. et al. (2026) Mitochondria contact lipid droplets through the mitochondrial import complex binding to lipid metabolism enzyme Ayr1., Nat Cell Biol, PMID 41748941

PXD070895 no publication (from MassIVE)
Dataset title: Chlamydial membrane vesicles deliver the beta barrel membrane protein OmpA to mitochondria to inhibit apoptosis
Possible reference: Mesesan, A. et al. (2026) Chlamydial membrane vesicles deliver the beta barrel outer membrane protein OmpA to mitochondria to inhibit apoptosis., PLoS Pathog, PMID 41628280

PXD070863 Dataset with its publication pending (from PRIDE)
Dataset title: A Rab1 interactome illuminates its dual role in autophagy and membrane trafficking
Possible reference: van Vliet, AR. et al. (2026) A Rab1 interactome illuminates a dual role in autophagy and membrane trafficking., J Cell Biol, PMID 41493270

PXD070823 Dataset with its publication pending (from iProX)
Dataset title: Photodynamic therapy with a novel photosensitizer inhibits BLM-induced pulmonary fibrosis in mice via MRC1-mediated pathway
Possible reference: Zhu, M. et al. (2025) Photodynamic therapy with a novel photosensitizer inhibits BLM-induced pulmonary fibrosis in mice via MRC1-mediated pathway., Front Pharmacol, PMID 41394130

PXD070784 Dataset with its publication pending (from PRIDE)
Dataset title: Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms
Possible reference: Bodel�n, A. et al. (2026) Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms., Nat Commun, PMID 42215459

PXD070780 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomics and phosphoproteomics analyses of glucocorticoid responses in breast cancer cell lines
Possible reference: Cho, H. et al. (2026) Glucocorticoid-Induced Proteome and Phosphoproteome Changes in Breast Cancer Cell Lines., J Proteome Res, PMID 41801802

PXD070776 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Profiling of Equine Airway Mucus Reveals Compositional Changes in Asthmatic Phenotypes
Possible reference: Bartenschlager, F. et al. (2026) Proteomic profiling of equine airway mucus reveals compositional changes in asthmatic phenotypes., Sci Rep, PMID 41667845

PXD070767 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of dimorphic sperm in the Cabbage White Butterfly, Pieris rapae
Possible reference: Plakke, M. et al. (2026) Proteomic analysis of dimorphic sperm in the cabbage white butterfly, Pieris rapae., Front Insect Sci, PMID 41958958

PXD070766 Dataset with its publication pending (from PRIDE)
Dataset title: PacL1-ALFA tag based proximity proteomics in Mycobacterium tuberculosis
Possible reference: Fay, A. et al. (2025) A split ALFA tag-nanobody system for protein localization and proximity proteomics in mycobacteria., mBio, PMID 40576343

PXD070750 no publication (from MassIVE)
Dataset title: Ketogenic diet dampens excitatory neurotransmission by shrinking synaptic vesicle pools
Possible reference: Stunault, MI. et al. (2025) Ketogenic diet dampens excitatory neurotransmission by shrinking synaptic vesicle pools., bioRxiv, PMID 40502031

PXD070720 Dataset with its publication pending (from iProX)
Dataset title: The role and mechanism of MMP3 in the proliferation and invasion processes of colorectal cancer
Possible reference: He, L. et al. (2022) The immunomodulatory role of matrix metalloproteinases in colitis-associated cancer., Front Immunol, PMID 36776395

PXD070715 Dataset with its publication pending (from iProX)
Dataset title: Mass spectrometry analysis of Cend1 interacting protein
Possible reference: Schmelter, C. et al. (2023) Glaucoma-Associated CDR1 Peptide Promotes RGC Survival in Retinal Explants through Molecular Interaction with Acidic Leucine Rich Nuclear Phosphoprotein 32A (ANP32A)., Biomolecules, PMID 37509196

PXD070675 no publication (from MassIVE)
Dataset title: Proteomic data of cytoplasmic male sterility in Capsicum annuum L.
Possible reference: Guo, J. et al. (2017) Proteomic analysis reveals strong mitochondrial involvement in cytoplasmic male sterility of pepper (Capsicum annuum L.)., J Proteomics, PMID 28847649

PXD070670 no publication (from MassIVE)
Dataset title: Microbial Co-Culture Circadian Control Proteomics
Possible reference: Bateman, RM. et al. (2016) 36th International Symposium on Intensive Care and Emergency Medicine : Brussels, Belgium. 15-18 March 2016., Crit Care, PMID 27885969

PXD070658 no publication (from MassIVE)
Dataset title: Commensal derived short chain fatty acids disrupt Staphylococcus aureus lipid membrane homeostasis
Possible reference: Fletcher, JR. et al. (2024) Commensal-derived short-chain fatty acids disrupt lipid membrane homeostasis in Staphylococcus aureus., bioRxiv, PMID 39185181

PXD070650 Dataset with its publication pending (from PRIDE)
Dataset title: Membrane-associated effluxosomes coordinate multi-metal resistance in Mycobacterium tuberculosis
Possible reference: Dupuy, P. et al. (2025) PacL-organized membrane-associated effluxosomes coordinate multi-metal resistance in Mycobacterium tuberculosis., bioRxiv, PMID 40196583

PXD070648 Dataset with its publication pending (from PRIDE)
Dataset title: The resting and ligand-bound states of the membrane-embedded human T-cell receptor–CD3 complex
Possible reference: Notti, RQ. et al. (2024) The resting and ligand-bound states of the membrane-embedded human T-cell receptor-CD3 complex., bioRxiv, PMID 37662363

PXD070610 Dataset with its publication pending (from iProX)
Dataset title: ASB9 promotes ubiquitin-mediated degradation of TNP2 to facilitate histone-to-protamine transition in humans and mice
Possible reference: Zhao, S. et al. (2026) ASB9 promotes ubiquitin-mediated degradation of TNP2 to facilitate histone-to-protamine transition in humans and mice., Proc Natl Acad Sci U S A, PMID 41915740

PXD070591 Dataset with its publication pending (from PRIDE)
Dataset title: Asymmetrically glycosylated IgG1 antibodies are universal and drive human disease
Possible reference: Azzam, T. et al. (2025) Asymmetrically glycosylated IgG1 antibodies are universal and drive human disease., Nat Commun, PMID 41387437

PXD070589 no publication (from MassIVE)
Dataset title: The RNA Exosome Maintains Cellular RNA Homeostasis by Controlling Transcript Abundance in the Brain
Possible reference: Higginson, LA. et al. (2024) The RNA exosome maintains cellular RNA homeostasis by controlling transcript abundance in the brain., bioRxiv, PMID 39554067

PXD070512 Dataset with its publication pending (from iProX)
Dataset title: The mechanism of AMPKÎ±2 in liver aging using AMPKÎ±2 knockout mouse
Possible reference: Hwang, SL. et al. (2013) AMP-activated protein kinase negatively regulates FcεRI-mediated mast cell signaling and anaphylaxis in mice., J Allergy Clin Immunol, PMID 23587332

PXD070503 no publication (from MassIVE)
Dataset title: Global profiling of post-translationally modified crustacean neuropeptidome trends affiliated with feeding activity
Possible reference: Fields, L. et al. (2026) Global Profiling of Post-Translationally Modified Crustacean Neuropeptidome Trends Affiliated with Feeding Activity., J Am Soc Mass Spectrom, PMID 41848780

PXD070500 Dataset with its publication pending (from PRIDE)
Dataset title: The proteome of bilateral macronodular adrenocortical disease (BMAD) shows different profiles correlating with the genetic causes and reveals specific dysregulation of RNA polymerase II and cholesterol biosynthesis enzymes.
Possible reference: Violon, F. et al. (2026) The Proteome of Bilateral Macronodular Adrenocortical Disease (BMAD) Shows Different Profiles Correlating with the Genetic Causes and Reveals Specific Dysregulation of RNA Polymerase II and Cholesterol Biosynthesis Enzymes., Endocr Pathol, PMID 41524866

PXD070464 no publication (from MassIVE)
Dataset title: Supercharging-Enhanced nDIA-MS Enables Global Profiling of Drug-Induced Proteome Solubility Shifts (Method evaluation)
Possible reference: Xiong, Y. et al. (2026) Supercharging-enhanced nDIA-MS enables global profiling of drug-induced proteome solubility shifts., Nat Commun, PMID 41617713

PXD070440 Dataset with its publication pending (from iProX)
Dataset title: THBS1 as a Candidate Biomarker and Fibrotic Mediator in Radiation-induced liver injury: Insights from TMT-Labeled Quantitative Proteomics
Possible reference: Wang, Z. et al. (2025) THBS1 as a candidate biomarker and fibrotic mediator in radiation-induced liver injury: insights from TMT-labeled quantitative proteomics., Front Pharmacol, PMID 41394148

PXD070439 Dataset with its publication pending (from iProX)
Dataset title: TRIM21 promotes K63-linked Ubiquitination of ALKBH5�and Suppresses�Cuproptosis via down-regulation of LIAS in�Esophageal Squamous Cell Carcinoma
Possible reference: Feng, A. et al. (2025) TRIM21 promotes K63-linked ubiquitination of ALKBH5 and suppresses cuproptosis via down-regulation of LIAS in esophageal squamous cell carcinoma., Commun Biol, PMID 41413718

PXD070437 Dataset with its publication pending (from iProX)
Dataset title: Psychological stress exacerbates vitiligo via dysregulated proteolysis of substance P and MRGPRX2-dependent mast cell activation
Possible reference: Geng, MM. et al. (2026) Psychological stress exacerbates vitiligo via dysregulated proteolysis of substance P and MRGPRX2-dependent mast cell activation., J Dermatol Sci, PMID 42251015

PXD070428 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profile of (Laser-dissected) Motoneurons, Ependymal Cells and Dorsal Root Ganglia Cells, and after Spinal Cord Injury in Rat
Possible reference: Gajewska-Woźniak, O. et al. (2026) Proteomic profile of Laser-dissected Motoneurons, Ependymal Cell Layer and Dorsal Root Ganglia after Spinal Cord Injury in the Rat., Sci Data, PMID 41932936

PXD070409 Dataset with its publication pending (from PRIDE)
Dataset title: SPOROCYTELESS/NOZZLE interacts with MADS-DOMAIN transcription factors during the megaspore mother cell differentiation in the Arabidopsis ovule
Possible reference: Cavalleri, A. et al. (2025) SPOROCYTELESS/NOZZLE cooperates with MADS-domain transcription factors to regulate an auxin-dependent network controlling Megaspore-Mother-Cell differentiation., Nat Commun, PMID 41392078

PXD070396 Dataset with its publication pending (from iProX)
Dataset title: Proteomic Profiling of Metastatic and Non-Metastatic Primary Tumors in Pancreatic Cancer
Possible reference: Saller, J. et al. (2019) EPB41L5 is Associated With the Metastatic Potential of Low-grade Pancreatic Neuroendocrine Tumors., Cancer Genomics Proteomics, PMID 31467225

PXD070395 Dataset with its publication pending (from iProX)
Dataset title: A group competition strategy for covalent ligand discovery
Possible reference: Huang, T. et al. (2021) Chemoproteomic profiling of kinases in live cells using electrophilic sulfonyl triazole probes., Chem Sci, PMID 34164099

PXD070376 no publication (from MassIVE)
Dataset title: Magnesium modulates the stress response of oral streptococci to environmental and antibiotic challenges by altering cell envelope and nutrient transport pathways
Possible reference: Mishra, S. et al. (2025) Magnesium modulates the stress responses of oral streptococci to environmental and antibiotic challenges by altering cell envelope and nutrient transport pathways., Front Microbiol, PMID 41568040

PXD070372 no publication (from MassIVE)
Dataset title: MiProChip A microfluidic device for high-throughput single-cell proteomics via multiplexed isobaric labeling
Possible reference: Chou, TF. et al. (2026) MiProChip: A Scalable Microfluidic Platform for Multiplexed Single-Cell Proteomics via Isobaric Labeling., Anal Chem, PMID 41740022

PXD070369 Dataset with its publication pending (from PRIDE)
Dataset title: HMGN1 and HMGN2 are recruited to acetylated and histone variant H2A.Z-containing nucleosomes to regulate chromatin state and transcription
Possible reference: Gohil, R. et al. (2026) HMGN1 and HMGN2 are recruited to acetylated and histone variant H2A.Z-containing nucleosomes to regulate chromatin state and transcription., J Biol Chem, PMID 41325801

PXD070354 Dataset with its publication pending (from PRIDE)
Dataset title: Chromatin architecture reprogramming reveals novel epigenetic dependencies in breast cancer
Possible reference: Garcia-Martinez, L. et al. (2026) Chromatin architecture reprogramming reveals novel epigenetic dependencies in breast cancer., Genes Dev, PMID 41412800

PXD070352 Dataset with its publication pending (from PRIDE)
Dataset title: UltraPlex: Expanding isobaric hyperplexing via orthogonal protease cleavage
Possible reference: Roumeliotis, TI. et al. (2026) UltraPlex-TMT: Expanding Isobaric Hyperplexing via Orthogonal Protease Cleavage., J Proteome Res, PMID 41622683

PXD070339 Dataset with its publication pending (from PRIDE)
Dataset title: Enhanced STEAP4 Ubiquitination in Obesity: Insights from Combined Proteome and Ubiquitylome Analysis of Visceral Adipose Tissue
Possible reference: Li, Y. et al. (2026) Enhanced STEAP4 Ubiquitination in Obesity: Insights From Combined Proteome and Ubiquitylome Analysis of Visceral Adipose Tissue., Mol Cell Proteomics, PMID 41317904

PXD070333 Dataset with its publication pending (from iProX)
Dataset title: 4D label-free N-glycoproteomics of milk fat globule membrane proteins reveal distinct profiles between yak colostrum and mature milk
Possible reference: Su, D. et al. (2025) Astral-DIA proteomics and 4D label-free N-glycoproteomics of milk fat globule membrane proteins reveal distinct profiles between yak colostrum and mature milk., Food Chem X, PMID 41378274

PXD070325 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting Prolyl 3-hydroxylase 1 Inhibits Pancreatic Cancer Progression and Macrophage Immunity
Possible reference: Bai, P. et al. (2026) Targeting Prolyl 3-hydroxylase 1 inhibits pancreatic cancer progression and macrophage immunity., Nat Commun, PMID 41826312

PXD070306 Dataset with its publication pending (from PRIDE)
Dataset title: The bile acid-CoA ligase, FATP5, is necessary for synthesis of N-acyl taurines in the liver
Possible reference: Kuentzel, KB. et al. (2026) The bile acid-CoA ligase, FATP5, is necessary for the synthesis of N-acyl taurines in the liver., J Lipid Res, PMID 41780593

PXD070290 no publication (from MassIVE)
Dataset title: Proteome Data - Dog Protein Atlas
Possible reference: Ivliev, AE. et al. (2012) Exploring the transcriptome of ciliated cells using in silico dissection of human tissues., PLoS One, PMID 22558177

PXD070283 no publication (from MassIVE)
Dataset title: Advancing DIA-Based Limited Proteolysis Workflows: Introducing DIA-LiPA
Possible reference: Van Leene, C. et al. (2026) Advancing DIA-Based Limited Proteolysis Workflows: Introducing DIA-LiPA., Anal Chem, PMID 41689503

PXD070242 no publication (from MassIVE)
Dataset title: Proteome Data - Non-human primate Protein Atlas
Possible reference: Mansi, L. et al. (2021) REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments., Nucleic Acids Res, PMID 33104797

PXD070204 Dataset with its publication pending (from iProX)
Dataset title: DCAF15-mediated EphA2 degradation triggers disruption of the blood-brain barrier during Streptococcus suis meningitis
Possible reference: Yin, H. et al. (2025) Dcaf15-mediated EphA2 degradation triggers disruption of the blood-brain barrier during Streptococcus suis meningitis., Commun Biol, PMID 41276610

PXD070201 Dataset with its publication pending (from PRIDE)
Dataset title: High-Throughput Label-free Single-Cell Proteomics Enabled by Multicolumn NanoLC with a 5-min Cycle Time
Possible reference: Wang, C. et al. (2025) High-Throughput Label-free Single-Cell Proteomics Enabled by Multicolumn NanoLC with a 5-min Cycle Time., Res Sq, PMID 41333401

PXD070180 Dataset with its publication pending (from PRIDE)
Dataset title: An abundant membrane protein in the NCAM superfamily is required for epithelial organization in sea anemone embryos
Possible reference: Postnikova, A. et al. (2025) An abundant membrane protein in the NCAM superfamily is required for epithelial organization in sea anemone embryos., Proc Natl Acad Sci U S A, PMID 41400995

PXD070177 Dataset with its publication pending (from PRIDE)
Dataset title: Targets of K27 polyubiquitin in the female hippocampus following contextual fear conditioning
Possible reference: Patrick, MB. et al. (2026) Non-canonical K27 polyubiquitination is a sex-specific regulator of contextual fear memory in the hippocampus but not the amygdala., Behav Brain Res, PMID 41905718

PXD070139 Dataset with its publication pending (from iProX)
Dataset title: CRISPR-free RNA Base Editing Mediated PTC-readthrough Restores Hearing in Mice with Otof Nonsense Mutation
Possible reference: Sun, H. et al. (2025) CRISPR-free RNA base editing mediated PTC-readthrough restores hearing in mice with Otof nonsense mutation., Nat Commun, PMID 41353207

PXD070126 Dataset with its publication pending (from iProX)
Dataset title: Therapeutic hypothermia reprograms nanocarrier protein corona via apolipoprotein C1 enrichment for precision cardiovascular therapy
Possible reference: Li, C. et al. (2025) Therapeutic hypothermia reprograms nanocarrier protein corona via apolipoprotein C1 enrichment for precision cardiovascular therapy., Proc Natl Acad Sci U S A, PMID 41231950

PXD070084 Dataset with its publication pending (from iProX)
Dataset title: Lactate Orchestrates the TGFÎ² Pathway and Ferroptosis Nexus in Organ Fibrosis via USP2 Lactylation
Possible reference: Xiang, J. et al. (2025) Lactate orchestrates the TGFβ pathway and ferroptosis nexus in organ fibrosis via USP2 lactylation., Commun Biol, PMID 41310079

PXD070070 Dataset with its publication pending (from iProX)
Dataset title: Mechanism of Hepatotoxicity Induced by Ethanol Extract of Emilia sonchifolia (L.) DC Revealed by Proteomics and Metabolomics
Possible reference: Chen, G. et al. (2025) Mechanism of hepatotoxicity induced by ethanol extract of Emilia sonchifolia (L.) DC revealed by proteomics and metabolomics., Front Pharmacol, PMID 41293248

PXD070069 Dataset with its publication pending (from iProX)
Dataset title: Pericyte-myofibroblast Transition: A novel mechanism in peritoneal fibrosis and the effect of Asiaticoside
Possible reference: Shi, J. et al. (2025) Pericyte-myofibroblast transition: a novel mechanism in peritoneal fibrosis and the effect of Asiaticoside., J Adv Res, PMID 41338386

PXD070066 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of Rhitymna verruca
Possible reference: Li, Z. et al. (2026) Serine proteases and serine protease inhibitors identified from the venom gland transcriptome of Rhitymna verruca., Comp Biochem Physiol Part D Genomics Proteomics, PMID 41435494

PXD070063 Dataset with its publication pending (from iProX)
Dataset title: Astral-DIA proteomics of milk fat globule membrane proteins reveal distinct profiles between yak colostrum and mature milk
Possible reference: Su, D. et al. (2025) Astral-DIA proteomics and 4D label-free N-glycoproteomics of milk fat globule membrane proteins reveal distinct profiles between yak colostrum and mature milk., Food Chem X, PMID 41378274

PXD070053 no publication (from MassIVE)
Dataset title: Proteomic profiling of adipose-derived mesenchymal stromal cell response to novel compounds targeting the Laminin Receptor PEDF interaction
Possible reference: Figueiredo, ML. et al. (2025) Proteomic profiling of adipose-derived mesenchymal stromal cell response to novel compounds targeting the Laminin Receptor - PEDF interaction., Biochem Biophys Rep, PMID 41378102

PXD070027 Dataset with its publication pending (from iProX)
Dataset title: Sec14L6 Is a Phosphoinositide Transporter That Regulates Phosphoinositide Homeostasis and Biogenesis of Lipid Droplet
Possible reference: Zhou, T. et al. (2025) Sec14L6 is a phosphoinositide transporter that regulates phosphoinositide homeostasis and biogenesis of lipid droplets., Nat Commun, PMID 41298368

PXD070012 Dataset with its publication pending (from iProX)
Dataset title: A simple and flexible strategy for single-cell proteomic analysis based on protein immobilization and digestion tube reactor
Possible reference: Zhang, W. et al. (2025) A Simple and Flexible Strategy for Single-Cell Proteomic Analysis Based on Protein Immobilization and Digestion Tube Reactor., Anal Chem, PMID 41186116

PXD070010 Dataset with its publication pending (from iProX)
Dataset title: Docosahexaenoic acid (DHA) alleviates hepatic lipid deposition in transitional dairy cows: An integrated in vitro and in vivo study
Possible reference: Zhang, X. et al. (2025) Docosahexaenoic acid (DHA) alleviates hepatic lipid deposition in dairy cows during the transition period: an integrated in vitro and in vivo study., J Anim Sci Biotechnol, PMID 41345683

PXD070000 no publication (from MassIVE)
Dataset title: Midbrain extracellular matrix and microglia are associated with cognition in aging mice
Possible reference: Gray, DT. et al. (2025) Midbrain extracellular matrix and microglia are associated with cognition in aging mice., Nat Commun, PMID 41309656

PXD069999 Dataset with its publication pending (from PRIDE)
Dataset title: Coordinated regulation of metabolic plasticity by the Hsp90 chaperones
Possible reference: Trčka, F. et al. (2016) [Mechanisms of Protein Homeostasis Regulation in Cancer Development]., Klin Onkol, PMID 27846716

PXD069947 no publication (from MassIVE)
Dataset title: Sphingosine Kinase-2 Inhibition Increases Acetyl-CoA Carboxylase Activity
Possible reference: Wang, X. et al. (2021) LINC00514 promotes lipogenesis and tumor progression in esophageal squamous cell carcinoma by sponging miR‑378a‑5p to enhance SPHK1 expression., Int J Oncol, PMID 34533201

PXD069942 Dataset with its publication pending (from PRIDE)
Dataset title: P. aeruginosa proteomics under the compound 7
Possible reference: Medić, A. et al. (2019) A comprehensive study of conditions of the biodegradation of a plastic additive 2,6-di-tert-butylphenol and proteomic changes in the degrader Pseudomonas aeruginosa san ai., RSC Adv, PMID 35530597

PXD069936 Dataset with its publication pending (from iProX)
Dataset title: The mass spectrometry data for Gp16
Possible reference: Dieterle, ME. et al. (2014) Exposing the secrets of two well-known Lactobacillus casei phages, J-1 and PL-1, by genomic and structural analysis., Appl Environ Microbiol, PMID 25217012

PXD069935 Dataset with its publication pending (from iProX)
Dataset title: Azeliragon for the treatment of Staphylococcus aureus proteome
Possible reference: Ma, J. et al. (2026) Repurposing Azeliragon as a novel antibacterial agent against methicillin-resistant Staphylococcus aureus via combined membrane phospholipids and cell wall targeting., Commun Biol, PMID 42135462

PXD069896 Dataset with its publication pending (from PRIDE)
Dataset title: The effect of ADAR1 depletion on mitochondrial proteins
Possible reference: Yin, X. et al. (2024) Exploration and Validation of Ferroptosis-Associated Genes in ADAR1 Deletion-Induced NAFLD through RNA-seq Analysis., Int Immunopharmacol, PMID 38696908

PXD069886 Christopher R. Below ? Oliver M. Bernhardt ? Stephanie Kaspar-Sch�nefeld ? Sander Willems ? Edoardo Coronado ? Ino D. Karemaker ? Bettina Streckenbach ? Monika Pepelnjak ? Luca R�ss ? Sandra Sch�r ? Dennis Trede ? Jonathan R. Krieger ? Tejas Gandhi ? Rola (from MassIVE)
Dataset title: Enhanced Identifications and Quantification through Retention Time Down-Sampling in Fast-Cycling diagonal-PASEF Methods
Possible reference: Below, CR. et al. (2026) Enhanced Identifications and Quantification Through Retention Time Down-Sampling in Fast-Cycling Diagonal-PASEF Methods., Mol Cell Proteomics, PMID 41380996

PXD069873 Dataset with its publication pending (from iProX)
Dataset title: ZmbZIP39 coordinates source-flow-sink relations to boost grain filling in maize
Possible reference: Yang, T. et al. (2026) ZmbZIP39 coordinates source-flow-sink relations to boost grain filling in maize., Plant Cell, PMID 41790798

PXD069856 no publication (from MassIVE)
Dataset title: Parallel Accumulation with Mobility-Aligned Fragmentation (PAMAF) datasets for xTracer
Possible reference: Song, J. et al. (2026) xTracer: Integrating chromatogram and mobiligram correlations for untargeted peptide identification in SLIM-based PAMAF data., bioRxiv, PMID 41726910

PXD069854 Dataset with its publication pending (from PRIDE)
Dataset title: A ZNF-nanobody fusion reveals SUMOylation-dependent changes in protein localization
Possible reference: Bouchard, AY. et al. (2026) A ZNF-nanobody fusion reveals SUMOylation-dependent changes in p53 protein localization., iScience, PMID 42063548

PXD069851 Dataset with its publication pending (from PRIDE)
Dataset title: Bovine Corpus Luteum Proteomics during Different Reproductive and Physiological Stages
Possible reference: Thaqi, G. et al. (2026) Bovine Corpus Luteum Proteomics during Different Reproductive and Physiological Stages., Sci Data, PMID 42236731

PXD069837 Dataset with its publication pending (from PRIDE)
Dataset title: Adhesion-derived condensates control component availability to regulate adhesion dynamics
Possible reference: Dibus, M. et al. (2026) Adhesion-derived condensates control component availability to regulate adhesion dynamics., Nat Commun, PMID 42248878

PXD069835 no publication (from MassIVE)
Dataset title: Monoclonal neutralizing antibodies elicited by infection with Kaposi sarcoma-associated herpesvirus reveal critical sites of vulnerability on gH/gL
Possible reference: Wan, YH. et al. (2026) Monoclonal neutralizing antibodies elicited by infection with Kaposi sarcoma-associated herpesvirus reveal critical sites of vulnerability on gH/gL., PLoS Pathog, PMID 41499715

PXD069821 no publication (from MassIVE)
Dataset title: Isolation defines identity: Functional consequences of EV purification strategies
Possible reference: Preu�er, C. et al. (2026) Isolation Defines Identity: Functional Consequences of Extracellular Vesicle Purification Strategies., Adv Healthc Mater, PMID 41555698

PXD069807 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic dataset of MECP2-deficient and wild-type human brain organoids under spaceflight and ground conditions
Possible reference: Martins, AMA. et al. (2026) Proteomic dataset of MECP2-deficient and wild-type human brain organoids under spaceflight and ground conditions., Sci Data, PMID 41714632

PXD069795 no publication (from MassIVE)
Dataset title: Lysosomal permeabilization by Group A Streptococcus releases proteins into the macrophage cytosol
Possible reference: Quezada, A. et al. (2025) Lysosomal permeabilization by Group A Streptococcus releases proteins into the macrophage cytosol., bioRxiv, PMID 41279162

PXD069758 Dataset with its publication pending (from iProX)
Dataset title: Proteomics and Acetyl-proteomics reveal the antibacterial mechanism of berberine sulfate against methicillin-resistant Staphylococcus aureus
Possible reference: Hu, Z. et al. (2025) Proteomics and acetyl-proteomics reveal the antibacterial mechanism of berberine sulfate against methicillin-resistant Staphylococcus aureus., Front Microbiol, PMID 41614126

PXD069757 Dataset with its publication pending (from iProX)
Dataset title: Integrative Dynamic proteomics and acyl-proteomics analyses in Clostridium butyricum
Possible reference: Li, G. et al. (2025) Integrative Dynamic Proteomics and Acyl-Proteomics Analyses in Clostridium butyricum., J Proteome Res, PMID 41224670

PXD069734 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-Pathway Regulatory role of miR-4693-5p in Rheumatoid Arthritis
Possible reference: Saquib, M. et al. (2025) Multi-pathway regulatory role of miR-4693-5p in the modulation of rheumatoid arthritis., Sci Rep, PMID 41430065

PXD069729 no publication (from MassIVE)
Dataset title: Combinatorial Use of VHL and KEAP1 PROTACs Reveals Unexpected Synergy and Hook Effect Relief
Possible reference: Islam, S. et al. (2026) Combinatorial use of VHL and KEAP1 PROTACs reveals unexpected synergy and hook effect relief., Genes Dev, PMID 41360670

PXD069719 Dataset with its publication pending (from iProX)
Dataset title: Comprehensive genome editing and signaling pathway engineering evolve potent and safe adenoviral producer cell
Possible reference: Deng, Z. et al. (2026) Comprehensive genome editing and signaling pathway engineering evolve potent and safe adenoviral producer cell., Commun Biol, PMID 42091678

PXD069706 Dataset with its publication pending (from PRIDE)
Dataset title: Syntaxin 4 (STX4) protects islet ï¢-cells from cytokine-induced senescence
Possible reference: Ahn, M. et al. (2026) Syntaxin 4 protects islet β-cells from cytokine-induced senescence., Front Endocrinol (Lausanne), PMID 41877925

PXD069696 Dataset with its publication pending (from iProX)
Dataset title: The proteomics of microalgal exosomes
Possible reference: Garaeva, L. et al. (2025) Microalgae-Derived Vesicles: Natural Nanocarriers of Exogenous and Endogenous Proteins., Plants (Basel), PMID 40805703

PXD069690 Dataset with its publication pending (from iProX)
Dataset title: Infectious EVs govern flavivirus infection in mosquitoes
Possible reference: Basak, S. et al. (2026) Persistent and Long-Term Infectivity of Dengue Virus in Mosquito Cells Revealed Reduced Replication in Vector Host and Human Endothelial Cells., Pathogens, PMID 41754454

PXD069689 Dataset with its publication pending (from iProX)
Dataset title: Orthogonal Ionic Liquid-based Extraction Strategy Enables Amyloid-Specific Profiling of the Aggregate Proteome
Possible reference: Zheng, S. et al. (2026) Orthogonal Ionic Liquid-Based Extraction Strategy Enables Amyloid-Specific Profiling of Aggregate Proteome., Adv Sci (Weinh), PMID 42007885

PXD069652 Dataset with its publication pending (from iProX)
Dataset title: Infectious EVs governs flavivirus infection in mosquitoes
Possible reference: Basak, S. et al. (2026) Persistent and Long-Term Infectivity of Dengue Virus in Mosquito Cells Revealed Reduced Replication in Vector Host and Human Endothelial Cells., Pathogens, PMID 41754454

PXD069645 Dataset with its publication pending (from iProX)
Dataset title: Regulation of Enrofloxacin drug resistance in bovine Pasteurella multocida strains by quorum-sensing acyl-homoserine lactone signaling molecules
Possible reference: Sun, M. et al. (2026) Regulation of drug resistance to enrofloxacin in Pasteurella multocida strains from cattle by quorum-sensing acyl-homoserine lactone signaling molecules., Front Microbiol, PMID 41668883

PXD069632 Dataset with its publication pending (from jPOST)
Dataset title: Mitochondrial contact site and cristae organizing system promotes modular assembly of cytochrome c oxidase
Possible reference: Colina-Tenorio, L. et al. (2026) Mitochondrial contact site and cristae organizing system promotes modular assembly of cytochrome c oxidase., Cell Rep, PMID 41420863

PXD069625 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery of Regulatory Complexes in Arabidopsis via Protein–Metabolite Mapping During Pseudomonas Infection
Possible reference: Kang, J. et al. (2026) Discovery of regulatory complexes in Arabidopsis via protein-metabolite mapping during Pseudomonas infection., Plant Physiol, PMID 42262578

PXD069604 no publication (from MassIVE)
Dataset title: A network of coiled-coil and actin-like proteins controls the cellular organization of magnetosome organelles in deep-branching magnetotactic bacteria
Possible reference: Russell, VV. et al. (2025) A network of coiled-coil and actin-like proteins controls the cellular organization of magnetosome organelles in deep-branching magnetotactic bacteria., bioRxiv, PMID 40060654

PXD069594 Dataset with its publication pending (from PRIDE)
Dataset title: A new role for lipoproteins LpqZ and FecB in orchestrating mycobacterial cell envelope biogenesis
Possible reference: Lissner, R. et al. (2026) A new role for lipoproteins LpqZ and FecB in orchestrating mycobacterial cell envelope biogenesis., mBio, PMID 41384969

PXD069585 Dataset with its publication pending (from jPOST)
Dataset title: Discovery of Chirally-dependent Protein O-2-Hydroxyglutarylation by D2HG and L2HG
Possible reference: Zhang, Z. et al. (2025) Discovery of Chirally-dependent Protein O-2-Hydroxyglutarylation by D2HG and L2HG., bioRxiv, PMID 39975355

PXD069576 Dataset with its publication pending (from iProX)
Dataset title: Tumor-derived CDC37 inhibits antigen cross-presentation in dendritic cells and impairs anti-tumor immunity in breast cancer
Possible reference: Wang, R. et al. (2026) Tumor-Derived CDC37 Inhibits Antigen Cross-Presentation in Dendritic Cells and Impairs Anti-Tumor Immunity in Breast Cancer., Adv Sci (Weinh), PMID 41215476

PXD069569 Dataset with its publication pending (from PRIDE)
Dataset title: G-CSF/NAMPT signaling drives neutrophil dysfunction and enhances bacterial infection susceptibility in cancer patients
Possible reference: Pylaeva, E. et al. (2025) G-CSF/NAMPT signaling drives neutrophil dysfunction and enhances bacterial infection susceptibility in cancer patients., Nat Commun, PMID 41387444

PXD069552 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of Ruegeria in response to coral tissue extract
Possible reference: Xie, M. et al. (2026) Trait-based signatures associated with persistence and thermal benefit in a genomically decayed coral probiotic., ISME J, PMID 42096550

PXD069550 Dataset with its publication pending (from PRIDE)
Dataset title: BORC assemblies integrate BLOC-1 subunits to diversify endosomal trafficking functions
Possible reference: de Araujo, MEG. et al. (2026) BORC assemblies integrate BLOC-1 subunits to diversify endosomal trafficking functions., Proc Natl Acad Sci U S A, PMID 41557793

PXD069538 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoprofile reorganization of the actin binding protein Drebrin during long term depression
Possible reference: Pedro Silva, R. et al. (2025) Phosphoprofile reorganization of the actin binding protein Drebrin during long term depression., Front Mol Neurosci, PMID 41268362

PXD069517 Dataset with its publication pending (from PRIDE)
Dataset title: Fecal metaproteome profiles of celiac disease patients with poly-autoimmunity
Possible reference: Abbondio, M. et al. (2026) A human fecal metaproteomic dataset from celiac disease patients on gluten-free diet with or without poly-autoimmunity., Data Brief, PMID 41657399

PXD069476 no publication (from MassIVE)
Dataset title: Asymmetric biphasic electric stimulation supports cardiac maturation and functionality
Possible reference: Sharpee, TO. et al. (2016) 25th Annual Computational Neuroscience Meeting: CNS-2016., BMC Neurosci, PMID 27534393

PXD069462 Dataset with its publication pending (from iProX)
Dataset title: Discovery of Novel MLKL PROTAC Degrader for the Treatment of Hepatocellular Carcinoma via Promoting Parthanatos
Possible reference: Chen, C. et al. (2026) Discovery of Novel MLKL PROTAC Degraders for the Treatment of Hepatocellular Carcinoma via Promoting Parthanatos., J Med Chem, PMID 41834604

PXD069456 no publication (from MassIVE)
Dataset title: Novel high-resolution ion mobility mass spectrometry for site-specific quantification of the sirtuin-5 regulated kidney succinylome
Possible reference: Schilling, B. et al. (2025) Novel high-resolution ion mobility mass spectrometry for site-specific quantification of the sirtuin-5 regulated kidney succinylome., bioRxiv, PMID 41279335

PXD069449 no publication (from MassIVE)
Dataset title: Secretory kinase FAM20C triggers adipocyte dysfunction inciting insulin resistance and inflammation in obesity
Possible reference: Gilani, A. et al. (2026) Secretory kinase FAM20C triggers adipocyte dysfunction, inciting insulin resistance and inflammation in obesity., J Clin Invest, PMID 41148235

PXD069435 Dataset with its publication pending (from iProX)
Dataset title: AutoGP 2: an improved fully automated high-throughput system for simultaneously enriching and separating intact glycopeptides
Possible reference: Hu, Z. et al. (2026) A fully automated high-throughput system for simultaneously enriching and separating intact glycopeptides., J Chromatogr A, PMID 41671804

PXD069433 Dataset with its publication pending (from iProX)
Dataset title: Macrophage MERTK restrains GRAMD1A‑driven mitochondrial cholesterol trafficking to limit colitis
Possible reference: Liu, J. et al. (2026) Macrophage MERTK restrains GRAMD1A-driven mitochondrial oxysterol trafficking to limit colitis., Redox Biol, PMID 42025057

PXD069422 Dataset with its publication pending (from iProX)
Dataset title: The Chinese mitten crab acetylation proteome
Possible reference: Cui, X. et al. (2025) Genome-wide identification of glutathione S-transferase (GST) gene family and its regulating characteristics responding to sperm capacitation in Eriocheir sinensis., Int J Biol Macromol, PMID 40054825

PXD069399 Dataset with its publication pending (from PRIDE)
Dataset title: An ATP-gated molecular switch orchestrates human messenger RNA export
Possible reference: Hohmann, U. et al. (2026) An ATP-gated molecular switch orchestrates human mRNA export., Nature, PMID 41198879

PXD069368 Dataset with its publication pending (from iProX)
Dataset title: A neurotoxic cryptic peptide arising from TDP-43-dependent cryptic splicing of PKN1
Possible reference: Yang, M. et al. (2026) A neurotoxic cryptic peptide arising from TDP-43-dependent cryptic splicing of PKN1., Nat Commun, PMID 41720774

PXD069347 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of Trichoderma harzianum gene expression and protein production in submerged cultures with inactivated oomycete mycelium
Possible reference: Anjago, WM. et al. (2026) Regulation of Trichoderma harzianum gene expression and protein production in submerged cultures with inactivated oomycete mycelium., Microbiol Res, PMID 41223685

PXD069320 no publication (from MassIVE)
Dataset title: Proteoform-Resolved Phosphorylation Dynamics in Kinase Complexes by Hybrid Precision Mass Spectrometry
Possible reference: Krichel, B. et al. (2025) Proteoform-Resolved Phosphorylation Dynamics in Kinase Complexes by Hybrid Precision Mass Spectrometry., bioRxiv, PMID 41279313

PXD069298 Dataset with its publication pending (from iProX)
Dataset title: Proteomics and Lactylome of osteoblast differentiation
Possible reference: Xu, X. et al. (2026) Lactylome-based investigation of osteoarthritic subchondral bone reveals cell-specific differential expression of histone H4K12 lactylation: an experimental study., Int J Surg, PMID 41677331

PXD069294 Dataset with its publication pending (from iProX)
Dataset title: Proteomic and metabolomic analysis of immune-related adverse events in patients treated with PD-1 inhibitors
Possible reference: Xu, B. et al. (2025) Multi-omics insights into gut microbial dysbiosis and metabolic alterations in immune checkpoint inhibitor-induced thrombocytopenia., Immunotherapy, PMID 41572827

PXD069286 Dataset with its publication pending (from iProX)
Dataset title: A novel tool for labeling intermediary proteins between two non-interacting proteins
Possible reference: Xie, L. et al. (2025) STUPPIT is a proximity labeling tool for labeling intermediary proteins that bridge two non-interacting proteins., PLoS Biol, PMID 41284752

PXD069282 Dataset with its publication pending (from PRIDE)
Dataset title: Degron models: a toolbox for rapid in vivo depletion of essential proteins regulating mRNA metabolism
Possible reference: Antczak, W. et al. (2026) Degron models: a toolbox for rapid in vivo depletion of essential proteins regulating mRNA metabolism., Commun Biol, PMID 41851445

PXD069251 Dataset with its publication pending (from PRIDE)
Dataset title: Small extracellular vesicles secreted by cisplatin-resistant neuroblastoma cells increase lactate secretion and alter metabolic pathways in primary human umbilical vein endothelial cells (HUVECs)
Possible reference: Frawley, T. et al. (2025) Small Extracellular Vesicles Secreted by Cisplatin-Resistant Neuroblastoma Cells Increase Lactate Secretion and Alter Metabolic Pathways in Primary Human Umbilical Vein Endothelial Cells (HUVECs)., J Pers Med, PMID 41440947

PXD069246 Dataset with its publication pending (from iProX)
Dataset title: TIGAR Regulates Intestinal Mucus Barrier Integrity by Inhibiting Lactylation of G6PD/6PGD in Ulcerative Colitis
Possible reference: Wu, D. et al. (2026) TIGAR regulates intestinal mucus barrier integrity by inhibiting lactylation of G6PD/6PGD in ulcerative colitis., Nat Commun, PMID 41776188

PXD069237 Dataset with its publication pending (from iProX)
Dataset title: Proteomic responses to progressive dehydration and rehydration in Xenopus laevis
Possible reference: Zhang, B. et al. (2025) Proteomic responses to progressive dehydration and rehydration in Xenopus laevis., Comp Biochem Physiol Part D Genomics Proteomics, PMID 41101171

PXD069229 Dataset with its publication pending (from iProX)
Dataset title: Qualitative detection of ASPHD1-interacting proteins in the glioblastoma cell line U87
Possible reference: Han, L. et al. (2018) Cytocidal effects of arenobufagin and hellebrigenin, two active bufadienolide compounds, against human glioblastoma cell line U-87., Int J Oncol, PMID 30272276

PXD069222 Dataset with its publication pending (from PRIDE)
Dataset title: The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration
Possible reference: Punga, T. et al. (2026) The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration., Sci Rep, PMID 42062449

PXD069221 Dataset with its publication pending (from PRIDE)
Dataset title: The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration
Possible reference: Punga, T. et al. (2026) The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration., Sci Rep, PMID 42062449

PXD069216 Dataset with its publication pending (from PRIDE)
Dataset title: The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration
Possible reference: Punga, T. et al. (2026) The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration., Sci Rep, PMID 42062449

PXD069211 no publication (from MassIVE)
Dataset title: What does next generation Mass Spectrometry offer for proteomics? A comprehensive platform comparison
Possible reference: Blasco Tavares Pereira Lopes, F. et al. (2026) What Does Next-Generation Mass Spectrometry Offer for Proteomics? A Comprehensive Platform Comparison., J Proteome Res, PMID 41882496

PXD069192 Dataset with its publication pending (from PRIDE)
Dataset title: The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration
Possible reference: Punga, T. et al. (2026) The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration., Sci Rep, PMID 42062449

PXD069175 Dataset with its publication pending (from PRIDE)
Dataset title: The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration.
Possible reference: Punga, T. et al. (2026) The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration., Sci Rep, PMID 42062449

PXD069174 Dataset with its publication pending (from PRIDE)
Dataset title: The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration.
Possible reference: Punga, T. et al. (2026) The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration., Sci Rep, PMID 42062449

PXD069168 no publication (from MassIVE)
Dataset title: The CTLH Ubiquitin Ligase Substrates ZMYND19 and MKLN1 Negatively Regulate mTORC1 at the Lysosomal Membrane
Possible reference: Wang, Y. et al. (2024) The CTLH Ubiquitin Ligase Substrates ZMYND19 and MKLN1 Negatively Regulate mTORC1 at the Lysosomal Membrane., Res Sq, PMID 38746323

PXD069158 Dataset with its publication pending (from PRIDE)
Dataset title: TIGAR Regulates Intestinal Mucus Barrier Integrity by Inhibiting Lactylation of G6PD/6PGD in Ulcerative Colitis
Possible reference: Wu, D. et al. (2026) TIGAR regulates intestinal mucus barrier integrity by inhibiting lactylation of G6PD/6PGD in ulcerative colitis., Nat Commun, PMID 41776188

PXD069097 no publication (from MassIVE)
Dataset title: Multiplexed Data-independent Acquisition-based Proteomics Enabled by TMTpro Complementary Ions
Possible reference: Wang, Z. et al. (2025) Multiplexed Data-Independent Acquisition-Based Proteomics Enabled by TMTpro Complementary Ions., Anal Chem, PMID 41293887

PXD069095 Dataset with its publication pending (from PRIDE)
Dataset title: Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells
Possible reference: Els�sser, F. et al. (2026) Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells., Mol Syst Biol, PMID 41526500

PXD069074 Dataset with its publication pending (from PRIDE)
Dataset title: Lung adenocarcinoma surfaceome remodeling with EGFR inhibitors uncovers placental alkaline phosphatase as a target for combination therapy
Possible reference: Chen, Y. et al. (2025) Lung adenocarcinoma surfaceome remodeling with EGFR inhibitors uncovers placental alkaline phosphatase as a target for combination therapy., Cell Rep Med, PMID 41406940

PXD069055 Dataset with its publication pending (from PRIDE)
Dataset title: Sialoglycans Modulate Siglec-5 – TLR4 Interactions in Osteoarthritis
Possible reference: R�berg, L. et al. (2025) Sialoglycans modulate Siglec-5-TLR4 interactions in osteoarthritis., iScience, PMID 41358156

PXD069053 Dataset with its publication pending (from PRIDE)
Dataset title: Retinal proteome in models with compromised lysosomal function
Possible reference: Kapphahn, RJ. et al. (2019) Lipid-derived and other oxidative modifications of retinal proteins in a rat model of Smith-Lemli-Opitz syndrome., Exp Eye Res, PMID 30114413

PXD069047 no publication (from MassIVE)
Dataset title: PHIP suppresses NuRD to enable the growth of SWI/SNF-mutant cancers
Possible reference: Malone, HA. et al. (2026) PHIP suppresses NuRD to enable the growth of SWI/SNF-mutant cancers., Nat Commun, PMID 41946722

PXD069037 Dataset with its publication pending (from PRIDE)
Dataset title: Spatiotemporal control of PIWI compartmentalization by mitochondrial scaffolds defines pachytene piRNA pathway organization
Possible reference: Yan, X. et al. (2025) Spatiotemporal control of PIWI compartmentalization by mitochondrial scaffolds defines pachytene piRNA pathway organization., bioRxiv, PMID 41280110

PXD069027 Dataset with its publication pending (from PRIDE)
Dataset title: Biallelic variants in CHCHD4 are associated with combined OXPHOS defect leading to mitochondrial disease
Possible reference: Mantecon, M. et al. (2026) Biallelic variants in CHCHD4 are associated with combined OXPHOS defect leading to mitochondrial disease., HGG Adv, PMID 41981912

PXD069004 Dataset with its publication pending (from PRIDE)
Dataset title: Peptidoglycan recycling is critical for cell division, cell wall integrity and Î²-lactam resistance in Caulobacter crescentus
Possible reference: Richter, P. et al. (2026) Peptidoglycan recycling is critical for cell division, cell wall integrity, and β-lactam resistance in Caulobacter crescentus., Elife, PMID 41925725

PXD069003 no publication (from MassIVE)
Dataset title: Expanding the human metaproteome: enhancing small open reading frame (smORF) prediction and ultra-deep detection of smORF-encoded proteins in the gut microbiome
Possible reference: Davin, ME. et al. (2026) High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome., Nat Commun, PMID 42106331

PXD068995 Dataset with its publication pending (from PRIDE)
Dataset title: PROTAC Mediated Structure-Function Disruption of CD26 A Therapeutic Strategy for Driver Negative NSCLC
Possible reference: Zhang, G. et al. (2025) PROTAC-mediated structure-function disruption of CD26: a therapeutic strategy for driver-negative non-small cell lung cancer., EBioMedicine, PMID 41237665

PXD068994 no publication (from MassIVE)
Dataset title: Hyaluronic acid decoration facilitates CD44-mediated targeting and alters protein corona formation of extracellular vesicles
Possible reference: Kyykallio, H. et al. (2026) Hyaluronic Acid Decoration Facilitates CD44-Mediated Targeting and Alters Protein Corona Formation of Extracellular Vesicles., J Extracell Vesicles, PMID 41885409

PXD068991 Dataset with its publication pending (from iProX)
Dataset title: Microglial NLRC5 Drives Lysosomal Dysfunction to Disrupt Autophagic Flux and Promote Post-Stroke Neuroinflammation
Possible reference: Xu, S. et al. (2025) Microglial NLRC5 drives lysosomal dysfunction to disrupt autophagic flux and promote post-stroke neuroinflammation., J Neuroinflammation, PMID 41174779

PXD068977 Dataset with its publication pending (from iProX)
Dataset title: Genomic and Proteomic Characterization of the Deltamethrin-Degrading Bacterium Paracoccus Sp. P-2.
Possible reference: Li, Q. et al. (2025) Genomic and Proteomic Characterization of the Deltamethrin-Degrading Bacterium Paracoccus sp. P-2., Microorganisms, PMID 41304166

PXD068969 no publication (from MassIVE)
Dataset title: Proteomics analysis of Hydractinia symbiolongicarpus nematocysts
Possible reference: Klompen, AML. et al. (2026) Proteomic analysis of FACS-enriched whole nematocysts from the colonial hydrozoan Hydractinia symbiolongicarpus., Toxicon X, PMID 41767043

PXD068963 no publication (from MassIVE)
Dataset title: PhosphoProteomic and Kinase Expression Networks Reveal Partial EMT and Adaptive Growth Programs in Pediatric Peutz-Jeghers Polyps
Possible reference: Pushel, I. et al. (2026) Phosphoproteomic and kinase networks reveal partial EMT and stress-adaptive growth programs in pediatric Peutz-Jeghers polyps., Pediatr Res, PMID 42082734

PXD068958 no publication (from MassIVE)
Dataset title: Urinary Proteomic Profiling in Pregnancies Affected by Fetal Aneuploidies
Possible reference: Jurca, RL. et al. (2025) Exploratory Urinary Proteomic Profiling in Pregnancies with Fetal Aneuploidies: Molecular Insights into Maternal-Fetal Metabolic Communication., Curr Issues Mol Biol, PMID 41614738

PXD068953 Dataset with its publication pending (from iProX)
Dataset title: Nearly complete redirection of insertion-type indel into recombination enhances knock-in and facilitates endogenous biomolecular condensate analysis
Possible reference: Huang, M. et al. (2025) Nearly complete redirection of insertion-type indel into recombination enhances knock-in and facilitates endogenous biomolecular condensate analysis., Cell Res, PMID 41152564

PXD068941 Dataset with its publication pending (from iProX)
Dataset title: PARP1-mediated TEAD4 PARylation stabilizes YAP1-TEAD4 complex and promotes the malignancy and immune evasion of breast cancer
Possible reference: Guo, Y. et al. (2025) PARP1-mediated PARylation of TEAD4 stabilizes the YAP1-TEAD4 complex and promotes growth and immune evasion in breast cancer cells., Sci Signal, PMID 41118450

PXD068932 Dataset with its publication pending (from iProX)
Dataset title: The H3K27me3 reader UAD-2 recruits a TAF-12-containing transcription machinery to initiate piRNA expression within heterochromatic clusters
Possible reference: Huang, X. et al. (2025) The H3K27me3 reader UAD-2 recruits a TAF-12-containing transcription machinery to initiate piRNA expression within heterochromatic clusters., Nat Commun, PMID 41298378

PXD068923 Dataset with its publication pending (from iProX)
Dataset title: UBE2S-Mediated Deubiquitination of GLUT1 via USP10 Regulates Glucose Metabolic Reprogramming and Immune Microenvironment to Promote Fibrosis in Endometriosis
Possible reference: Wang, B. et al. (2025) UBE2S-mediated deubiquitination of GLUT1 via USP10 regulates glucose metabolic reprogramming and immune microenvironment to promote fibrosis in endometriosis., J Transl Med, PMID 41351058

PXD068918 Dataset with its publication pending (from iProX)
Dataset title: OTUD7B promotes cardiac hypertrophy by deubiquitinating SERCA2a
Possible reference: Huang, Z. et al. (2026) Cardiomyocyte-derived OTUD7B promotes cardiac hypertrophy by deubiquitinating SERCA2a., Theranostics, PMID 41695487

PXD068917 Dataset with its publication pending (from iProX)
Dataset title: Promoting Astrocyte-Neuron Triiodothyronine Shuttling Attenuates Brain Damage in Neonatal Hypoxic-Ischemic Encephalopathy
Possible reference: Yu, G. et al. (2025) Promoting astrocyte-neuron triiodothyronine shuttling attenuates brain damage in neonatal hypoxic-ischemic encephalopathy., J Neuroinflammation, PMID 41331484

PXD068912 Dataset with its publication pending (from PRIDE)
Dataset title: Arginine deprivation of ASS1-deficient cancers drives mistranslation and shared neoepitope production
Possible reference: Nagel, R. et al. (2026) Arginine Deprivation of ASS1-Deficient Cancers Drives Mistranslation and Shared Neoepitope Production., Cancer Res, PMID 42095547

PXD068911 Dataset with its publication pending (from PRIDE)
Dataset title: Enterohemorrhagic Escherichia coli O157:H7 responds to norepinephrine gradients by tRNA reprogramming and codon-biased translation of virulence genes
Possible reference: McShane, AE. et al. (2026) Enterohemorrhagic Escherichia coli O157:H7 responds to norepinephrine gradients by tRNA reprogramming and codon-biased translation of virulence genes., mSystems, PMID 42017662

PXD068909 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated tissue and serum proteomics on magnet-guided photothermal therapy using Au/Fe/Au trilayer nanodiscs
Possible reference: Lee, SY. et al. (2025) Integrated tissue and serum proteomics on magnet-guided photothermal therapy using Au/Fe/Au trilayer nanodiscs., Sci Rep, PMID 41361001

PXD068884 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanisms affecting fluoride tolerance in the environmental bacterium Pseudomonas putida
Possible reference: Calero, P. et al. (2022) Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride., Environ Microbiol, PMID 35726888

PXD068880 no publication (from MassIVE)
Dataset title: Integrated PhosphoProteomic and Kinase Expression Networks Reveal Partial EMT and Adaptive Growth Programs in Pediatric Peutz-Jeghers Polyps
Possible reference: Pushel, I. et al. (2026) Phosphoproteomic and kinase networks reveal partial EMT and stress-adaptive growth programs in pediatric Peutz-Jeghers polyps., Pediatr Res, PMID 42082734

PXD068863 Dataset with its publication pending (from iProX)
Dataset title: MIAT-DHX9 spatiotemporal expression drives venous neointimal hyperplasia through nucleolar homeostasis and mitotic progression
Possible reference: Lou, Y. et al. (2025) MIAT-DHX9 spatiotemporal expression drives venous neointimal hyperplasia through nucleolar homeostasis and mitotic progression., Cell Rep, PMID 41259202

PXD068816 Dataset with its publication pending (from iProX)
Dataset title: Anisodine Hydrobromide Targets Matk and Prevents Delayed rtPA Thrombolysis-Induced Vasogenic Cerebral Edema in Ischemic Stroke
Possible reference: Guo, S. et al. (2026) Anisodine hydrobromide targets matk and prevents delayed rtPA thrombolysis-induced vasogenic cerebral edema in ischemic stroke., Nat Commun, PMID 42259802

PXD068736 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omics of barley Fusarium Head Blight converge on pathogen-triggered biosynthesis of aromatic amino acid derived chemical defense compounds
Possible reference: Hein, S. et al. (2026) Multi-omics of barley Fusarium Head Blight converge on pathogen-triggered biosynthesis of aromatic amino acid derived chemical defense compounds., Stress Biol, PMID 42223798

PXD068723 Dataset with its publication pending (from iProX)
Dataset title: H3K4me1 directs H3K36me2 and H3K36me3 deposition in land plants
Possible reference: Wu, J. et al. (2026) H3K4me1 directs H3K36me2 and H3K36me3 deposition in land plants., Nat Commun, PMID 41698948

PXD068708 Dataset with its publication pending (from iProX)
Dataset title: Multi-Omics Profiling Uncovers Metabolic Regulation in Cumulus Cells During Oocyte Maturation
Possible reference: Kassim, Y. et al. (2026) Multi-omics profiling uncovers metabolic regulation in cumulus cells during oocyte maturation., Anim Reprod Sci, PMID 41679094

PXD068690 no publication (from MassIVE)
Dataset title: Dictyostelium CAGE complex: a hollow, megadalton, protein assembly
Possible reference: McCafferty, CL. et al. (2025) The CAGE complex: a hollow, megadalton, protein assembly in prokaryotic and eukaryotic microbes., bioRxiv, PMID 41040395

PXD068658 Dataset with its publication pending (from iProX)
Dataset title: Onobrychis viciifolia Proteomics
Possible reference: Gazzonis, AL. et al. (2023) In Vitro Evaluations and Comparison of the Efficacy of Two Commercial Products Containing Condensed Tannins and of Saifoin (Onobrychis viciifolia Scop.) Hay against Gastrointestinal Nematodes of Goats., Animals (Basel), PMID 36766435

PXD068645 Dataset with its publication pending (from iProX)
Dataset title: IBT16plex-based Quantitative Proteomics: Enabling Protein Profiles of Mouse Spleen Tissues at the Single Cell Level
Possible reference: Ning, X. et al. (2025) IBT-16plex-Based Quantitative Proteomics at the Single-Cell Level: Enabling Protein Profiles toward the Single Cells from Mouse Spleen., Anal Chem, PMID 41257469

PXD068642 Dataset with its publication pending (from iProX)
Dataset title: Metabolomics data of bamboo under stress treatment
Possible reference: Liu, S. et al. (2026) PagMYB74 orchestrates flavonoid-mediated plant-microbe feedback for drought resilience in poplar., New Phytol, PMID 41840421

PXD068629 Dataset with its publication pending (from iProX)
Dataset title: A PSAT1 buff of YBX1 transcriptionally sustains HLA-E-mediated�evasion of NK immunity
Possible reference: Zhang, Y. et al. (2025) A PSAT1 buff of YBX1 transcriptionally sustains HLA-E-mediated evasion of NK immunity., Proc Natl Acad Sci U S A, PMID 41428871

PXD068628 Dataset with its publication pending (from iProX)
Dataset title: Nicotinamide mononucleotide treatment improves spermatogenesis in obese mice by reducing lysine acetylation of lactate dehydrogenase C
Possible reference: Liu, K. et al. (2025) Nicotinamide mononucleotide treatment improves spermatogenesis in obese mice by reducing lysine acetylation of lactate dehydrogenase C., Commun Biol, PMID 41298813

PXD068582 no publication (from MassIVE)
Dataset title: The proteomics and phosphoproteomics landscape of melanoma under T cell attack
Possible reference: Franciosa, G. et al. (2026) The proteomics and phosphoproteomics landscape of melanoma under T cell attack., Cell Rep Med, PMID 42167233

PXD068569 Dataset with its publication pending (from PRIDE)
Dataset title: Nucleoside Binding by a Surface Lipoprotein Governs Conjugative ICE Acquisition in Ruminant Mycoplasmas
Possible reference: Derriche, M. et al. (2026) Nucleoside binding by a surface lipoprotein governs conjugative ICE acquisition in mycoplasmas., mBio, PMID 41467788

PXD068568 Dataset with its publication pending (from jPOST)
Dataset title: Arabidopsis root lipid droplets are hubs for membrane homeostasis under heat stress, and triterpenoid synthesis and storage
Possible reference: Scholz, P. et al. (2026) Arabidopsis root lipid droplets are hubs for membrane homeostasis under heat stress, and triterpenoid synthesis and storage., New Phytol, PMID 41292132

PXD068555 Dataset with its publication pending (from PRIDE)
Dataset title: A genetic screen reveals a key role for Reg1 in 2-deoxyglucose sensing and yeast AMPK inhibition
Possible reference: Ballin, A. et al. (2025) A genetic screen reveals a key role for Reg1 in 2-deoxyglucose sensing and yeast AMPK inhibition., PLoS Genet, PMID 41066605

PXD068553 Dataset with its publication pending (from PRIDE)
Dataset title: Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
Possible reference: Konstantinou, A. et al. (2026) Systematic discovery of motif-based interactions of the auxiliary domains of USP family deubiquitinases., Nat Commun, PMID 42151178

PXD068521 Dataset with its publication pending (from jPOST)
Dataset title: Sequential Denaturation and Protein Precipitation assay (SDPP) improves the sensitivity for ligand target identification at the proteome level
Possible reference: Ma, Y. et al. (2025) Sequential denaturation and protein precipitation assay (SDPP) improves the sensitivity for ligand target identification at the proteome level., Anal Chim Acta, PMID 41167885

PXD068506 Dataset with its publication pending (from iProX)
Dataset title: Colon-Targeted Astragalus Polysaccharide Nanoparticles Prevent NAFLD-Driven Hepatocarcinogenesis via Microbiota Remodeling and NF-ÎºB Inhibition
Possible reference: Liu, D. et al. (2025) Colon-Targeted astragalus polysaccharide nanoparticles prevent NAFLD-Driven hepatocarcinogenesis via microbiota remodeling and NF-κB Inhibition., J Exp Clin Cancer Res, PMID 41422246

PXD068504 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping the complexity of ME/CFS: Evidence for abnormal energy metabolism, altered immune profile and vascular dysfunction
Possible reference: Heng, B. et al. (2025) Mapping the complexity of ME/CFS: Evidence for abnormal energy metabolism, altered immune profile, and vascular dysfunction., Cell Rep Med, PMID 41406947

PXD068468 Dataset with its publication pending (from PRIDE)
Dataset title: High-purity isolation and chemical composition of stabilisomes from thermophilic cyanobacteria
Possible reference: Wang, C. et al. (2026) High-Purity Isolation of Polyphosphate-Rich Stabilisomes Defines Their Conserved Chemical Architecture in Thermophilic Cyanobacteria., Plants (Basel), PMID 41681662

PXD068459 Dataset with its publication pending (from iProX)
Dataset title: Gut microbial genetic variation prolongs host healthy longevity and remodels metabolome and proteome in Drosophila melanogaster
Possible reference: Wang, L. et al. (2025) Gut Microbial Genetic Variation Prolongs Host Healthy Longevity and Remodels Metabolome and Proteome in Drosophila Melanogaster., Adv Sci (Weinh), PMID 41013900

PXD068448 Dataset with its publication pending (from iProX)
Dataset title: Serum metabolomics reveal metabolic changes in coal workers’ pneumoconiosis progression
Possible reference: Xu, J. et al. (2026) Serum metabolomics reveal metabolic changes in coal workers' pneumoconiosis progression., J Pharm Biomed Anal, PMID 41687223

PXD068434 no publication (from MassIVE)
Dataset title: A mouse model of MEPAN demonstrates a role for mitochondrial fatty acid synthesis in iron sulfur cluster and supercomplex formation
Possible reference: Murdock, DG. et al. (2025) A mouse model of MEPAN demonstrates a role for mitochondrial fatty acid synthesis in iron-sulfur cluster and supercomplex formation., Proc Natl Acad Sci U S A, PMID 41021813

PXD068429 Dataset with its publication pending (from PRIDE)
Dataset title: Mitotic entry is controlled by the plant-specific phosphatase BSL1 and cyclin-dependent kinase B
Possible reference: Tulin, F. et al. (2025) Mitotic entry is controlled by the plant-specific phosphatase BSL1 and cyclin-dependent kinase B., bioRxiv, PMID 40777456

PXD068425 Dataset with its publication pending (from PRIDE)
Dataset title: Deciphering Photosynthetic Protein Networks: A Crosslinking-MS Strategy for Studying Functional Thylakoid Membranes
Possible reference: Frances, N. et al. (2026) Deciphering photosynthetic protein networks: a�crosslinking-MS strategy for studying functional thylakoid�membranes., Plant J, PMID 42251534

PXD068387 Dataset with its publication pending (from PRIDE)
Dataset title: Dysregulation of muscle myosin biochemical states in X-linked myotubular myopathy
Possible reference: Laitila, J. et al. (2024) Myosin ATPase inhibition fails to rescue the metabolically dysregulated proteome of nebulin-deficient muscle., J Physiol, PMID 39216086

PXD068359 no publication (from MassIVE)
Dataset title: Patch-Clamp Single-Cell Proteomics of Rat Prefrontal Cortex Neurons
Possible reference: Rodriguez, L. et al. (2025) Patch-Clamp Single-Cell Proteomics in Acute Brain Slices: A Framework for Recording, Retrieval, and Interpretation., bioRxiv, PMID 41000636

PXD068321 no publication (from MassIVE)
Dataset title: Structural Basis for TRF2-RAP1 Recruitment by EBNA1 at the EBV origin of replication
Possible reference: Lieberman, P. et al. (2025) Structural Basis for TRF2-RAP1 Recruitment by EBNA1 at the EBV origin of replication., Res Sq, PMID 41282254

PXD068299 Dataset with its publication pending (from iProX)
Dataset title: Inhibition of apoptosis in breast cancer cells by si-FoxO3a through the protein digestion and absorption signaling pathway
Possible reference: Sun, L. et al. (2025) Inhibition of apoptosis in breast cancer cells by si-FoxO3a through the protein digestion and absorption signaling pathway., Oncol Lett, PMID 41169349

PXD068295 no publication (from PanoramaPublic)
Dataset title: Quantitative protein analysis and glycan profiling of umbilical cord plasma and corresponding maternal plasma samples
Possible reference: Benešová, E. et al. (2026) Quantitative protein analysis and glycan profiling of umbilical cord plasma and corresponding maternal plasma samples., Sci Rep, PMID 41813832

PXD068280 Dataset with its publication pending (from iProX)
Dataset title: Intracellular macroproteomics analysis
Possible reference: Guo, W. et al. (2022) Stem cells from human exfoliated deciduous teeth affect mitochondria and reverse cognitive decline in a senescence-accelerated mouse prone 8 model., Cytotherapy, PMID 34598900

PXD068270 Dataset with its publication pending (from iProX)
Dataset title: Pyruvate metabolism enzyme Dlat induces mitochondria protein hyperacetylation to limit fatty acid oxidation in the HFpEF heart
Possible reference: Wang, Y. et al. (2026) Pyruvate metabolism enzyme Dlat induces mitochondria protein hyperacetylation to limit fatty acid oxidation in the HFpEF heart., Nat Commun, PMID 41826295

PXD068257 Dataset with its publication pending (from PRIDE)
Dataset title: Antigen-specific IgG Glycosylation Profiles in Hamsters and Macaques Following COVID-19 Vaccination
Possible reference: Claushuis, B. et al. (2026) Antigen-specific IgG glycosylation profiles in hamsters and macaques following COVID-19 vaccination., iScience, PMID 41953001

PXD068246 Dataset with its publication pending (from iProX)
Dataset title: Alteration of the Secretome in Airway Epithelial Cells by air pollutes: Evidence from an Air-Liquid Interface Model
Possible reference: Lu, H. et al. (2025) Alteration of the Secretome in Airway Epithelial Cells by Air Pollutants: Evidence from an Air-Liquid Interface Model., Lung, PMID 41081902

PXD068239 Dataset with its publication pending (from iProX)
Dataset title: IP-MS identifies TRIM3-interacting proteins in H1299 cells
Possible reference: Mao, CG. et al. (2020) BCAR1 promotes proliferation and cell growth in lung adenocarcinoma via upregulation of POLR2A., Thorac Cancer, PMID 33001583

PXD068214 no publication (from MassIVE)
Dataset title: PHF19 drives the formation of PRC2 clusters to enhance motility in TNBC cells
Possible reference: Pelzer, N. et al. (2025) PHF19 drives the formation of PRC2 clusters to enhance motility in TNBC cells., Cell Rep, PMID 41066230

PXD068208 Dataset with its publication pending (from jPOST)
Dataset title: Notch signaling regulates the secretion of pro-metastatic factors in extracellular vesicles in liposarcoma
Possible reference: Quan, M. et al. (2026) Notch signaling regulates the secretion of pro-metastatic factors in extracellular vesicles in liposarcoma., Cancer Lett, PMID 42036011

PXD068183 Dataset with its publication pending (from PRIDE)
Dataset title: Vesicle-mediated mitochondrial clearance presents an actionable metabolic vulnerability in triple-negative breast cancer
Possible reference: Vykoukal, J. et al. (2025) Vesicle-mediated mitochondrial clearance presents an actionable metabolic vulnerability in triple-negative breast cancer., Cell Rep Med, PMID 41406946

PXD068170 Dataset with its publication pending (from iProX)
Dataset title: Functional S-persulfidation Exploration Reveals a Novel Regulatory Mechanism of HNF1Î±
Possible reference: Huang, Y. et al. (2025) Functional S-persulfidation exploration reveals a novel regulatory mechanism of HNF1α., Redox Biol, PMID 41274036

PXD068154 Dataset with its publication pending (from iProX)
Dataset title: mTORC1 Regulates Autophagosomal Components Recycling 1 through SNX16 Phosphorylation
Possible reference: Que, H. et al. (2025) mTORC1 regulates autophagosomal components recycling through SNX16 phosphorylation., Proc Natl Acad Sci U S A, PMID 41237209

PXD068129 Dataset with its publication pending (from PRIDE)
Dataset title: On the feasibility of clinical studies with cross-linking mass spectrometry
Possible reference: Park, SG. et al. (2026) On the Feasibility of Clinical Studies with Cross-Linking Mass Spectrometry., J Proteome Res, PMID 41529186

PXD068123 Mona Gr�nwald, Nabil Adrar, George Francis, Nils Rugen, Matthias D�ring, Hans-Peter Braun, Tuba Esatbeyoglu. A comparative study of the nutritional and physiological potential of Xuta (edible Jatropha curcas L.) protein: Insights into its digestibility an (from MassIVE)
Dataset title: Nutritional Potential of Xuta (Jatropha curcas L.) Protein
Possible reference: Gr�nwald, M. et al. (2026) A comparative study of the nutritional and physiological potential of Xuta (edible Jatropha curcas L.) protein: Insights into its digestibility and effects on the intestinal barrier., Curr Res Food Sci, PMID 41477029

PXD068122 Dataset with its publication pending (from PRIDE)
Dataset title: Locus-specific proteomics identifies CHD4 and Polycomb PRC1 as novel repressors of Epstein-Barr virus lytic reactivation
Possible reference: Greaves, DE. et al. (2026) Locus-specific proteomics identifies novel regulators of Epstein-Barr virus lytic reactivation., J Virol, PMID 41841741

PXD068119 Dataset with its publication pending (from PRIDE)
Dataset title: A developmental condensin I complex assists the Paramecium PiggyMac domesticated transposase during programmed DNA elimination
Possible reference: Balan, T. et al. (2026) A developmental condensin I complex assists the Paramecium PiggyMac domesticated transposase during programmed DNA elimination., Nucleic Acids Res, PMID 42003548

PXD068115 Dataset with its publication pending (from iProX)
Dataset title: Plasma lipidomics for Biomarker Identification In non-muscle invasive bladder cancer
Possible reference: Zhao, Y. et al. (2025) Plasma lipidomics for biomarker identification in non-muscle invasive bladder cancer., BMC Cancer, PMID 41188770

PXD068106 no publication (from MassIVE)
Dataset title: Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome
Possible reference: Becker, AP. et al. (2024) Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome., bioRxiv, PMID 39229057

PXD068104 no publication (from MassIVE)
Dataset title: Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome
Possible reference: Becker, AP. et al. (2024) Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome., bioRxiv, PMID 39229057

PXD068092 Dataset with its publication pending (from jPOST)
Dataset title: Notch signaling regulates the secretion of pro-metastatic factors in extracellular vesicles in liposarcoma
Possible reference: Quan, M. et al. (2026) Notch signaling regulates the secretion of pro-metastatic factors in extracellular vesicles in liposarcoma., Cancer Lett, PMID 42036011

PXD068050 Dataset with its publication pending (from iProX)
Dataset title: ProteomicsAnalyzer: A Scalable and Integrated Platform for Robust Multi-Source Proteomics Data Harmonization
Possible reference: Ren, Y. et al. (2026) ProteoIntegrator: A Scalable and Integrated Platform for Robust Multi-Source Proteomics Data Harmonization, Differential and Functional Analysis., Anal Chem, PMID 42175890

PXD068043 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic evaluation and comparison of native and decellularized human saphenous vein extracellular matrices
Possible reference: Niemi, EM. et al. (2026) Proteomic evaluation and comparison of native and decellularized human saphenous vein extracellular matrices., Front Bioeng Biotechnol, PMID 41982326

PXD068042 Dataset with its publication pending (from jPOST)
Dataset title: TAG-PL: A Universal Proximity Labeling Platform for Mapping Mitochondrial Proteomes and Organelle Interactions Under Stress
Possible reference: Miao, E. et al. (2026) TAG-PL: A Universal Proximity Labeling Platform for Mapping Mitochondrial Proteomes and Organelle Interactions under Stress., J Proteome Res, PMID 41432230

PXD068021 Dataset with its publication pending (from PRIDE)
Dataset title: Structural basis of T-loop-independent recognition and activation of CDKs by the CDK-activating kinase
Possible reference: Cushing, VI. et al. (2025) Structural basis of T-loop-independent recognition and activation of CDKs by the CDK-activating kinase., Science, PMID 41100585

PXD068012 Dataset with its publication pending (from PRIDE)
Dataset title: VE-cadherin interaction proteomics identifies ARVCF as a key stabilizer of endothelial adherens junctions
Possible reference: Schoon, RM. et al. (2026) VE-cadherin interaction proteomics identifies ARVCF as stabilizer of endothelial adherens junctions., iScience, PMID 42006337

PXD068011 Dataset with its publication pending (from iProX)
Dataset title: Gastric mucosal proteomic analysis reveals the role of TGF-Î² signaling pathway in gastritis associated with Helicobacter pylori infection
Possible reference: Zhu, C. et al. (2025) Gastric mucosal proteomic analysis reveals the role of the TGF-β signaling pathway in gastritis associated with Helicobacter pylori infection., Front Microbiol, PMID 41035878

PXD068006 Dataset with its publication pending (from PRIDE)
Dataset title: Plastic associated endocrine disruptors reduce Nicastrin protein and potentiate inflammation in Hidradenitis Suppurativa skin disease
Possible reference: Williams, KL. et al. (2025) Plastic associated endocrine disruptors reduce Nicastrin protein and potentiate inflammation in hidradenitis suppurativa skin disease., Nat Commun, PMID 41315355

PXD067996 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative analysis of proteomic changes in monoclonal MDCK cell lines infected with human influenza A virus
Possible reference: K�chler, J. et al. (2025) Quantitative analysis of proteomic changes in two monoclonal suspension MDCK cell lines infected with human influenza A virus (H1N1)., PLoS One, PMID 41118376

PXD067973 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic characterization of adipose tissue from cold-exposed mice
Possible reference: Zhu, Q. et al. (2026) Temporal transcriptomic and proteomic characterization of adipose tissue from cold-exposed mice., Sci Data, PMID 41629358

PXD067966 Dataset with its publication pending (from iProX)
Dataset title: A Cancer-Specific Antigen Drives Histone Acetylation by Stabilizing the Acetyltransferases
Possible reference: Fu, X. et al. (2025) A cancer-specific antigen drives histone acetylation by stabilizing the acetyltransferases., Cell Rep, PMID 41060806

PXD067955 Dataset with its publication pending (from PRIDE)
Dataset title: Florigen activation complex forms via multifaceted assembly in Arabidopsis
Possible reference: Gao, H. et al. (2025) Florigen activation complex forms via multifaceted assembly in Arabidopsis., Nature, PMID 41225013

PXD067949 Dataset with its publication pending (from PRIDE)
Dataset title: Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation
Possible reference: Worpenberg, L. et al. (2025) Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation., Genome Biol, PMID 41015776

PXD067947 Dataset with its publication pending (from PRIDE)
Dataset title: Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides
Possible reference: Ghosh Dastidar, N. et al. (2025) Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides., Nat Commun, PMID 41162373

PXD067940 Dataset with its publication pending (from iProX)
Dataset title: Nanomaterial signatures program biomolecular condensates via triphasic separation for chemoplasticity remodeling
Possible reference: Zheng, LT. et al. (2025) Nanomaterial signatures program biomolecular condensates via triphasic separation for chemoplasticity remodeling., Nat Commun, PMID 41162367

PXD067919 Dataset with its publication pending (from iProX)
Dataset title: The SCOOP12-MIK2 module regulates Arabidopsis root meristem development via the PLETHORA transcription factors
Possible reference: Chen, M. et al. (2025) The SCOOP12-MIK2 module regulates Arabidopsis root meristem development via the PLETHORA transcription factors., Plant J, PMID 41364809

PXD067916 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of chronic hepatitis B across distinct clinical stages
Possible reference: Xie, J. et al. (2026) Proteomics Insight into the Pathogenic Evolution of Chronic Hepatitis B across Distinct Clinical Stages., J Proteome Res, PMID 41468387

PXD067913 Dataset with its publication pending (from iProX)
Dataset title: HOXC10 protects from aging by targeting FZD6/Wnt/Î²-catenin signaling pathway
Possible reference: Zhong, Y. et al. (2025) HOXC10 Protects from Skin Aging by Targeting the FZD6/Wnt/β-Catenin Signaling Pathway., Research (Wash D C), PMID 41268215

PXD067911 Dataset with its publication pending (from PRIDE)
Dataset title: Specialisation of meiotic kinetochores revealed through a synthetic spindle assembly checkpoint strategy.
Possible reference: Koch, LB. et al. (2026) Specialisation of meiotic kinetochores revealed through a synthetic spindle assembly checkpoint strategy., Elife, PMID 41954595

PXD067902 no publication (from MassIVE)
Dataset title: Proteomic Profiling of EUS-FNA Samples Differentiates PDAC and MFP
Possible reference: Teodorescu, C. et al. (2025) Proteomic Profiling of EUS-FNA Samples Differentiates Pancreatic Adenocarcinoma from Mass-Forming Chronic Pancreatitis., Biomedicines, PMID 41007761

PXD067862 Dataset with its publication pending (from iProX)
Dataset title: Zebrafish Study Provides Evidence for Porphyromonas gingivalis Outer Membrane Vesicles Eliciting Alzheimer's Disease-Like Pathologies
Possible reference: Guo, J. et al. (2026) Zebrafish study provides evidence for Porphyromonas gingivalis outer membrane vesicles eliciting Alzheimer's disease-like pathologies., Front Cell Infect Microbiol, PMID 41868145

PXD067856 Dataset with its publication pending (from PRIDE)
Dataset title: Human RNA ligase 1 as a novel regulator of ribosome function and translation under oxidative stress
Possible reference: Stumpf, FM. et al. (2026) Human RNA ligase 1 as a novel regulator of ribosome function and translation under oxidative stress., Nucleic Acids Res, PMID 42258534

PXD067850 Dataset with its publication pending (from PRIDE)
Dataset title: PRC2 loss impairs small cell lung cancer tumorigenesis and enhances sensitivity to G9a/GLP inhibition
Possible reference: Kopparam, J. et al. (2026) PRC2 loss impairs small cell lung cancer tumorigenesis and enhances sensitivity to G9a/GLP inhibition., Commun Biol, PMID 41723269

PXD067835 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics analysis of Stra8-Pdcd5-/- mouse elongating spermatids
Possible reference: Li, M. et al. (2020) Comparative proteomic analysis of round and elongated spermatids during spermiogenesis in mice., Biomed Chromatogr, PMID 31994209

PXD067830 no publication (from MassIVE)
Dataset title: GPCR kinases shape ACKR4 functions via differential C-terminal phosphorylation
Possible reference: Gerken, OJ. et al. (2026) GPCR kinases shape ACKR4 functions via differential C-terminal phosphorylation., Nat Commun, PMID 42143096

PXD067822 Dataset with its publication pending (from iProX)
Dataset title: Targeting the UFL1-PARP1 axis amplifies anti-tumor immunity
Possible reference: Song, W. et al. (2025) Targeting the UFL1-PARP1 axis amplifies anti-tumor immunity., Cell Rep, PMID 41105513

PXD067817 Dataset with its publication pending (from iProX)
Dataset title: The m6A reader IGF2BP2 promotes homologous recombination-mediated DNA repair by eliminating DNA-RNA hybrids
Possible reference: Sun, Y. et al. (2025) The m6A reader IGF2BP2 promotes homologous recombination-mediated DNA repair by eliminating DNA-RNA hybrids., Cell Rep, PMID 41100254

PXD067816 Dataset with its publication pending (from iProX)
Dataset title: AMPK-activated BAP1 Regulates pVHL Stability and Tumor-suppressive Function
Possible reference: Li, M. et al. (2026) AMPK-activated BAP1 regulates pVHL stability and tumor-suppressive functions., Cell Death Differ, PMID 41015595

PXD067795 no publication (from MassIVE)
Dataset title: Mitochondrial Complex I in the diatom Phaeodactylum tricornutum
Possible reference: Li, Y. et al. (2017) Ocean acidification modulates expression of genes and physiological performance of a marine diatom., PLoS One, PMID 28192486

PXD067760 Dataset with its publication pending (from PRIDE)
Dataset title: CUT&Tag Overcomes Biases of ChIP and Establishes Chromatin Patterns for Repetitive Genomic Loci
Possible reference: Park, BJ. et al. (2025) CUT&Tag overcomes biases of ChIP and establishes chromatin patterns for repetitive genomic loci., iScience, PMID 41234774

PXD067725 Dataset with its publication pending (from iProX)
Dataset title: Comprehensive Phosphoproteomic Profiling Reveals Sex-Specific Regulatory Mechanisms in HrasG12V-Driven Hepatocarcinogenesis
Possible reference: Yang, C. et al. (2025) Comprehensive phosphoproteomic profiling reveals sex-specific regulatory mechanisms in HrasG12V-driven hepatocarcinogenesis., Cancer Cell Int, PMID 41126211

PXD067721 Dataset with its publication pending (from iProX)
Dataset title: Activity-Based Ubiquitin Probes Capture the Sulfenylated State of Deubiquitinases
Possible reference: Chen, Z. et al. (2025) Activity-Based Ubiquitin Probes Capture the Sulfenylated State of Deubiquitinases., Angew Chem Int Ed Engl, PMID 40916186

PXD067716 Dataset with its publication pending (from PRIDE)
Dataset title: A Phosphoinositide Interacting Protein Coordinates Stress Precursor Activities
Possible reference: Baumann, V. et al. (2024) Faa1 membrane binding drives positive feedback in autophagosome biogenesis via fatty acid activation., J Cell Biol, PMID 38573225

PXD067712 Dataset with its publication pending (from iProX)
Dataset title: Exploring potential biomarkers for myasthenia gravis based on serum proteomics
Possible reference: Jin, M. et al. (2024) Exploring Potential Biomarkers of Early Thymoma based on Serum Proteomics., Protein Pept Lett, PMID 38053354

PXD067699 Dataset with its publication pending (from PRIDE)
Dataset title: Deciphering Membrane Protein Complexes in Plasmodium falciparum Gametocytes via Cross-Linking Mass Spectrometry and Structural Modeling
Possible reference: Mostafavi, S. et al. (2026) Deciphering Membrane Protein Complexes in Plasmodium falciparum Gametocytes via Integrative Structural Systems Biology., Mol Cell Proteomics, PMID 41966402

PXD067694 Dataset with its publication pending (from iProX)
Dataset title: NEK7 induced phosphorylation of EGFR on serine 1070 drive the acquired lenvatinib resistance in hepatocellular carcinoma
Possible reference: Huang, Q. et al. (2025) NEK7-induced phosphorylation of EGFR on serine 1070 drives the acquired lenvatinib resistance in hepatocellular carcinoma., Hepatology, PMID 40694824

PXD067693 Dataset with its publication pending (from iProX)
Dataset title: Chaperonin TRiC bridges radial spokes for folding proteins locally translated in mammalian sperm flagella
Possible reference: Meng, X. et al. (2026) Chaperonin TRiC bridges radial spokes for folding locally translated proteins to sustain mammalian sperm flagellar motility., Mol Cell, PMID 41932310

PXD067680 no publication (from MassIVE)
Dataset title: Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability
Possible reference: Rosenberger, G. et al. (2025) Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability., bioRxiv, PMID 41040394

PXD067668 Dataset with its publication pending (from iProX)
Dataset title: Role of the oncogene PIM1 in mammalian erythroblast enucleation
Possible reference: Zhang, H. et al. (2025) The oncogene protein kinase PIM1 regulates mammalian erythroblast enucleation., Commun Biol, PMID 41094106

PXD067667 Dataset with its publication pending (from iProX)
Dataset title: Phosphorylation of Plectin by Akt3 Promotes Triple-Negative Breast Cancer Cell Invasive Migration�
Possible reference: Zheng, S. et al. (2025) Phosphorylation of plectin by Akt3 promotes triple-negative breast cancer cell invasive migration., iScience, PMID 41079612

PXD067666 Dataset with its publication pending (from iProX)
Dataset title: Mycobacterial tyrosine phosphatases PtpA/PtpB affected host proteome and tyrosine phosphoproteome
Possible reference: Liu, T. et al. (2025) Mycobacterial Tyrosine Phosphatase PtpB Affects Host Cytokine Expression by Dephosphorylating ERK1/2 and STAT3., Mol Cell Proteomics, PMID 40935154

PXD067659 Dataset with its publication pending (from PRIDE)
Dataset title: Cross-linking mass spectrometry for structure analysis of the intrinsically disordered Tau and phosphorylated Tau protein
Possible reference: Arsene, C. et al. (2026) Cross-linking mass spectrometry for structure analysis of the intrinsically disordered Tau and phosphorylated Tau protein., PLoS Comput Biol, PMID 41533746

PXD067649 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluating the Robustness of Micro-Pillar Array Columns for High-Throughput Proteomics
Possible reference: Schroeter, CB. et al. (2026) Evaluating the Robustness of Micro-Pillar Array Columns for Quantitative Proteomics Applications., J Proteome Res, PMID 41343703

PXD067642 no publication (from MassIVE)
Dataset title: Proteomic Analyses of Blood Samples of Highly Trained Athletes
Possible reference: Jones, PR. et al. (2022) Uncovering the effects of gender affirming hormone therapy on skeletal muscle and epigenetics: protocol for a prospective matched cohort study in transgender individuals (the GAME study)., BMJ Open, PMID 35545400

PXD067624 Dataset with its publication pending (from PRIDE)
Dataset title: DNA-Protein Crosslinks Promote cGAS-STING-driven Premature Aging and Embryonic Lethality
Possible reference: Tomaskovic, I. et al. (2026) DNA-protein cross-links promote cGAS-STING-driven premature aging and embryonic lethality., Science, PMID 41610251

PXD067622 Dataset with its publication pending (from PRIDE)
Dataset title: DNA-Protein Crosslinks Promote cGAS-STING-driven Premature Aging and Embryonic Lethality
Possible reference: Tomaskovic, I. et al. (2026) DNA-protein cross-links promote cGAS-STING-driven premature aging and embryonic lethality., Science, PMID 41610251

PXD067620 Dataset with its publication pending (from PRIDE)
Dataset title: DNA-Protein Crosslinks Promote cGAS-STING-driven Premature Aging and Embryonic Lethality
Possible reference: Tomaskovic, I. et al. (2026) DNA-protein cross-links promote cGAS-STING-driven premature aging and embryonic lethality., Science, PMID 41610251

PXD067619 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of pericyte and smooth muscle cell contributions to CADASIL pathology
Possible reference: Huang, Y. et al. (2026) Multi-omic profiling reveals pericyte and smooth muscle cell contributions to CADASIL pathology in cell-specific Notch3 mutant mice., Cell Rep, PMID 41996236

PXD067615 Dataset with its publication pending (from PRIDE)
Dataset title: Human RNA ligase 1 as a novel regulator of ribosome function and translation under oxidative stress
Possible reference: Stumpf, FM. et al. (2026) Human RNA ligase 1 as a novel regulator of ribosome function and translation under oxidative stress., Nucleic Acids Res, PMID 42258534

PXD067614 Dataset with its publication pending (from PRIDE)
Dataset title: Cooperative Aldehyde Chemistry Maps an Orthogonal Lysine Reactivity Landscape
Possible reference: Galindo, AV. et al. (2026) Cooperative Aldehyde Chemistry Maps an Orthogonal Lysine Reactivity Landscape., J Am Chem Soc, PMID 41926330

PXD067610 no publication (from MassIVE)
Dataset title: AURKB-driven dissolution of CIZ1-RNA assemblies from the inactive X chromosome in mitosis
Possible reference: Byrom, L. et al. (2026) AURKB-driven dissolution of CIZ1-RNA assemblies from the inactive X chromosome in mitosis., Nucleic Acids Res, PMID 41626693

PXD067578 Dataset with its publication pending (from PRIDE)
Dataset title: A Structural Mechanism for Noncanonical GPCR Signal Transduction in the Hedgehog Pathway
Possible reference: Arensdorf, AM. et al. (2016) Smoothened Regulation: A Tale of Two Signals., Trends Pharmacol Sci, PMID 26432668

PXD067574 Dataset with its publication pending (from PRIDE)
Dataset title: Prenatal Valproic Acid Exposure Alters Striatal Proteomic Signatures Associated with Autism Spectrum Disorder in Mice
Possible reference: Jo, EH. et al. (2026) Prenatal valproic acid exposure alters striatal proteomic signatures associated with autism spectrum disorder in mice., Transl Psychiatry, PMID 42204145

PXD067557 Dataset with its publication pending (from PRIDE)
Dataset title: Functional dissection of SPOP in the amino acid level reveals comprehensive functional landscape of variants on tumorigenesis
Possible reference: Park, SK. et al. (2026) Functional dissection of SPOP at the amino acid level reveals a comprehensive functional landscape of variants during tumorigenesis., Proc Natl Acad Sci U S A, PMID 42090249

PXD067522 no publication (from MassIVE)
Dataset title: Chemical genetics reveals Leishmania KKT2 and CRK9 kinase activity is required for cell cycle progression
Possible reference: Carnielli, JBT. et al. (2026) Chemical genetics reveals Leishmania KKT2 and CRK9 kinase activity is required for cell cycle progression., PLoS Pathog, PMID 42127156

PXD067507 Dataset with its publication pending (from iProX)
Dataset title: Functions of the three common fungal extracellular membrane (CFEM) domain-containing genes of Arthrobotrys flagrans in the process of nematode trapping
Possible reference: Shi, T. et al. (2025) Functions of the Three Common Fungal Extracellular Membrane (CFEM) Domain-Containing Genes of Arthrobotrys flagrans in the Process of Nematode Trapping., Microorganisms, PMID 41011333

PXD067503 Dataset with its publication pending (from jPOST)
Dataset title: Characterization of Difficult-to-Remove Host Cell Proteins in Adeno-Associated Virus Downstream Processing
Possible reference: Leibiger, TM. et al. (2025) Characterization of difficult-to-remove host cell proteins in adeno-associated virus downstream processing., Mol Ther Methods Clin Dev, PMID 41321396

PXD067493 Dataset with its publication pending (from iProX)
Dataset title: Optimized light supply strategy comprehensively increases the synthesis of high-value cell inclusions in Rhodopseudomonas palustris using food waste fermentation broth: Process optimization and biosynthetic mechanism
Possible reference: Sun, Y. et al. (2025) Optimized light supply strategy comprehensively increases the synthesis of high-value cell inclusions in Rhodopseudomonas palustris using food waste fermentation broth: Process optimization and biosynthetic mechanism., Bioresour Technol, PMID 40912577

PXD067489 Dataset with its publication pending (from iProX)
Dataset title: Exploring Potential Mechanistic Aspects of "Biaoben acupoint " acupuncture for Lumbar Disc Herniation using 4D Proteomics
Possible reference: Shi, F. et al. (2025) Exploring potential mechanistic aspects of "Biaoben acupoint" acupuncture for lumbar disc herniation using 4D proteomics., Front Neurol, PMID 40963934

PXD067480 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics Reveals Altered Lipid Biosynthesis and Keratin Hyperphosphorylation in Pachyonychia Congenita
Possible reference: Ceccacci, S. et al. (2026) Proteomics reveals altered lipid biosynthesis and keratin hyperphosphorylation in pachyonychia congenita., J Invest Dermatol, PMID 41581590

PXD067474 Dataset with its publication pending (from PRIDE)
Dataset title: Human Lyme Neuroborreliosis LC-MS (CSF)
Possible reference: Biernacki, M. et al. (2026) Assessment of lipid mediators in the urine of patients with Lyme disease, tick-borne encephalitis and human granulocytic anaplasmosis., Sci Rep, PMID 41764219

PXD067472 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting Ubiquitin Signaling vulnerabilities in KEAP1-Inactivated Lung Cancer
Possible reference: Shah, VJ. et al. (2026) Targeting ubiquitin signaling vulnerabilities in KEAP1-inactivated lung cancer., EMBO J, PMID 41862643

PXD067454 Dataset with its publication pending (from iProX)
Dataset title: Fgk3-0 60 120 Immunoprecipitation-mass spectrometry
Possible reference: Schindler, SE. et al. (2022) Effect of Race on Prediction of Brain Amyloidosis by Plasma Aβ42/Aβ40, Phosphorylated Tau, and Neurofilament Light., Neurology, PMID 35450967

PXD067453 Dataset with its publication pending (from iProX)
Dataset title: Liver-breast communication of adipocyte-oriented exosomes drives primary mammary cancer progression
Possible reference: Li, C. et al. (2025) Liver-breast communication of adipocyte-oriented exosomes drives primary mammary cancer progression., Cell Metab, PMID 40997802

PXD067451 Dataset with its publication pending (from PRIDE)
Dataset title: Nanobody-mediated modulation of long RSH enzymes Rel and RelA catalysis by restriction of their conformational landscape
Possible reference: Van Nerom, K. et al. (2026) Nanobody-mediated control of long RSH Rel and RelA catalysis by restriction of their conformational landscape., Nat Commun, PMID 42129208

PXD067447 Dataset with its publication pending (from PRIDE)
Dataset title: Akkermansia muciniphila MucT – Polyphenols interactions.
Possible reference: Elmassry, MM. et al. (2020) Osteoprotective effect of green tea polyphenols and annatto-extracted tocotrienol in obese mice is associated with enhanced microbiome vitamin K2 biosynthetic pathways., J Nutr Biochem, PMID 32920088

PXD067442 Dataset with its publication pending (from iProX)
Dataset title: Nidogen 1-Enriched Extracellular Vesicles Promote Liver Metastasis by Inducing EMT and Activating Stellate Cells
Possible reference: Chen, H. et al. (2025) Nidogen 1-enriched extracellular vesicles promote liver metastasis by inducing EMT and activating stellate cells., iScience, PMID 41377661

PXD067441 Dataset with its publication pending (from iProX)
Dataset title: Effects of parthenolide on amino acid metabolism and oxidative stress in lung adenocarcinoma based on quantitative proteomic analysis, targeted amino acid metabolomics, network pharmacology, and experimental validation
Possible reference: Liu, J. et al. (2025) Effects of parthenolide on amino acid metabolism and oxidative stress in lung adenocarcinoma based on quantitative proteomic analysis, targeted amino acid metabolomics, network pharmacology, and experimental validation., Front Oncol, PMID 40958860

PXD067421 Dataset with its publication pending (from PRIDE)
Dataset title: VCPIP1 Drives Diabetic Cardiomyopathy by Deubiquitinating AMPKÎ³1 and Preventing AMPKÎ±-Î³ Subunit Assembly in Cardiomyocytes
Possible reference: Han, X. et al. (2026) VCPIP1 drives diabetic cardiomyopathy by deubiquitinating AMPKγ1 and preventing AMPKα-γ subunit assembly in cardiomyocytes., Signal Transduct Target Ther, PMID 42144399

PXD067415 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics- and BRET-screens identify SPRY2 as interactor of active Ras the impacts on its membrane organisation
Possible reference: Pavic, K. et al. (2025) Proteomics- and BRET- screens identify SPRY2 as a Ras effector that impacts its membrane organization., iScience, PMID 41362608

PXD067357 no publication (from MassIVE)
Dataset title: Turning waste into insight: a novel proteomic approach to non-invasive wound biomarker discovery
Possible reference: Soto, V. et al. (2025) Turning Waste Into Insight: A Novel Proteomic Approach to Non-Invasive Wound Biomarker Discovery., Mol Cell Proteomics, PMID 40848928

PXD067347 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamic proteomic changes and ultrastructural insights into Pochonia chlamydosporia's parasitism of Parascaris equorum Eggs
Possible reference: Hao, L. et al. (2025) Dynamic proteomic changes and ultrastructural insights into Pochonia chlamydosporia's parasitism of Parascaris equorum eggs., Front Cell Infect Microbiol, PMID 40909343

PXD067303 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular Vesicle Proteomics in Staphylococcus aureus-Treated Blood and Sepsis Reveals Coordinated Acute Phase, Neutrophil, and Exocytosis Responses
Possible reference: Chiang, DM. et al. (2026) Extracellular vesicle proteomics in staphylococcus aureus-treated blood and sepsis reveals coordinated complement, acute phase, neutrophil, and exocytosis responses., Sci Rep, PMID 42225697

PXD067281 Dataset with its publication pending (from jPOST)
Dataset title: Condensation-dependent interactome of a chromatin remodeler underlies tumor suppressor activities.
Possible reference: Tsukamoto, Y. et al. (2025) Condensation-dependent interactome of a chromatin remodeler underlies tumor suppressor activities., Nat Commun, PMID 41168190

PXD067251 Dataset with its publication pending (from PRIDE)
Dataset title: An engineered insulin analog with dual insulin and IGF-1 receptor agonism and distinct signaling
Possible reference: Selicharov�, I. et al. (2026) An engineered insulin analog with dual insulin and IGF-1 receptor agonism and distinct signaling., Sci Adv, PMID 42139356

PXD067247 Dataset with its publication pending (from iProX)
Dataset title: Region-specific effects of drugs on the gut ecosystem
Possible reference: Alziny, N. et al. (2025) The Impact of Microplastics in Food and Drugs on Human Health: A Review of the MENA Region., Int J Environ Res Public Health, PMID 40238422

PXD067246 no publication (from MassIVE)
Dataset title: Quantitative Decoding of Pathway Fluxes that Couple Carbon and Energy Metabolism in Lignin Carbon Utilization
Possible reference: Zhou, N. et al. (2025) Quantitative decoding of coupled carbon and energy metabolism in Pseudomonas putida for lignin carbon utilization., Commun Biol, PMID 40883435

PXD067235 Dataset with its publication pending (from PRIDE)
Dataset title: Functional Microbial Shifts and Host-Microbiome Crosstalk in Colorectal Cancer: Evidence from a Metaproteomic Approach
Possible reference: Sobhy, EE. et al. (2026) Functional microbial shifts and host-microbiome crosstalk in colorectal cancer: insights from a metaproteomic approach., BMC Microbiol, PMID 41742010

PXD067217 no publication (from MassIVE)
Dataset title: Dimethyl labeled murine liver LC-MS data
Possible reference: Wilson-Grady, JT. et al. (2013) Quantitative comparison of the fasted and re-fed mouse liver phosphoproteomes using lower pH reductive dimethylation., Methods, PMID 23567750

PXD067197 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular mechanism of co-transcriptional H3K36 methylation by SETD2
Possible reference: Walshe, JL. et al. (2025) Molecular mechanism of co-transcriptional H3K36 methylation by SETD2., Nat Commun, PMID 41162378

PXD067172 Dataset with its publication pending (from iProX)
Dataset title: A glucose kinase independent HK2 activity prevents TNF-induced cell death by phosphorylating RIPK1
Possible reference: Zou, T. et al. (2025) A glucose kinase-independent HK2 activity prevents TNF-induced cell death by phosphorylating RIPK1., Nat Commun, PMID 41233370

PXD067171 Dataset with its publication pending (from iProX)
Dataset title: A Newly Evolved Small Secretory Peptide Enhances Mechanical Properties of Spider Silk
Possible reference: Jia, A. et al. (2025) A newly evolved small secretory peptide enhances mechanical properties of spider silk., Nat Commun, PMID 41253802

PXD067162 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of Anoplocephala perfoliata elucidate lineage-specific features of a “neglected” equine tapeworm
Possible reference: Young, ND. et al. (2026) Chromosome-scale nuclear genome and proteome of Anoplocephala perfoliata elucidate lineage-specific features of a 'neglected' equine tapeworm., BMC Genomics, PMID 41566420

PXD067120 Dataset with its publication pending (from PRIDE)
Dataset title: Role of SPOP in cardiac hypertrophy and heart failure
Possible reference: Wu, H. et al. (2025) SPOP Is a Key Trigger of Pathological Cardiac Hypertrophy and Heart Failure., Circ Res, PMID 40948188

PXD067104 no publication (from PanoramaPublic)
Dataset title: Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to a precursor of advanced aviation fuel
Possible reference: Kang, CW. et al. (2026) Multi-layered metabolic remodeling of Pseudomonas putida for efficient conversion of lignocellulosic sugars to the precursors of advanced aviation fuel., Metab Eng Commun, PMID 41858775

PXD067103 no publication (from MassIVE)
Dataset title: DIA workflow optimization with 3 species for low input
Possible reference: Yang, Z. et al. (2026) Systematic Evaluation of Data-independent Acquisition Workflows for High-Throughput and Low-Input Proteomics Analysis with an Astral Mass Spectrometer., J Proteome Res, PMID 41738589

PXD067098 no publication (from MassIVE)
Dataset title: Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells
Possible reference: McLean, IC. et al. (2025) Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells., iScience, PMID 41054517

PXD067080 Dataset with its publication pending (from PRIDE)
Dataset title: The Perijunctional Zone Is a Molecularly Distinct Muscle Subdomain Altered in Duchenne Muscular Dystrophy
Possible reference: Haddix, SG. et al. (2026) The perijunctional zone is a molecularly distinct muscle subdomain altered in Duchenne muscular dystrophy., Nat Commun, PMID 42168231

PXD067019 Dataset with its publication pending (from PRIDE)
Dataset title: Fine-Tuning of Label-Free Single-Cell Proteomics Workflows
Possible reference: Perdu-Alloy, P. et al. (2026) Fine-Tuning of Label-Free Single-Cell Proteomics Workflows., J Proteome Res, PMID 41779902

PXD067015 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-scale classification decodes the complexity of the human E3 ligome
Possible reference: Dutta, A. et al. (2025) Multi-scale classification decodes the complexity of the human E3 ligome., Nat Commun, PMID 41449181

PXD066983 Dataset with its publication pending (from iProX)
Dataset title: Th9/IL-9 axis mediates airway fibrosis in traumatic tracheal stenosis via TGF-Î²1/SMAD2/3 signaling
Possible reference: Feng, T. et al. (2025) Th9/IL-9 axis mediates airway fibrosis in traumatic tracheal stenosis via TGF-β1/SMAD2/3 signaling., Respir Res, PMID 41275206

PXD066971 no publication (from MassIVE)
Dataset title: Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex
Possible reference: Chung, Y. et al. (2024) Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex., J Cell Biol, PMID 39565596

PXD066965 no publication (from MassIVE)
Dataset title: KIF13B controls ciliary protein content by promoting endocytic retrieval and suppressing release of large extracellular vesicles from cilia
Possible reference: Rezi, CK. et al. (2025) KIF13B controls ciliary protein content by promoting endocytic retrieval and suppressing release of large extracellular vesicles from cilia., Curr Biol, PMID 40930094

PXD066949 no publication (from MassIVE)
Dataset title: Overexpression of the signaling-coordinator GAB2 can play an important role in Acute Myeloid Leukemia progression
Possible reference: Kramer, MH. et al. (2025) Overexpression of the signaling coordinator GAB2 can play an important role in acute myeloid leukemia progression., J Clin Invest, PMID 40773291

PXD066933 Dataset with its publication pending (from PRIDE)
Dataset title: Characterisation of the Active Kinome of Leishmania
Possible reference: Bendjeddou, LZ. et al. (2017) Exploration of the imidazo[1,2-b]pyridazine scaffold as a protein kinase inhibitor., Eur J Med Chem, PMID 27721154

PXD066928 Dataset with its publication pending (from jPOST)
Dataset title: p1/s1, a 3â€™-nucleotidase/nuclease, allows Leishmania to circumvent innate immune response mechanisms
Possible reference: Schmelzle, SM. et al. (2026) p1/s1, a 3'-nucleotidase/nuclease, allows Leishmania major to circumvent host innate immune response mechanisms., PLoS Pathog, PMID 42160378

PXD066917 Dataset with its publication pending (from iProX)
Dataset title: Site-specific Profiling of RNA-binding Proteins Enabled by Isotopic Signature Enhanced Mass Spectrometry
Possible reference: Liu, Y. et al. (2025) Site-Specific Profiling of RNA-Binding Proteins Enabled by Isotopic Signature-Enhanced Mass Spectrometry., J Am Chem Soc, PMID 41036732

PXD066909 Dataset with its publication pending (from iProX)
Dataset title: HSPA1A can alleviate CFA-induced inflammatory pain by modulating macrophages
Possible reference: Zhang, W. et al. (2025) HSPA1A Can Alleviate CFA-Induced Inflammatory Pain by Modulating Macrophages., Int J Mol Sci, PMID 41096856

PXD066890 Dataset with its publication pending (from PRIDE)
Dataset title: A trypanosome-specific complex mediates late-stage processing of cytosolic LSU rRNA
Possible reference: Amodeo, S. et al. (2025) A trypanosome-specific complex mediates late-stage processing of cytosolic LSU rRNA., Nucleic Acids Res, PMID 41391488

PXD066883 no publication (from MassIVE)
Dataset title: WhiB6 transduces contact-dependent signaling in Mycobacterium smegmatis and coordinately induces both ESX-1 and ESX-4
Possible reference: Canestrari, JG. et al. (2025) WhiB6 Transduces Contact-Dependent Signaling in Mycobacterium smegmatis and Coordinately Induces Both ESX-1 and ESX-4., Mol Microbiol, PMID 41137460

PXD066854 Dataset with its publication pending (from jPOST)
Dataset title: VCPIP1 Drives Diabetic Cardiomyopathy by Deubiquitinating AMPKÎ³1 and Preventing AMPKÎ±-Î³ Subunit Assembly in Cardiomyocytes
Possible reference: Han, X. et al. (2026) VCPIP1 drives diabetic cardiomyopathy by deubiquitinating AMPKγ1 and preventing AMPKα-γ subunit assembly in cardiomyocytes., Signal Transduct Target Ther, PMID 42144399

PXD066814 no publication (from MassIVE)
Dataset title: Plasma Extracellular-Vesicle Proteomics Identifies Candidate Biomarkers of 177Lu-PSMA-617 Outcomes in Metastatic Prostate Cancer Patients
Possible reference: Arafa, AT. et al. (2026) Plasma extracellular vesicle proteomics nominates candidate biomarkers of 177Lu-PSMA-617 outcomes in metastatic prostate cancer patients., Cell Rep Med, PMID 42013849

PXD066795 Dataset with its publication pending (from PRIDE)
Dataset title: Structural characterization of atrial natriuretic peptide amyloid fibrils from patients with atrial fibrillation
Possible reference: Broggini, L. et al. (2025) Structural characterization of atrial natriuretic peptide amyloid fibrils from patients with atrial fibrillation., Nat Commun, PMID 41162370

PXD066792 Dataset with its publication pending (from iProX)
Dataset title: Circulating Proteins and Metabolites Panel for Noninvasive Preoperative Diagnosis of Epithelial Ovarian Cancer
Possible reference: Jia, Y. et al. (2025) Circulating proteins and metabolites panel for noninvasive preoperative diagnosis of epithelial ovarian cancer., BMC Med, PMID 40846961

PXD066782 Dataset with its publication pending (from PRIDE)
Dataset title: Essential role of Protein kinase R in the pathogenesis of pulmonary veno-occlusive disease
Possible reference: Prabhakar, A. et al. (2025) Essential role of protein kinase R in the pathogenesis of pulmonary veno-occlusive disease., JCI Insight, PMID 40839386

PXD066772 no publication (from MassIVE)
Dataset title: Identifying time-of-day- and Bmal1- dependent liver secreted proteomes
Possible reference: Litwin, C. et al. (2026) Timed secreted proteomes reveal regulation of hepatokines by the liver circadian clock., Nat Commun, PMID 42230628

PXD066763 Dataset with its publication pending (from PRIDE)
Dataset title: Stereo-random Oligonucleotides Enable Efficient Recruitment of ADAR in vitro and in vivo
Possible reference: Pfeiffer, LS. et al. (2025) Stereo-random oligonucleotides enable efficient recruitment of ADAR in vitro and in vivo., Nat Commun, PMID 41044092

PXD066736 Dataset with its publication pending (from iProX)
Dataset title: Molecular Glue Degraders of the HuR RNA Binding Protein to Treat BRAF-Mutant Colorectal Cancer
Possible reference: Lu, X. et al. (2026) Molecular glue degraders of HuR suppress BRAF-mutant colorectal cancer., Nature, PMID 42271059

PXD066683 Dataset with its publication pending (from PRIDE)
Dataset title: New proteomic signature in circulating extracellular vesicles from tumor-draining and peripheral veins of patients with lung adenocarcinoma
Possible reference: Tricard, J. et al. (2026) New proteomic signature in circulating extracellular vesicles from tumor-draining and peripheral veins of patients with lung adenocarcinoma., Cancer Cell Int, PMID 41923119

PXD066656 Dataset with its publication pending (from PRIDE)
Dataset title: Follicle-like niches outside the cortex? 3D phase-contrast �CT revealed medullary B cell nodules in mucosa-draining lymph nodes
Possible reference: Sch�tz, P. et al. (2025) Follicle-like niches outside the cortex? 3D phase-contrast �CT revealed medullary B cell nodules in mucosa-draining lymph nodes., Front Immunol, PMID 41346636

PXD066638 Dataset with its publication pending (from iProX)
Dataset title: Attenuate host susceptibility to respiratory virus invasion by inhibiting interactions between host proteins SLC16A3 and AP1G1
Possible reference: Deng, X. et al. (2025) Attenuate host susceptibility to respiratory virus invasion by inhibiting interactions between host proteins SLC16A3 and AP1G1., Microbiol Spectr, PMID 40919783

PXD066637 Dataset with its publication pending (from PRIDE)
Dataset title: SLC25-family transporters of choline and branched-chain and methylated amino acids regulate mitochondrial protein synthesis
Possible reference: Rudler, DL. et al. (2026) Specific SLC25 carriers regulate mitochondrial protein synthesis., Sci Adv, PMID 41739937

PXD066635 Dataset with its publication pending (from iProX)
Dataset title: FAM3A drives uncoupling of muscle lipid accumulation and insulin resistance depending on insulin receptor
Possible reference: Yang, D. et al. (2025) FAM3A drives uncoupling of muscle lipid accumulation and insulin resistance depending on insulin receptor., Cell Death Dis, PMID 41353211

PXD066633 Dataset with its publication pending (from iProX)
Dataset title: CRISPR/Cas9 library screening uncovered CCT2 as a critical driver of acquired resistance to EGFR-targeted therapy by stabilizing TMX1 in non-small cell lung cancer
Possible reference: Ke, Z. et al. (2026) CRISPR/Cas9 library screening uncovered CCT2 as a critical driver of acquired resistance to EGFR-targeted therapy by stabilizing TMX1 in non-small cell lung cancer., Cell Death Differ, PMID 41168408

PXD066622 Dataset with its publication pending (from PRIDE)
Dataset title: Single molecule dynamics of the TRiC chaperonin system in vivo
Possible reference: Li, R. et al. (2026) Single-molecule dynamics of the TRiC chaperonin system in vivo., Nature, PMID 41639457

PXD066577 Dataset with its publication pending (from iProX)
Dataset title: Streptococcus mutans biofilm enhances drug resistance of Helicobacter pylori
Possible reference: Lalezadeh, A. et al. (2025) A Critical Review on the Potential of Inactivated Bacteria in Counteracting Human Pathogens., Curr Microbiol, PMID 40394322

PXD066573 Dataset with its publication pending (from iProX)
Dataset title: Machine Learning-Driven Extracellular Vesicles Peptidomics Powers Precision Classification of Endometrial Cancer Molecular Subtypes
Possible reference: Yang, Y. et al. (2025) Machine Learning-Driven Extracellular Vesicles Peptidomics Powers Precision Classification of Endometrial Cancer., Anal Chem, PMID 41403007

PXD066565 Dataset with its publication pending (from PRIDE)
Dataset title: Multiomics profiling of zebrafish embryonic cell line PAC2 across growth phases to assess its relevance for toxicological studies
Possible reference: Degeratu, MO. et al. (2026) Multiomics profiling of zebrafish embryonic cell line PAC2 across growth phases to assess its relevance for toxicological studies., PLoS One, PMID 41996304

PXD066551 Dataset with its publication pending (from PRIDE)
Dataset title: Role of activating transcription factor 4 (ATF4) in mGluR-LTD
Possible reference: Mahmood, N. et al. (2026) The ISR downstream effector ATF4 promotes mGluR-dependent long-term depression and associated behavior., Proc Natl Acad Sci U S A, PMID 41706892

PXD066544 no publication (from MassIVE)
Dataset title: Lysosomal reduced thiols are essential for mouse embryonic development
Possible reference: Adelmann, CH. et al. (2024) Lysosomal reduced thiols are essential for mouse embryonic development., bioRxiv, PMID 39764028

PXD066533 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of Cullin 5 in myeloid cells protects against autoimmune neuroinflammation
Possible reference: Ortega-Burgos, Y. et al. (2025) Loss of Cullin 5 in myeloid cells protects against autoimmune neuroinflammation., Front Immunol, PMID 40842987

PXD066528 no publication (from MassIVE)
Dataset title: Dual AAV gene therapy using laminin-linking proteins ameliorates muscle and nerve defects in LAMA2-related muscular dystrophy
Possible reference: Reinhard, JR. et al. (2026) Dual AAV gene therapy using laminin-linking proteins ameliorates muscle and nerve defects in LAMA2-related muscular dystrophy., Mol Ther, PMID 41635088

PXD066524 Dataset with its publication pending (from iProX)
Dataset title: Antifungal activity of cinnamaldehyde against Aspergillus fumigatus involves disruption of the TCA cycle and protein metabolism
Possible reference: Li, F. et al. (2025) Antifungal activity of cinnamaldehyde against Aspergillus fumigatus involves disruption of the TCA cycle and protein metabolism., Front Microbiol, PMID 40919208

PXD066488 Dataset with its publication pending (from PRIDE)
Dataset title: Bacterial supplementation shapes honey bee gut microbiota, metabolism and proteome under controlled and field conditions
Possible reference: Lee, S. et al. (2026) Bacterial supplementation shapes honey bee gut microbiota and host metabolism under controlled and field conditions., mSystems, PMID 42165584

PXD066462 Dataset with its publication pending (from PRIDE)
Dataset title: The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain
Possible reference: Wong, J. et al. (2025) The assembly of a hybrid type IV secretion system by a Crohn's disease-associated Escherichia coli strain., Nat Commun, PMID 41038829

PXD066441 Dataset with its publication pending (from PRIDE)
Dataset title: Algal carbon concentrating drives fatty acid biosynthesis beyond photosynthesis
Possible reference: You, T. et al. (2025) Algal carbon concentrating drives fatty acid biosynthesis beyond photosynthesis., Cell Rep, PMID 41091597

PXD066440 Dataset with its publication pending (from iProX)
Dataset title: Sub-inhibitory concentrations of oxacillin modulate biogenesis and function of extracellular vesicles secreted by oxacillin-sensitive methicillin-resistant Staphylococcus aureus
Possible reference: Ran, Z. et al. (2025) Sub-inhibitory concentrations of oxacillin modulate biogenesis and function of extracellular vesicles secreted by oxacillin-sensitive methicillin-resistant Staphylococcus aureus., Front Microbiol, PMID 40831641

PXD066435 Dataset with its publication pending (from iProX)
Dataset title: Site-specific alterations of N-glycans define the glycoproteomic landscape of thymic aging in rats
Possible reference: Zhang, Z. et al. (2025) Structural and site-specific N-glycan alterations define the glycoproteomic landscape of thymic aging in rats., Carbohydr Polym, PMID 41116571

PXD066400 Dataset with its publication pending (from iProX)
Dataset title: Stenotrophomonas maltophilia P373 impedes biocontrol effects of Bacillus lipopeptides against tomato wilt disease
Possible reference: Peng, J. et al. (2025) Stenotrophomonas maltophilia impedes Bacillus biocontrol of tomato wilt disease by degrading its lipopeptide antibiotics., ISME J, PMID 40985535

PXD066391 Dataset with its publication pending (from PRIDE)
Dataset title: Adipocyte FMO3-derived TMAO induces WAT dysfunction and metabolic disorders by promoting inflammasome activation in ageing
Possible reference: Ganapathy, T. et al. (2025) Adipocyte FMO3-derived TMAO induces WAT dysfunction and metabolic disorders by promoting inflammasome activation in ageing., Nat Commun, PMID 41053195

PXD066374 Dataset with its publication pending (from iProX)
Dataset title: Identification of the malonylation modification in staphylococcus aureus and insight into the regulators in biofilm Formation.
Possible reference: Yu, X. et al. (2025) Identification of the malonylation modification in Staphylococcus aureus and insight into the regulators in biofilm formation., Front Microbiol, PMID 40904684

PXD066373 Dataset with its publication pending (from iProX)
Dataset title: Comparative Proteomics Identified Proteins iMung Bean SproutsUnder Different Concentrations of Urea
Possible reference: Wu, L. et al. (2025) Comparative Proteomics Identified Proteins in Mung Bean Sprouts Under Different Concentrations of Urea., Molecules, PMID 40807351

PXD066351 Dataset with its publication pending (from iProX)
Dataset title: From Gut to Proteomics: The Impact of Roseburia intestinalis on Chromatin Modifications in Colorectal Cancer
Possible reference: Li, L. et al. (2025) From gut to proteomics: the impact of Roseburia intestinalis on post-translational modifications in colorectal cancer., Front Oncol, PMID 40900785

PXD066349 Dataset with its publication pending (from iProX)
Dataset title: Identification of the malonylation modification in staphylococcus aureus and insight into the regulators in biofilm Formation
Possible reference: Yu, X. et al. (2025) Identification of the malonylation modification in Staphylococcus aureus and insight into the regulators in biofilm formation., Front Microbiol, PMID 40904684

PXD066332 Dataset with its publication pending (from PRIDE)
Dataset title: March5-mediated Trim28 degradation preserves islet Î²-cell function in mice
Possible reference: Chen, Y. et al. (2025) March5-mediated Trim28 degradation preserves islet β-cell function in mice., Nat Commun, PMID 40750777

PXD066324 no publication (from MassIVE)
Dataset title: All-trans retinoic acid destabilizes ADAR1 protein through retinoylation-mediated USP7 dissociation and improves immunotherapy in pancreatic cancer
Possible reference: Li, CF. et al. (2026) All-trans retinoic acid destabilizes ADAR1 protein through retinoylation-mediated USP7 dissociation and improves immunotherapy in pancreatic cancer., Nat Commun, PMID 42115161

PXD066317 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles from obese visceral adipose promote pancreatic cancer development and resistance to immune checkpoint blockade therapy
Possible reference: Xue, C. et al. (2025) Extracellular vesicles from obese visceral adipose promote pancreatic cancer development and resistance to immune checkpoint blockade therapy., Cell Metab, PMID 41338178

PXD066297 Dataset with its publication pending (from PRIDE)
Dataset title: Genome-scale CRISPR screens identify PTGES3 as a direct modulator of AR function in advanced prostate cancer
Possible reference: Li, H. et al. (2025) Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer., Nat Genet, PMID 41193657

PXD066273 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles from obese visceral adipose promote pancreatic cancer development and resistance to immune checkpoint blockade therapy
Possible reference: Xue, C. et al. (2025) Extracellular vesicles from obese visceral adipose promote pancreatic cancer development and resistance to immune checkpoint blockade therapy., Cell Metab, PMID 41338178

PXD066247 Dataset with its publication pending (from iProX)
Dataset title: Hexosamine Biosynthetic Pathway Drives Tumor Immune Evasion via Translational Control of PD-L1 at the Elongation Level
Possible reference: Liu, B. et al. (2025) The hexosamine biosynthetic pathway drives tumor immune evasion via translational control of PD-L1 at the elongation level., Cell Rep, PMID 40938752

PXD066243 Dataset with its publication pending (from iProX)
Dataset title: Multi-omics profiling reveals the role of 4-Ethylbenzoic Acid in promoting proliferation and invasion of cervical cancer
Possible reference: Huang, X. et al. (2025) Multi-omics profiling reveals the role of 4-ethylbenzoic acid in promoting proliferation and invasion of cervical cancer., Front Med (Lausanne), PMID 41158463

PXD066242 Chen, S., J. L. Baumert, and M. L. Downs. 2025. Quantification, Risk Assessment, and Mitigation of Cashew Allergen Cross-Contact in Shared Roasting Oil Systems. Journal of Food Protection:100678. (from PanoramaPublic)
Dataset title: Quantification, Risk Assessment, and Mitigation of Cashew Allergen Cross-Contact in Shared Roasting Oil Systems
Possible reference: Chen, S. et al. (2026) Quantification, Risk Assessment, and Mitigation of Cashew Allergen Cross-Contact in Shared Roasting Oil Systems., J Food Prot, PMID 41349907

PXD066219 no publication (from MassIVE)
Dataset title: SLFN11 counteracts the RFWD3-PRIMPOL DNA damage tolerance pathway to restrain gapped DNA synthesis in response to replication stress
Possible reference: Coleman, KE. et al. (2025) SLFN11 counteracts the RFWD3-PRIMPOL DNA damage tolerance axis to restrain gapped DNA synthesis in response to replication stress., Nat Commun, PMID 41372167

PXD066160 Dataset with its publication pending (from PRIDE)
Dataset title: Generalizable direct protein sequencing with InstaNexus
Possible reference: Reverenna, M. et al. (2026) Generalizable Direct Protein Sequencing With InstaNexus., Mol Cell Proteomics, PMID 41780890

PXD066120 Dataset with its publication pending (from iProX)
Dataset title: Negative pressure-induced fibroblast activation for wound healing through the Piezo1-Ca2+-NFAT3 signaling pathway
Possible reference: Xiao, SA. et al. (2026) Negative pressure-induced fibroblast activation for wound healing through the Piezo1-Ca2+-NFAT3 signaling pathway., Burns Trauma, PMID 42181011

PXD066110 Dataset with its publication pending (from PRIDE)
Dataset title: PROTAC repurposing uncovers a noncanonical binding surface that mediates chemical degradation of nuclear receptors
Possible reference: Huber, AD. et al. (2025) PROTAC repurposing uncovers a noncanonical binding surface that mediates chemical degradation of nuclear receptors., Nat Commun, PMID 41198675

PXD066100 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles from obese visceral adipose promote pancreatic cancer development and resistance to immune checkpoint blockade therapy
Possible reference: Xue, C. et al. (2025) Extracellular vesicles from obese visceral adipose promote pancreatic cancer development and resistance to immune checkpoint blockade therapy., Cell Metab, PMID 41338178

PXD066098 Dataset with its publication pending (from PRIDE)
Dataset title: VMAT2 dysfunction impairs vesicular dopamine sequestration, driving oxidation and Î±-synuclein pathology in DJ-1-linked Parkinsonâs disease neurons
Possible reference: Heger, LM. et al. (2026) VMAT2 dysfunction impairs vesicular dopamine uptake, driving its oxidation and α-synuclein pathology in DJ-1-linked Parkinson's neurons., Sci Adv, PMID 41671379

PXD066077 no publication (from MassIVE)
Dataset title: Proteomics of ovarian cancer stem like cells SKOV-3 treated with mDivi-1
Possible reference: Raina, M. et al. (2025) An altered proteome in ovarian cancer stem-like cells: profiling of the mDivi-1 induced proteome and its clinical significance., Mol Omics, PMID 41060254

PXD066076 no publication (from MassIVE)
Dataset title: Therapeutic targeting of eIF4E cap-binding domain reveals control of lineage fate in prostate cancer
Possible reference: Mishra, R. et al. (2026) Therapeutic targeting of the eIF4E cap-binding domain reveals control of lineage fate in prostate cancer., J Clin Invest, PMID 41984598

PXD066074 no publication (from MassIVE)
Dataset title: Detection and Characterization of Protein Methylation in Bacteriophages and Their Host, Cellulophaga baltica, During Infection
Possible reference: Stai, AJ. et al. (2026) Detection and characterization of protein methylation in bacteriophages and their host, Cellulophaga baltica, during infection., mSystems, PMID 42148748

PXD066062 no publication (from MassIVE)
Dataset title: Discovery of a paralog-selective p300 protein degrader with potent anti-cancer activity in hematological malignancies
Possible reference: Asem, MS. et al. (2026) Discovery of a paralog-selective p300 protein degrader with potent anti-cancer activity in hematological malignancies., Nat Commun, PMID 42091886

PXD066029 Dataset with its publication pending (from PRIDE)
Dataset title: Scalable Acid-Aided Lysis of Skin Samples Improves Proteome Coverage
Possible reference: Sauerland, MB. et al. (2026) Scalable Acid-Aided Lysis of Skin Samples Improves Proteome Coverage., J Invest Dermatol, PMID 40914411

PXD066019 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of a shared persistence program in triple-negative breast cancer across treatments and patients
Possible reference: , . et al. (2025) Global burden of 292 causes of death in 204 countries and territories and 660 subnational locations, 1990-2023: a systematic analysis for the Global Burden of Disease Study 2023., Lancet, PMID 41092928

PXD066017 Dataset with its publication pending (from PRIDE)
Dataset title: Defining the Ovarian Cancer Precancerous Landscape through Modeling Fallopian Tube Epithelium Reprogramming Driven by Extracellular Vesicles
Possible reference: Sipes, J. et al. (2025) Defining the Ovarian Cancer Precancerous Landscape through Modeling Fallopian Tube Epithelium Reprogramming Driven by Extracellular Vesicles., Cancer Res Commun, PMID 40689422

PXD065988 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic Exploration of the Recently Re-classified Forest Cobra Naja Species and the Potential Cytotoxic Activity in Cancer Cell Lines
Possible reference: Motsa, P. et al. (2026) Proteomic exploration of the recently Re-classified forest cobra Naja species and the potential cytotoxic activity in cancer cell lines., J Proteomics, PMID 41115607

PXD065987 Dataset with its publication pending (from iProX)
Dataset title: Glycosylation Inhibition as a Therapeutic Strategy for Neuroinflammatory Disorders: The Potential of Tanshinone IIA
Possible reference: Li, Y. et al. (2026) Glycosylation modulation as a therapeutic strategy for neuroinflammatory disorders: The potential of Tanshinone IIA., iScience, PMID 42211131

PXD065981 Dataset with its publication pending (from iProX)
Dataset title: IKKÎ² and USP28 govern HEY1 stability to enhance cancer stemness and immune evasion in hepatocellular carcinoma
Possible reference: Shao, N. et al. (2026) IKKβ and USP28 Regulate HEY1 Stability to Promote Cancer Stemness and Immune Evasion in Hepatocellular Carcinoma., Adv Sci (Weinh), PMID 42189121

PXD065979 Dataset with its publication pending (from iProX)
Dataset title: kinase activity of RIOK2 transports FADD–RIPK1–Caspase-8 complex from lysosome to ER and triggers spatial cleavage of GSDMD
Possible reference: Ma, M. et al. (2025) RIOK2 kinase regulates the translocation of the FADD-RIPK1-Caspase-8 complex to the ER and the cleavage of Gasdermin D to drive pyroptosis., Nat Commun, PMID 41249793

PXD065977 Dataset with its publication pending (from jPOST)
Dataset title: Functional and proteomic analysis of Lactobacillus rhamnosus-derived extracellular vesicles with antioxidant and anti-inflammatory activity
Possible reference: Wang, H. et al. (2025) Functional and proteomic analysis of Lactobacillus rhamnosus-derived extracellular vesicles with antioxidant and anti-inflammatory activity., Sci Rep, PMID 41413220

PXD065965 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular Domain Shedding of TROP2 Activates EGFR Signaling to Drive Prostate Cancer Metastasis
Possible reference: Liu, S. et al. (2025) Extracellular Domain Shedding of TROP2 Activates EGFR Signaling to Drive Prostate Cancer Metastasis., Cancer Res, PMID 40911783

PXD065931 no publication (from MassIVE)
Dataset title: Pseudomonadal itaconate degradation gene cluster encodes enzymes for methylsuccinate utilization
Possible reference: Gonner, L. et al. (2025) Pseudomonadal itaconate degradation gene cluster encodes enzymes for methylsuccinate utilization., Commun Biol, PMID 40707647

PXD065896 no publication (from MassIVE)
Dataset title: AlphaDIA enables DIA Transfer Learning for Feature-Free Proteomics
Possible reference: Wallmann, G. et al. (2025) AlphaDIA enables DIA transfer learning for feature-free proteomics., Nat Biotechnol, PMID 41120665

PXD065893 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics investigation into the alkaline pH-driven metabolic plasticity of Lactococcus lactis FM03
Possible reference: Bendig, TAL. et al. (2025) Alkaline pH-Driven Metabolic Plasticity of Lactococcus lactis FM03., Environ Microbiol, PMID 41199611

PXD065882 Dataset with its publication pending (from iProX)
Dataset title: C-Reactive Protein Is A Broad-Spectrum Capsule-Binding Receptor For Hepatic Capture of Blood-Borne Bacteria
Possible reference: Chen, D. et al. (2025) C-reactive protein is a broad-spectrum capsule-binding receptor for hepatic capture of blood-borne bacteria., EMBO J, PMID 41214213

PXD065881 Dataset with its publication pending (from iProX)
Dataset title: Spatiotemporal profiling of modification-specific proteome secretion uncovers an itaconation-activated tyrosine kinase
Possible reference: Lu, W. et al. (2025) Spatiotemporal profiling of modification-specific proteome secretion uncovers an itaconation-activated tyrosine kinase., Nat Commun, PMID 41345137

PXD065845 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of evolved strong biofilm producer strains of Listeria monocytogenes
Possible reference: Bombelli, A. et al. (2026) Evolution of Listeria monocytogenes to a strong biofilm producer via the overexpression of Lmo1799., Microbiol Res, PMID 41187561

PXD065844 Dataset with its publication pending (from PRIDE)
Dataset title: Unlocking the Zn-enriching Potential of Industrial Yeast Strains – an experimental journey from metal analysis to proteomics
Possible reference: Grimmer, G. et al. (2026) Unlocking the Zn-enriching potential of industrial yeast strains-an experimental journey from metal analysis to proteomics., Appl Microbiol Biotechnol, PMID 41520026

PXD065840 Dataset with its publication pending (from iProX)
Dataset title: Deciphering metabolic regulation in overripe grapes through multi-omics analysis of non-targeted metabolome, proteome, and transcriptome
Possible reference: Shi, N. et al. (2025) Deciphering metabolic regulation in overripe grapes through multi-omics analysis of non-targeted metabolome, proteome, and transcriptome., BMC Plant Biol, PMID 40898034

PXD065835 Dataset with its publication pending (from iProX)
Dataset title: Plasma Proteome Profiling Reveals Potential Biomarkers for the Early Diagnosis of Alzheimer’s Disease
Possible reference: Latifi-Navid, H. et al. (2025) AI-assisted multi-OMICS analysis reveals new markers for the prediction of AD., Biochim Biophys Acta Mol Basis Dis, PMID 40441366

PXD065818 Dataset with its publication pending (from iProX)
Dataset title: Precise and in vivo-compatible spatial proteomics via biolumines-cence-triggered photocatalytic proximity labeling
Possible reference: Sun, X. et al. (2025) Precise and In Vivo-Compatible Spatial Proteomics via Bioluminescence-Triggered Photocatalytic Proximity Labeling., ACS Cent Sci, PMID 41019118

PXD065815 Dataset with its publication pending (from jPOST)
Dataset title: A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation
Possible reference: Yang, SL. et al. (2025) A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation., Nat Commun, PMID 41006205

PXD065810 Dataset with its publication pending (from jPOST)
Dataset title: Phosphoproteomic analysis of signal transduction by Pas2r12 or Pas2r12–EGFP
Possible reference: Okuda, A. et al. (2025) Phosphoproteomic analysis of signal transduction dynamics induced by a modified cell-penetrating peptide-protein complex., Biochem Biophys Res Commun, PMID 40700806

PXD065807 Dataset with its publication pending (from jPOST)
Dataset title: Chemical-induced colitis lowers mitochondrial bioenergetic function in the colonic epithelium with minimal impacts on the proteome
Possible reference: Montgomery, MM. et al. (2025) Chemical-induced colitis lowers mitochondrial bioenergetic function in the colonic epithelium with minimal impacts on the proteome., Res Sq, PMID 41282096

PXD065801 Dataset with its publication pending (from iProX)
Dataset title: Site-Specific N-Glycosylation Alterations in Serum Proteins Across Subtypes of Adolescent Depressive Disorder
Possible reference: Hu, X. et al. (2026) Site-specific N-glycosylation alterations in serum proteins across subtypes of adolescent depressive disorder., BMC Psychiatry, PMID 42237277

PXD065790 Dataset with its publication pending (from PRIDE)
Dataset title: AuxB interacts directly with GpsB and PknB to coordinate cell envelope processes that contribute to intrinsic antibiotic resistance in Staphylococcus aureus
Possible reference: Sisley, TA. et al. (2025) AuxB interacts directly with GpsB and PknB to coordinate cell envelope processes that contribute to intrinsic antibiotic resistance in Staphylococcus aureus., mBio, PMID 40852988

PXD065780 no publication (from MassIVE)
Dataset title: Activation of the HPV16 late promoter by viral E2 and cellular BRD4 and ZC3H4 proteins
Possible reference: Renner, J. et al. (2025) Activation of the HPV16 late promoter by viral E2 and cellular BRD4 and ZC3H4 proteins., J Virol, PMID 40801544

PXD065777 Dataset with its publication pending (from jPOST)
Dataset title: Development of endogenous protein probes for characterizing surface proteins and cellular interactors of extracellular vesicles
Possible reference: Zheng, W. et al. (2026) Development of Endogenous Protein Probes for Characterizing Surface Proteins and Cellular Interactors of Extracellular Vesicles., Adv Sci (Weinh), PMID 41387095

PXD065769 Dataset with its publication pending (from PRIDE)
Dataset title: 5′-triphosphate guanosine RNAs recruit GTP-binding proteins to suppress RIG-I/IFN type I signalling
Possible reference: Wolczyk, M. et al. (2026) 5'-Triphosphate guanosine RNAs recruit GTP-binding proteins to suppress RIG-I/IFN type I signaling., Mol Cell, PMID 42105765

PXD065751 Dataset with its publication pending (from PRIDE)
Dataset title: Bacterial extracellular vesicles as recyclable nutrient reservoirs
Possible reference: Laimer-Digruber, A. et al. (2026) Bacterial extracellular vesicles as recyclable nutrient reservoirs., Nat Commun, PMID 41942463

PXD065743 Dataset with its publication pending (from PRIDE)
Dataset title: Integrating Cell Painting and Thermal Proteome Profiling for Inference of Targets and Mechanism of Action
Possible reference: Johansson, C. et al. (2026) Cell painting and thermal proteome profiling for inference of drug targets and mechanism of action., Mol Syst Biol, PMID 42141265

PXD065693 no publication (from MassIVE)
Dataset title: Leishmania donovani co-fractionation
Possible reference: Azimi, A. et al. (2026) A global protein interaction network of Leishmania donovani., Int J Parasitol, PMID 41072706

PXD065685 Dataset with its publication pending (from PRIDE)
Dataset title: Structure of ATTRv-F64S fibrils isolated from skin tissue of a living patient
Possible reference: Yu, J. et al. (2025) Structure of ATTRv-F64S fibrils isolated from skin tissue of a living patient., Nat Commun, PMID 41402329

PXD065676 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial components secretion in extracellular vesicles promotes alveolar epithelial mitochondrial quality control
Possible reference: Liu, B. et al. (2025) Mitochondrial components secretion in extracellular vesicles promotes alveolar epithelial mitochondrial quality control., Nat Commun, PMID 41350534

PXD065670 Dataset with its publication pending (from iProX)
Dataset title: AMPK alters proteasome phosphorylation status and prevents persistent proteasome condensates
Possible reference: Li, J. et al. (2025) AMPK alters proteasome phosphorylation status and prevents persistent proteasome condensates., bioRxiv, PMID 40631302

PXD065659 Dataset with its publication pending (from PRIDE)
Dataset title: Polyamine-dependent metabolic shielding regulates alternative splicing
Possible reference: Zabala-Letona, A. et al. (2026) Polyamine-dependent metabolic shielding regulates alternative splicing., Nature, PMID 41535471

PXD065637 Dataset with its publication pending (from iProX)
Dataset title: Profiling of SFTS virus and host protein interactions by Affinity purification-mass spectrometry
Possible reference: Hou, W. et al. (2025) Profiling of SFTS virus and host protein interactions by affinity purification-mass spectrometry., Mol Immunol, PMID 40929771

PXD065627 Dataset with its publication pending (from jPOST)
Dataset title: Exploration of charge reduction on sequence coverage of proteins by 193 nm ultraviolet photodissociation
Possible reference: Dunham, SD. et al. (2023) Impact of Internal Fragments on Top-Down Analysis of Intact Proteins by 193 nm UVPD., J Proteome Res, PMID 36503236

PXD065625 Dataset with its publication pending (from PRIDE)
Dataset title: Periplasmic Protein Quality Control at Atomic Level in Live Cells
Possible reference: Gonz�lez, LJ. et al. (2025) Periplasmic protein quality control at atomic level in live cells., Nat Commun, PMID 40993131

PXD065621 Dataset with its publication pending (from PRIDE)
Dataset title: Fbxo42 promotes the degradation of Ataxin-2 granules to trigger terminal Xbp1 signaling
Possible reference: Santos, CC. et al. (2025) Fbxo42 promotes the degradation of Ataxin-2 granules to trigger terminal Xbp1 signaling., Nat Commun, PMID 40804044

PXD065617 Dataset with its publication pending (from iProX)
Dataset title: Proteomic data of NCR1 negatively regulates drought tolerance in Arabidopsis thaliana
Possible reference: Li, L. et al. (2025) The small nucleolar RNA NON-CODING RNA 1 negatively regulates drought tolerance in Arabidopsis thaliana., Plant J, PMID 40842199

PXD065585 Dataset with its publication pending (from PRIDE)
Dataset title: AP2X-1 is a negative regulator of Toxoplasma gondii sexual commitment
Possible reference: Sun, L-X. et al. (2025) AP2X-1 is a negative regulator of Toxoplasma gondii sexual commitment., mBio, PMID 40823841

PXD065564 no publication (from MassIVE)
Dataset title: Mono-mix strategy enables proteomic analysis of a cross-kingdom microbial symbiosis
Possible reference: Dupuis, S. et al. (2025) Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis., bioRxiv, PMID 40777375

PXD065561 Dataset with its publication pending (from PRIDE)
Dataset title: Cooperative clamp-mediated promoter recognition by poxviral RNA polymerase and its TBP/TFIIB-like partner
Possible reference: Jungwirth, S. et al. (2026) Cooperative clamp-mediated promoter recognition by poxviral RNA polymerase and its TBP/TFIIB-like partner., Nat Commun, PMID 41708602

PXD065536 no publication (from MassIVE)
Dataset title: Characterization of Usher Syndrome Type 2-Associated Retinal Proteins via Affinity Purification-Mass Spectrometry
Possible reference: Zou, J. et al. (2026) Characterization of Usher Syndrome Type 2-Associated Proteins in the Retina via Affinity Purification-Mass Spectrometry., Mol Cell Proteomics, PMID 41654259

PXD065529 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibition of AhR improves cortical bone and skeletal muscle function via preservation of neuromuscular junctions
Possible reference: Yu, K. et al. (2025) Inhibition of AhR improves cortical bone and skeletal muscle function via preservation of neuromuscular junctions., JCI Insight, PMID 40663393

PXD065528 no publication (from MassIVE)
Dataset title: Membrane-Associated Rhes Slc4a7 Complex Orchestrates Tunneling Nanotube Formation and Mutant Huntingtin Spread
Possible reference: Dagar, S. et al. (2026) Membrane-associated Rhes-Slc4a7 complex orchestrates tunneling nanotube formation and mutant Huntingtin spread., Sci Adv, PMID 41861004

PXD065487 Dataset with its publication pending (from iProX)
Dataset title: Human umbilical cord MSC DIA analysis
Possible reference: Li, S. et al. (2024) Proteomic characterization of hUC-MSC extracellular vesicles and evaluation of its therapeutic potential to treat Alzheimer's disease., Sci Rep, PMID 38472335

PXD065479 Dataset with its publication pending (from iProX)
Dataset title: Aggresomes protect mRNA under stress in Escherichia coli
Possible reference: Pei, L. et al. (2025) Aggresomes protect mRNA under stress in Escherichia coli., Nat Microbiol, PMID 40830717

PXD065473 no publication (from MassIVE)
Dataset title: Proteome-wide analysis and surface protein isolation for secretome characterization reveal insights into the biology of the leaf-cutter ant Acromyrmex echinatior
Possible reference: Huang, P. et al. (2025) Proteome-Wide Analysis and Surface Protein Isolation for Secretome Characterization Reveal Insights into the Biology of the Leaf-Cutter Ant Acromyrmex echinatior., Anal Chem, PMID 41378770

PXD065469 no publication (from MassIVE)
Dataset title: SynchroSep-MS: Parallel LC Separations for Multiplexed Proteomics
Possible reference: Lancaster, NM. et al. (2025) SynchroSep-MS: Parallel LC Separations for Multiplexed Proteomics., J Am Soc Mass Spectrom, PMID 40736054

PXD065465 Dataset with its publication pending (from PRIDE)
Dataset title: Stress-induced ribosome degradation in Bacillus subtilis is mediated by the RNase Y-specificity complex
Possible reference: Cornejo, FA. et al. (2026) Stress-induced ribosome degradation in Bacillus subtilis is mediated by the RNase Y-specificity complex., Nat Commun, PMID 42230597

PXD065461 Dataset with its publication pending (from PRIDE)
Dataset title: Hypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity
Possible reference: Sanchez-Garcia, MA. et al. (2025) Hypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity., Nat Immunol, PMID 41152617

PXD065449 Dataset with its publication pending (from PRIDE)
Dataset title: A H3K27me3 reader complex couples H3K27me3 accumulation to nascent transcription of transposable elements in Paramecium
Possible reference: Balan, T. et al. (2026) A H3K27me3 reader complex couples H3K27me3 accumulation to nascent transcription of transposable elements in Paramecium., Genome Biol, PMID 41913290

PXD065428 Dataset with its publication pending (from PRIDE)
Dataset title: Light chain amyloid fibrils from multiple myeloma patient (case 2), abdominal fat biopsy
Possible reference: Tomberli, B. et al. (2017) Abrupt Onset of Refractory Heart Failure Associated With Light-Chain Amyloidosis in Hypertrophic Cardiomyopathy., JAMA Cardiol, PMID 27806176

PXD065413 no publication (from MassIVE)
Dataset title: Bacteria covalently incorporate polyfluoroalkyl carboxylates into membrane lipids
Possible reference: Xie, Y. et al. (2026) Bacteria covalently incorporate polyfluoroalkyl carboxylates into membrane lipids., Nat Microbiol, PMID 41896601

PXD065407 Dataset with its publication pending (from PRIDE)
Dataset title: PARG regulates the proteosomal degradation of TARG1
Possible reference: Groslambert, J. et al. (2026) PARG regulates the proteasomal degradation of TARG1., Cell Rep, PMID 41499238

PXD065388 no publication (from MassIVE)
Dataset title: Defective Olfactomedin-2 connects adipocyte dysfunction to obesity
Possible reference: Lluch, A. et al. (2025) Defective Olfactomedin-2 connects adipocyte dysfunction to obesity., Nat Commun, PMID 40759652

PXD065376 Dataset with its publication pending (from iProX)
Dataset title: Screening and metabolic utilization of rice straw cellulose-degrading bacteria
Possible reference: Chen, ZJ. et al. (2023) [Screening, enzyme activity and genomic analysis of Paenibacillus silvae CH2]., Ying Yong Sheng Tai Xue Bao, PMID 38511380

PXD065374 Dataset with its publication pending (from PRIDE)
Dataset title: GOT1 inhibition induces extracellular matrix remodeling in pancreatic cancer
Possible reference: Curvello, R. et al. (2026) GOT1 Inhibition Induces Extracellular Matrix Remodeling in Pancreatic Cancer., Adv Sci (Weinh), PMID 41527462

PXD065360 Dataset with its publication pending (from iProX)
Dataset title: Proteomic profiles of different subtypes of M2 macrophages
Possible reference: Sun, H. et al. (2020) Specific TP53 subtype as biomarker for immune checkpoint inhibitors in lung adenocarcinoma., EBioMedicine, PMID 32927274

PXD065349 no publication (from MassIVE)
Dataset title: Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis
Possible reference: Minetti, A. et al. (2025) Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis., Nat Cell Biol, PMID 41286441

PXD065348 no publication (from MassIVE)
Dataset title: Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis
Possible reference: Minetti, A. et al. (2025) Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis., Nat Cell Biol, PMID 41286441

PXD065347 Dataset with its publication pending (from PRIDE)
Dataset title: Astral-based DIA proteomics analysis reveals the effects of selenium on Pleurotus pulmonarius
Possible reference: Xu, C. et al. (2025) Astral-based DIA proteomics analysis reveals the effects of selenium on Pleurotus pulmonarius., Sci Rep, PMID 40715524

PXD065345 Dataset with its publication pending (from PRIDE)
Dataset title: Neuronal Pentraxin 2 as a Potential Biomarker for Nusinersen Therapy Response in Adults with Spinal Muscular Atrophy: A Pilot Study
Possible reference: Neuhoff, S. et al. (2025) Neuronal Pentraxin 2 as a Potential Biomarker for Nusinersen Therapy Response in Adults with Spinal Muscular Atrophy: A Pilot Study., Biomedicines, PMID 40868076

PXD065322 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of glomeruli from Thsd7a podocyte knockout and WT mice
Possible reference: Huang, M. et al. (2026) Functional characterization of podocyte-expressed THSD7A in experimental membranous nephropathy., JCI Insight, PMID 41746732

PXD065305 Dataset with its publication pending (from iProX)
Dataset title: Glutamine Synthetase Shields Triple-negative Breast Cancer Cells from Ferroptosis in Metastasis Triggered by Glutamine Deprivation
Possible reference: Yang, Z. et al. (2025) Glutamine synthetase shields triple-negative breast cancer cells from ferroptosis in metastasis triggered by glutamine deprivation., Breast Cancer Res, PMID 41013471

PXD065303 Dataset with its publication pending (from iProX)
Dataset title: Hypoxia Induces HIF-1Î± Activation in Tendon Stem Cells to Enhance Extracellular Vesicle-mediated Tendon Repair
Possible reference: Wu, Y. et al. (2025) Hypoxia Induces HIF-1α Activation in Tendon Stem Cells to Enhance Extracellular Vesicle-Mediated Tendon Repair., ACS Appl Mater Interfaces, PMID 40675622

PXD065292 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer
Possible reference: Luo, J. et al. (2025) Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer., Nat Genet, PMID 41044247

PXD065279 Dataset with its publication pending (from PRIDE)
Dataset title: MHC1-TIP: scalable multimodal immunopeptidome profiling of low-input samples
Possible reference: Bathini, M. et al. (2025) MHC1-TIP enables single-tube multimodal immunopeptidome profiling and uncovers intratumoral heterogeneity in antigen presentation., bioRxiv, PMID 40777321

PXD065260 no publication (from MassIVE)
Dataset title: Larval ascariasis elicits a prominent IgA and IgG1/2 antibody response to adult Ascaris excretory/secretory antigens in pigs
Possible reference: Musimbi, ZD. et al. (2025) Larval ascariasis elicits a prominent IgA and IgG1/2 antibody response to adult Ascaris excretory/secretory antigens in pigs., Front Immunol, PMID 40808955

PXD065247 Dataset with its publication pending (from iProX)
Dataset title: Proteome-wide analysis by LC-MS/MS reveals the role of ATRA during adipogenesis in hBMSCs
Possible reference: Peng, J. et al. (2026) Proteome-wide analysis by liquid chromatography tandem mass spectrometry reveals the role of retinoic acid during adipogenesis in human bone mesenchymal stem cells., PeerJ, PMID 41704236

PXD065245 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibition of rhizobial cheaters by the host Medicago truncatula involves repression of symbiotic functions and induction of defense, dataset1.2
Possible reference: Chen, M. et al. (2025) Inhibition of rhizobial cheaters by the host Medicago truncatula involves repression of symbiotic functions and induction of defense., New Phytol, PMID 40910153

PXD065238 Dataset with its publication pending (from iProX)
Dataset title: Proteome of the sporoplasm of Ameson portunus (Microsporidia)
Possible reference: Xu, YL. et al. (2025) Morphology, proteome and metabolome characterization of the sporoplasm of Ameson portunus (Microsporidia)., J Invertebr Pathol, PMID 40513983

PXD065234 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of KDM6A-mediated genomic instability and metabolic reprogramming regulates response to therapeutic perturbations in bladder cancer
Possible reference: Singh, P. et al. (2026) Loss of KDM6A-mediated genomic instability and metabolic reprogramming regulates response to therapeutic perturbations in bladder cancer., Nat Commun, PMID 41501085

PXD065228 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer
Possible reference: Luo, J. et al. (2025) Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer., Nat Genet, PMID 41044247

PXD065225 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibition of rhizobial cheaters by the host Medicago truncatula involves repression of symbiotic functions and induction of defense, dataset1.1
Possible reference: Chen, M. et al. (2025) Inhibition of rhizobial cheaters by the host Medicago truncatula involves repression of symbiotic functions and induction of defense., New Phytol, PMID 40910153

PXD065222 Dataset with its publication pending (from PRIDE)
Dataset title: Enamel peptide analysis to determine chromosomal sex of human remains (kÅiwi tangata) of MÄori-era individuals from New Zealand (Aotearoa)
Possible reference: Kinaston, RL. et al. (2026) Horticultural intensification and plant-based diets of 18th century CE Waikato Māori in Aotearoa New Zealand., Nat Commun, PMID 41946702

PXD065221 Dataset with its publication pending (from PRIDE)
Dataset title: The immune response against cancer is modulated by stromal cell fibronectin
Possible reference: Lubosch, A. et al. (2025) The immune response against cancer is modulated by stromal cell fibronectin., Neoplasia, PMID 40592236

PXD065220 Dataset with its publication pending (from PRIDE)
Dataset title: A Rab1 interactome illuminates its dual role in autophagy and membrane trafficking
Possible reference: van Vliet, AR. et al. (2026) A Rab1 interactome illuminates a dual role in autophagy and membrane trafficking., J Cell Biol, PMID 41493270

PXD065203 Dataset with its publication pending (from iProX)
Dataset title: Comparative Proteomic Analysis of Brassica Species under Lead (Pb) Stress
Possible reference: Wei, J. et al. (2021) Comparative Transcriptomics and Proteomics Analyses of Leaves Reveals a Freezing Stress-Responsive Molecular Network in Winter Rapeseed (Brassica rapa L.)., Front Plant Sci, PMID 33995460

PXD065171 no publication (from MassIVE)
Dataset title: AAV2 induced RPA exhaustion generates cellular DNA damage and restricts viral gene expression
Possible reference: Summers, MF. et al. (2025) Adeno-Associated Virus 2 (AAV2) - Induced RPA exhaustion generates cellular DNA damage and restricts viral gene expression., PLoS Pathog, PMID 40825038

PXD065125 Dataset with its publication pending (from PRIDE)
Dataset title: The Parkinson’s disease kinase LRRK2 impairs release sites of vulnerable dopamine axons
Possible reference: Chen, C. et al. (2025) Leucine-rich repeat kinase 2 impairs the release sites of Parkinson's disease vulnerable dopamine axons., bioRxiv, PMID 40909700

PXD065079 Dataset with its publication pending (from iProX)
Dataset title: Gansu Alpine Fine-Wool Sheep Wool Proteome
Possible reference: He, Z. et al. (2025) Screening of Protein Related to Wool Development and Fineness in Gansu Alpine Fine-Wool Sheep., Animals (Basel), PMID 40941372

PXD065063 Tim MG MacKenzie, Lucia Ramirez, Ruiqi Jian, Lihua Jiang, Michael P Snyder. Comprehensive Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2. https://www.biorxiv.org/content/10.1101/2025.07.10.663086v1. (from MassIVE)
Dataset title: In Depth Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2
Possible reference: MacKenzie, TMG. et al. (2026) In Depth Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2., Mol Cell Proteomics, PMID 42025763

PXD065038 no publication (from MassIVE)
Dataset title: Neuronal Idol deletion ameliorates amyloid pathology
Possible reference: Karahan, H. et al. (2025) Deletion of neuronal Idol ameliorates Alzheimer's disease-related pathologies via APOE receptors., Alzheimers Dement, PMID 41384508

PXD065001 Dataset with its publication pending (from PRIDE)
Dataset title: Tetraspanin-enriched Membrane Domains Regulate Vascular Leakage by Membrane Cholesterol Accessibility to Balance Antagonistic GTPases.
Possible reference: Ding, Y. et al. (2025) Tetraspanin-enriched membrane domains regulate vascular leakage by altering membrane cholesterol accessibility to balance antagonistic GTPases., Nat Cardiovasc Res, PMID 40731107

PXD064997 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omic responses of mouse liver and skeletal muscle to chronic alcohol drinking
Possible reference: Willis, CRG. et al. (2026) Comparative multi-omics in female mice reveals tissue-specific vulnerabilities to chronic alcohol intake., Alcohol Clin Exp Res (Hoboken), PMID 41612900

PXD064979 Dataset with its publication pending (from iProX)
Dataset title: proteomics exploratory analysis of urine from neuroblastoma before and after chemotherapy
Possible reference: Ma, Y. et al. (2025) The changes of immune function after neuroblastoma chemotherapy and the prediction of potential immune targets., BMC Med Genomics, PMID 40835926

PXD064973 Dataset with its publication pending (from jPOST)
Dataset title: Secretome MTB infected macrophage and neutrophil
Possible reference: Kaewseekhao, B. et al. (2021) Characterisation of secretome-based immune responses of human leukocytes infected with various Mycobacterium tuberculosis lineages., PeerJ, PMID 34141493

PXD064941 Dataset with its publication pending (from jPOST)
Dataset title: Plasma Proteomic Biomarkers for Predicting Chemoradiation Response in Locally Advanced Cervical Cancer
Possible reference: Leetanaporn, K. et al. (2024) Enhancing outcome prediction of concurrent chemoradiation treatment in patients with locally advanced cervical cancer through plasma extracellular vesicle proteomics., Heliyon, PMID 39262965

PXD064939 Dataset with its publication pending (from PRIDE)
Dataset title: Autoimmunity-associated DIORA1 binds the MRCK family of serine/threonine kinases and controls cell motility
Possible reference: Tršelič, T. et al. (2025) Autoimmunity-associated DIORA1 binds the MRCK family of serine/threonine kinases and controls cell motility., Proc Natl Acad Sci U S A, PMID 41042840

PXD064926 Dataset with its publication pending (from PRIDE)
Dataset title: Proteolytic Cleavage Activates the Mitochondrial Isoform of TOP3A
Possible reference: Erdinc, D. et al. (2025) Proteolytic cleavage activates the mitochondrial isoform of TOP3A., Nucleic Acids Res, PMID 41189053

PXD064921 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting synergetic endothelial inflammation by inhibiting NFKB and JAK-STAT pathways
Possible reference: Groten, SA. et al. (2025) Targeting synergetic endothelial inflammation by inhibiting NFKB and JAK-STAT pathways., iScience, PMID 40894883

PXD064903 Dataset with its publication pending (from iProX)
Dataset title: In vitro activity of quisinostat against Toxoplasma gondii
Possible reference: Qiu, H-J. et al. (2025) In vitro and in vivo activity of quisinostat against Toxoplasma gondii., Antimicrob Agents Chemother, PMID 40741955

PXD064863 no publication (from MassIVE)
Dataset title: Oxidative stress decreases deubiquitylases and proteasome activity during vertebrate brain aging
Possible reference: Sahu, AK. et al. (2026) Oxidative stress causes a reversible decrease of deubiquitylases activity in old vertebrate brains., Nat Commun, PMID 42014687

PXD064862 no publication (from MassIVE)
Dataset title: Oxidative stress decreases deubiquitylases and proteasome activity during vertebrate brain aging
Possible reference: Sahu, AK. et al. (2026) Oxidative stress causes a reversible decrease of deubiquitylases activity in old vertebrate brains., Nat Commun, PMID 42014687

PXD064860 no publication (from MassIVE)
Dataset title: Oxidative stress decreases deubiquitylases and proteasome activity during vertebrate brain aging
Possible reference: Sahu, AK. et al. (2026) Oxidative stress causes a reversible decrease of deubiquitylases activity in old vertebrate brains., Nat Commun, PMID 42014687

PXD064857 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of Sporobolomyces pararoseus ZRQ01
Possible reference: Li, X. et al. (2022) Torularhodin Alleviates Hepatic Dyslipidemia and Inflammations in High-Fat Diet-Induced Obese Mice via PPARα Signaling Pathway., Molecules, PMID 36234935

PXD064795 Dataset with its publication pending (from PRIDE)
Dataset title: Deciphering Mutational Effects on Inducible Nitric Oxide Synthase Conformational Dynamics via Quantitative Cross-Linking Mass Spectrometry and AlphaFold2 Subsampling
Possible reference: Jiang, T. et al. (2025) Deciphering mutational effects on inducible NO synthase conformational dynamics via quantitative cross-linking mass spectrometry and AlphaFold2 subsampling., J Biol Chem, PMID 40889679

PXD064794 Dataset with its publication pending (from PRIDE)
Dataset title: IsoBayes: a Bayesian approach for single-isoform proteomics inference
Possible reference: Bollon, J. et al. (2025) IsoBayes: a Bayesian approach for single-isoform proteomics inference., bioRxiv, PMID 38915658

PXD064774 Dataset with its publication pending (from iProX)
Dataset title: Comparison of Nigerian Snake Venom composition
Possible reference: Adeyi, AO. et al. (2026) Preliminary Insights into Geographic Variation in Venom Profiles and Functional Activities of Nigerian Snakes, Bitis arietans and Naja nigricollis., Toxins (Basel), PMID 42188623

PXD064771 Dataset with its publication pending (from iProX)
Dataset title: Phylloporia crataegi and Phylloporia fontanesiae proteomics
Possible reference: Fu, Y. et al. (2025) Comparative Multi-Omics Analysis and Antitumor Activity of Phylloporia crataegi and Phylloporia fontanesiae., J Microbiol Biotechnol, PMID 40877012

PXD064764 Dataset with its publication pending (from iProX)
Dataset title: Snhg18 regulates Yap subcellular localization to maintain bone homeostasis
Possible reference: Huang, J. et al. (2025) Snhg18 regulates Yap subcellular localization to maintain bone homeostasis., Nat Commun, PMID 40813368

PXD064751 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics of MYDGF knockdown in lung adenocarcinoma cells
Possible reference: Hsiao, TF. et al. (2025) Myeloid-Derived Growth Factor-Regulated Oncogenesis in Lung Adenocarcinoma Is Associated with EGFR Status and Cancer Aggressiveness., J Proteome Res, PMID 40752010

PXD064741 Dataset with its publication pending (from jPOST)
Dataset title: Reducing OGT and O-GlcNAcylation enhance the anticancer effects of oxaliplatin in SW620 metastatic colorectal cancer cells
Possible reference: Bunsuk, T. et al. (2026) Reducing OGT and O-GlcNAcylation enhance the anticancer effects of oxaliplatin in SW620 metastatic colorectal cancer cells., PLoS One, PMID 41666153

PXD064724 Dataset with its publication pending (from PRIDE)
Dataset title: Global Matrisome changes in the obese lung are linked to fibroblastic stroma and premature aging
Possible reference: Rottmann, S. et al. (2025) Global matrisome changes in obese lung are linked to fibroblastic stroma and premature aging., Cell Rep, PMID 40944912

PXD064706 Dataset with its publication pending (from iProX)
Dataset title: Radiation IP of HDAC6 in OMM2.3
Possible reference: Meng, X. et al. (2025) Ultrasound-assisted enzyme extraction of Citri Exocarpium Rubrum (Juhong) polysaccharides and its structural characteristics and evaluation of improving Parkinson's disease through HDAC6/NLRP3 pathway., Ultrason Sonochem, PMID 41135205

PXD064683 Dataset with its publication pending (from PRIDE)
Dataset title: Kinase activity of DYRK family members is required for regulating primary cilium length, stability and morphology
Possible reference: Arslanhan, MD. et al. (2025) Kinase activity of DYRK family members is required for regulating primary cilium length, stability and morphology., Commun Biol, PMID 40841441

PXD064681 Dataset with its publication pending (from PRIDE)
Dataset title: Global Matrisome changes in the obese lung are linked to fibroblastic stroma and premature aging
Possible reference: Rottmann, S. et al. (2025) Global matrisome changes in obese lung are linked to fibroblastic stroma and premature aging., Cell Rep, PMID 40944912

PXD064677 Dataset with its publication pending (from PRIDE)
Dataset title: Control of flagellar gene expression by the receptor-like regulator in pathogenic Escherichia coli
Possible reference: Lee, JW. et al. (2025) Control of flagellar gene expression by a chemotaxis receptor-like regulator in pathogenic Escherichia coli., EMBO J, PMID 41083908

PXD064675 Dataset with its publication pending (from PRIDE)
Dataset title: Complex II assembly drives metabolic adaptation to OXPHOS dysfunction.
Possible reference: Kugapreethan, R. et al. (2025) Complex II assembly drives metabolic adaptation to OXPHOS dysfunction., Sci Adv, PMID 40815660

PXD064660 Dataset with its publication pending (from iProX)
Dataset title: Phosphoproteomics Profiling Reveals Key Proteins Involved in Neuroinflammation and Impaired Axon Guidance Induced by Bilirubin Deficiency
Possible reference: Chen, M. et al. (2025) Phosphoproteomics Profiling Reveals Key Proteins Involved in Neuroinflammation and Impaired Axon Guidance Induced by Bilirubin Deficiency., ACS Chem Neurosci, PMID 40621869

PXD064659 Dataset with its publication pending (from iProX)
Dataset title: Deletion of SH2D5 alleviates epileptic seizures and NMDAR expression via autophagic degradation of STAT1
Possible reference: Guo, H. et al. (2025) Deletion of SH2D5 alleviates epileptic seizures and NMDAR expression via autophagic degradation of STAT1., JCI Insight, PMID 40857409

PXD064658 Dataset with its publication pending (from PRIDE)
Dataset title: Complex II assembly drives metabolic adaptation to OXPHOS dysfunction
Possible reference: Kugapreethan, R. et al. (2025) Complex II assembly drives metabolic adaptation to OXPHOS dysfunction., Sci Adv, PMID 40815660

PXD064655 Dataset with its publication pending (from PRIDE)
Dataset title: Thermal Liquid Biopsy for Early Colorectal Cancer Diagnosis integrating mass spectrometry proteomic biomarker discovery
Possible reference: Hermoso-Dur�n, S. et al. (2026) Integrating thermal liquid biopsy, clinical data, and mass spectrometry for early diagnosis and biomarker discovery in colorectal cancer., iScience, PMID 41704751

PXD064653 Dataset with its publication pending (from PRIDE)
Dataset title: Complex II assembly drives metabolic adaptation to OXPHOS dysfunction
Possible reference: Kugapreethan, R. et al. (2025) Complex II assembly drives metabolic adaptation to OXPHOS dysfunction., Sci Adv, PMID 40815660

PXD064651 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of Pacific oyster (Crassostrea gigas) mucus during Vibrio infection
Possible reference: Song, J. et al. (2024) Machine Learning-Driven Discovery and Evaluation of Antimicrobial Peptides from Crassostrea gigas Mucus Proteome., Mar Drugs, PMID 39330266

PXD064649 Dataset with its publication pending (from PRIDE)
Dataset title: Complex II assembly drives metabolic adaptation to OXPHOS dysfunction
Possible reference: Kugapreethan, R. et al. (2025) Complex II assembly drives metabolic adaptation to OXPHOS dysfunction., Sci Adv, PMID 40815660

PXD064634 Dataset with its publication pending (from PRIDE)
Dataset title: PBMC proteomics in paediatric obesity
Possible reference: Petek, M. et al. (2025) PBMC proteome is altered in children with high body fat percentage., Sci Rep, PMID 41257907

PXD064627 Dataset with its publication pending (from PRIDE)
Dataset title: Human neutrophils treated with glucocorticoids LC-MS/MS
Possible reference: Kant, R. et al. (2025) Dexamethasone mitigates sulfur mustard-induced stem cell deficiency in vivo in rabbit limbal tissue by reducing inflammation and oxidative stress., Arch Toxicol, PMID 39904901

PXD064618 Dataset with its publication pending (from PRIDE)
Dataset title: A clinic responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice
Possible reference: Zhou, H. et al. (2026) A clinic-responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice., Nat Microbiol, PMID 41803498

PXD064610 Dataset with its publication pending (from jPOST)
Dataset title: SARS-CoV-2 coreceptor candidate in CaCo-2 cell
Possible reference: Kotani, N. et al. (2022) Host cell membrane proteins located near SARS-CoV-2 spike protein attachment sites are identified using proximity labeling and proteomic analysis., J Biol Chem, PMID 36152751

PXD064609 Dataset with its publication pending (from jPOST)
Dataset title: SARS-CoV-2 coreceptor candidate in A549 cell
Possible reference: Chen, J. et al. (2021) Nonmuscle myosin heavy chain IIA facilitates SARS-CoV-2 infection in human pulmonary cells., Proc Natl Acad Sci U S A, PMID 34873039

PXD064602 Dataset with its publication pending (from iProX)
Dataset title: Nanoscale distribution of bioactive ligands on biomaterials regulates cell mechanosensing through translocation of actin into the nucleus
Possible reference: Liu, X. et al. (2025) Nanoscale distribution of bioactive ligands on biomaterials regulates cell mechanosensing through translocation of actin into the nucleus., Proc Natl Acad Sci U S A, PMID 40042901

PXD064598 Dataset with its publication pending (from iProX)
Dataset title: Lignocellulose adaptation drives polysaccharide biosynthesis in Tremella fuciformis: Metabolomic and proteomic insights
Possible reference: Xu, Y. et al. (2025) Lignocellulose adaptation drives polysaccharide biosynthesis in Tremella fuciformis: metabolomic and proteomic insights into CAZyme regulation., Front Fungal Biol, PMID 40718677

PXD064585 Dataset with its publication pending (from iProX)
Dataset title: RSK Inhibition Rewires Kinase Networks in Esophageal Cancer (proteomics)
Possible reference: Cheng, L. et al. (2025) RSK Inhibition Rewires Kinase Networks and Triggers Cascading Pathway Disruption in Esophageal Cancer., J Proteome Res, PMID 41157826

PXD064582 Dataset with its publication pending (from PRIDE)
Dataset title: Identifying interactions of the CLAVATA-related receptors FEA3 and BAM1D with TurboID-based proximity labeling in maize meristems
Possible reference: Lindsay, PL. et al. (2026) Antagonistic interactions between CLAVATA receptors shape maize ear development., New Phytol, PMID 41582630

PXD064571 Dataset with its publication pending (from PRIDE)
Dataset title: Radical footprinting in mammalian whole blood
Possible reference: Zhao, M. et al. (2025) Radical Footprinting in Mammalian Whole Blood., bioRxiv, PMID 39386581

PXD064570 Dataset with its publication pending (from PRIDE)
Dataset title: Large scale cerebrospinal fluid proteomics reveals biomarkers of Multiple Sclerosis
Possible reference: Bader, JM. et al. (2026) Large-scale proteomics across neurological disorders uncovers biomarker panel and targets in multiple sclerosis., Cell, PMID 41747728

PXD064568 Dataset with its publication pending (from PRIDE)
Dataset title: Chaperone Dependency during Primary Protein Biogenesis Does Not Correlate with Chaperone Dependency during in vitro Refolding
Possible reference: Yadav, D. et al. (2025) Chaperone Dependency during Primary Protein Biogenesis Does Not Correlate with Chaperone Dependency during in vitro Refolding., bioRxiv, PMID 40611891

PXD064562 Dataset with its publication pending (from PRIDE)
Dataset title: The adaptive molecular landscape to reprogrammed telomeric sequences
Possible reference: D'Angiolo, M. et al. (2026) The adaptive molecular landscape of reprogrammed telomeric sequences., Nat Commun, PMID 41957005

PXD064556 Dataset with its publication pending (from PRIDE)
Dataset title: Membrane protein changes during syntrophic interactions of an archaeal-bacterial coculture.
Possible reference: Fiege, K. et al. (2025) Membrane changes during syntrophic interactions of an archaeal-bacterial coculture., BMC Microbiol, PMID 41331417

PXD064548 Dataset with its publication pending (from iProX)
Dataset title: RSK Inhibition Rewires Kinase Networks in Esophageal Cancer
Possible reference: Cheng, L. et al. (2025) RSK Inhibition Rewires Kinase Networks and Triggers Cascading Pathway Disruption in Esophageal Cancer., J Proteome Res, PMID 41157826

PXD064538 Dataset with its publication pending (from PRIDE)
Dataset title: E3 ubiquitin ligase Listerin regulates macrophage cholesterol efflux and atherosclerosis by targeting ABCA1
Possible reference: Cao, L. et al. (2025) E3 ubiquitin ligase Listerin regulates macrophage cholesterol efflux and atherosclerosis by targeting ABCA1., J Clin Invest, PMID 40526435

PXD064532 Dataset with its publication pending (from PRIDE)
Dataset title: E3 ubiquitin ligase Listerin regulates macrophage cholesterol efflux and atherosclerosis by targeting ABCA1
Possible reference: Cao, L. et al. (2025) E3 ubiquitin ligase Listerin regulates macrophage cholesterol efflux and atherosclerosis by targeting ABCA1., J Clin Invest, PMID 40526435

PXD064516 Dataset with its publication pending (from PRIDE)
Dataset title: The intracellular bacterium Orientia tsutsugamushi uses the autotransporter ScaC to activate BICD adaptors for dynein-based motility.
Possible reference: Manigrasso, G. et al. (2025) The intracellular bacterium Orientia tsutsugamushi uses the autotransporter ScaC to activate BICD adaptors for dynein-based motility., Nat Commun, PMID 40610402

PXD064513 Dataset with its publication pending (from PRIDE)
Dataset title: Large scale cerebrospinal fluid proteomics reveals biomarkers of Multiple Sclerosis
Possible reference: Bader, JM. et al. (2026) Large-scale proteomics across neurological disorders uncovers biomarker panel and targets in multiple sclerosis., Cell, PMID 41747728

PXD064487 Dataset with its publication pending (from PRIDE)
Dataset title: A simplified perchloric acid workflow with neutralization (PCA-N) for democratizing deep plasma proteomics at population scale - Submission04
Possible reference: Albrecht, V. et al. (2025) A Simplified Perchloric Acid Workflow With Neutralization (PCA N) for Democratizing Deep Plasma Proteomics at Population Scale., Mol Cell Proteomics, PMID 40976565

PXD064431 Dataset with its publication pending (from iProX)
Dataset title: UBE2T mediated HP1Î± ubiquitination enhances nucleolar function and promote the progression of IDH1/TP53-mutant glioma
Possible reference: Zhou, F. et al. (2025) UBE2T-Mediated HP1α Ubiquitination Enhances Nucleolar Function and Promotes the Progression of IDH1/TP53-Mutant Glioma., Clin Cancer Res, PMID 40627452

PXD064413 no publication (from MassIVE)
Dataset title: Markers of neutrophil degranulation in the lung microenvironment linked to idiopathic pulmonary fibrosis severity and survival
Possible reference: Matson, SM. et al. (2026) Neutrophil degranulation in the lung microenvironment linked to idiopathic pulmonary fibrosis severity and survival., iScience, PMID 41531731

PXD064409 Dataset with its publication pending (from jPOST)
Dataset title: Evaluation of Cannabidiol Oil’s Effects on Sedation, Behavioral Responses to Handling, and Nociceptive Thresholds in Healthy Cats
Possible reference: Wanapinit, K. et al. (2025) Evaluation of Cannabidiol Oil's Effects on Sedation, Behavioral Responses to Handling, and Nociceptive Thresholds in Healthy Cats., Animals (Basel), PMID 40646886

PXD064403 Dataset with its publication pending (from iProX)
Dataset title: Fungal CeRNase T2 from Cunninghamella echinulata disrupts detoxification pathways and cause behavioral inhibition in invasive ant, Solenopsis invicta (Buren)
Possible reference: Li, S. et al. (2025) Fungal CeRNase T2 from Cunninghamella echinulata disrupts detoxification pathways and cause behavioral inhibition in invasive ant Solenopsis invicta (Buren)., Int J Biol Macromol, PMID 40675277

PXD064379 no publication (from MassIVE)
Dataset title: Desulfovibrio marinus single-subunit oligosaccharyltransferase and its human IgG substrates
Possible reference: Sotomayor, B. et al. (2024) Discovery of a single-subunit oligosaccharyltransferase that enables glycosylation of full-length IgG antibodies in Escherichia coli., bioRxiv, PMID 39574765

PXD064348 Dataset with its publication pending (from PRIDE)
Dataset title: Plasmodium parasite proteomics of iron deficiency
Possible reference: Song, X. et al. (2023) Regulation of Mitochondrial Energy Metabolism by Glutaredoxin 5 in the Apicomplexan Parasite Neospora caninum., Microbiol Spectr, PMID 36541793

PXD064347 Dataset with its publication pending (from iProX)
Dataset title: Non-invasive Urinary Proteomic Biomarkers for Prognostic Assessment in Sepsis
Possible reference: Bateman, RM. et al. (2016) 36th International Symposium on Intensive Care and Emergency Medicine : Brussels, Belgium. 15-18 March 2016., Crit Care, PMID 27885969

PXD064328 Dataset with its publication pending (from jPOST)
Dataset title: Modulation of Core-Fucosylation Oxidation for Selective Enrichment and Characterization of Cell Surface Glycoprotein
Possible reference: Guo, X. et al. (2025) Modulation of Core-Fucosylation Oxidation for Selective Enrichment and Characterization of Cell Surface Glycoprotein., ACS Chem Biol, PMID 41363663

PXD064324 no publication (from MassIVE)
Dataset title: Early microglia progenitors colonize the embryonic CNS via integrin-mediated transmigration from the pial surface
Possible reference: Petry, P. et al. (2026) Early microglia progenitors colonize the embryonic CNS via integrin-mediated migration from the pial surface., Dev Cell, PMID 40934928

PXD064286 no publication (from MassIVE)
Dataset title: Multiomic analysis identifies VPA induced changes in neural progenitor cells, ventricular-like regions and cellular microenvironment in dorsal forebrain organoids
Possible reference: Yent�r, Z. et al. (2026) Multiomics analysis identifies VPA-induced changes in neural progenitor cells, ventricular-like regions, and cellular microenvironment in dorsal forebrain organoids., Mol Psychiatry, PMID 42032298

PXD064272 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring the Cytotoxic Mechanisms and Anticancer Potentials of Silver Nanoparticles in Cisplatin-Sensitive and -Resistant Lung Adenocarcinoma: Insights from Proteomic and Mice Xenograft Studies
Possible reference: Wong, TY. et al. (2025) Exploring the Potentials of Silver Nanoparticles in Overcoming Cisplatin Resistance in Lung Adenocarcinoma: Insights from Proteomic and Xenograft Mice Studies., ACS Nano, PMID 40999704

PXD064268 Dataset with its publication pending (from PRIDE)
Dataset title: Exploration of phosphoproteins in Acinetobacter baumannii
Possible reference: Luo, J. et al. (2018) Exploring a phage-based real-time PCR assay for diagnosing Acinetobacter baumannii bloodstream infections with high sensitivity., Anal Chim Acta, PMID 30442396

PXD064265 Dataset with its publication pending (from PRIDE)
Dataset title: Ubiquitin-Proteasome System Dyeregulation in Alzheimer's Disease Impacts Protein Abundance.
Possible reference: Collins, M. et al. (2025) Ubiquitin-Proteasome System Dysregulation in Alzheimer's Disease Impacts Protein Abundance., bioRxiv, PMID 40501941

PXD064226 Dataset with its publication pending (from PRIDE)
Dataset title: The PP2A-2 holoenzyme orchestrates daughter cell emergence during cytokinesis in Toxoplasma gondii
Possible reference: Wang, JL. et al. (2025) The PP2A-2 holoenzyme orchestrates daughter cell emergence during cytokinesis in Toxoplasma gondii., PLoS Pathog, PMID 40901993

PXD064211 no publication (from MassIVE)
Dataset title: Extracellular Matrix Alterations in Chronic Ischemic Cardiomyopathy Revealed by Quantitative Proteomics
Possible reference: Buck, KM. et al. (2025) Extracellular Matrix Alterations in Chronic Ischemic Cardiomyopathy Revealed by Quantitative Proteomics., bioRxiv, PMID 40501991

PXD064185 Dataset with its publication pending (from PRIDE)
Dataset title: Supercharging-Enhanced nDIA-MS Enables Global Profiling of Drug-Induced Proteome Solubility Shifts (solubility proteomics)
Possible reference: Xiong, Y. et al. (2026) Supercharging-enhanced nDIA-MS enables global profiling of drug-induced proteome solubility shifts., Nat Commun, PMID 41617713

PXD064174 no publication (from MassIVE)
Dataset title: Overexpression of the signaling coordinator GAB2: a missing link in AML progression
Possible reference: Kramer, MH. et al. (2025) Overexpression of the signaling coordinator GAB2 can play an important role in acute myeloid leukemia progression., J Clin Invest, PMID 40773291

PXD064166 no publication (from MassIVE)
Dataset title: Turning waste into insight: a novel proteomic approach to non-invasive wound biomarker discovery
Possible reference: Soto, V. et al. (2025) Turning Waste Into Insight: A Novel Proteomic Approach to Non-Invasive Wound Biomarker Discovery., Mol Cell Proteomics, PMID 40848928

PXD064145 no publication (from MassIVE)
Dataset title: Impact of clozapine and risperidone on the proteome of the rat prefrontal cortex (PFC) and remaining cortex (CX)
Possible reference: Kedracka-Krok, S. et al. (2025) Clozapine's Molecular Signature: Selective 5-HT2A Receptor Downregulation and Signalling in Rat Brain Cortical Regions., J Neurochem, PMID 40952174

PXD064141 Dataset with its publication pending (from PRIDE)
Dataset title: Pathogenic phosphorylation of linear ubiquitin machinery causes inflammasome sensor degradation [Mouse]
Possible reference: Yu, Y. et al. (2025) Pathogenic phosphorylation of linear ubiquitin machinery causes inflammasome sensor degradation., Cell Rep, PMID 40944911

PXD064137 Dataset with its publication pending (from PRIDE)
Dataset title: The citrullinating enzyme PADI4 governs progenitor cell proliferation and translation in developing hair follicles
Possible reference: Vikhe Patil, K. et al. (2025) The citrullinating enzyme PADI4 governs progenitor cell proliferation and translation in developing hair follicles., Sci Adv, PMID 40938992

PXD064130 Dataset with its publication pending (from jPOST)
Dataset title: Cysteine redoxome landscape in the liver of male mice fed a high-fat high-sucrose diet
Possible reference: Galicia-Medina, CM. et al. (2025) Cysteine redoxome landscape in the liver of male mice fed a high-fat high-sucrose diet., J Biol Chem, PMID 40967437

PXD064126 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of oncogene-induced HCC in mouse models
Possible reference: Marquard, S. et al. (2020) Yes-associated protein (YAP) induces a secretome phenotype and transcriptionally regulates plasminogen activator Inhibitor-1 (PAI-1) expression in hepatocarcinogenesis., Cell Commun Signal, PMID 33097058

PXD064067 Dataset with its publication pending (from PRIDE)
Dataset title: A heterotrimeric protein complex assembles the metazoan V-ATPase upon dissipation of proton gradients
Possible reference: Nardone, C. et al. (2025) A heterotrimeric protein complex assembles the metazoan V-ATPase upon dissipation of proton gradients., Nat Struct Mol Biol, PMID 40646309

PXD064066 Dataset with its publication pending (from PRIDE)
Dataset title: Rapid expansion of primary human vocal fold epithelial cells via targeted pathway inhibition and anchorage-independent sphere culture
Possible reference: Shi, X. et al. (2026) Rapid expansion of primary human vocal fold epithelial cells via targeted pathway inhibition and anchorage-independent sphere culture., Cell Rep Methods, PMID 41794022

PXD064049 Dataset with its publication pending (from PRIDE)
Dataset title: Extrachromosomal DNA-driven oncogene dosage heterogeneity promotes rapid adaptation to therapy in MYCN-amplified cancers
Possible reference: Montuori, G. et al. (2025) Extrachromosomal DNA-Driven Oncogene Dosage Heterogeneity Promotes Rapid Adaptation to Therapy in MYCN-Amplified Cancers., Cancer Discov, PMID 40773595

PXD064039 Dataset with its publication pending (from iProX)
Dataset title: Extracellular vesicles from antler blastema progenitor cells reverse bone loss and mitigate aging related phenotypes in mice and macaques
Possible reference: Hao, Y. et al. (2025) Extracellular vesicles from antler blastema progenitor cells reverse bone loss and mitigate aging-related phenotypes in mice and macaques., Nat Aging, PMID 40660003

PXD064018 Dataset with its publication pending (from PanoramaPublic)
Dataset title: Combination of in vivo and in vitro phosphoproteomics determines the PP2A target repertoire on proteome scale
Possible reference: Brunner, M. et al. (2025) Combination of in vivo and in vitro phosphoproteomics determines the PP2A target repertoire on proteome scale., Cell Rep Methods, PMID 40541179

PXD064007 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicle-associated transcriptomic and proteomic biomarkers show in vitro potential for vandetanib treatment monitoring in anaplastic thyroid cancer
Possible reference: Gr�tz, C. et al. (2025) Extracellular vesicle-associated transcriptomic and proteomic biomarkers show in vitro potential for vandetanib treatment monitoring in anaplastic thyroid cancer., Sci Rep, PMID 40940449

PXD063991 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative Proteomic Analysis of Capillary and Micropillar Array Columns Using DIA: Insights from the TKO Yeast Standard
Possible reference: Zhang, T. et al. (2025) Comparative Proteomic Analysis of Capillary and Micropillar Array Columns Using DIA: Insights from the TKO Yeast Standard., J Proteome Res, PMID 40829030

PXD063981 Dataset with its publication pending (from PRIDE)
Dataset title: Activation of an initiating phosphoglycosyl transferase by a single-domain response regulator
Possible reference: Schwabe, J. et al. (2026) A single-domain response regulator activates exopolysaccharide biosynthesis by interaction with the initiating phosphoglycosyl transferase., mBio, PMID 41313210

PXD063973 Dataset with its publication pending (from PRIDE)
Dataset title: Activation of an initiating phosphoglycosyl transferase by a single-domain response regulator
Possible reference: Schwabe, J. et al. (2026) A single-domain response regulator activates exopolysaccharide biosynthesis by interaction with the initiating phosphoglycosyl transferase., mBio, PMID 41313210

PXD063971 Dataset with its publication pending (from PRIDE)
Dataset title: The raw proteomic data of overexpressing hCDK3 in neuron
Possible reference: Heidler, J. et al. (2016) Data file of a deep proteome analysis of the prefrontal cortex in aged mice with progranulin deficiency or neuronal overexpression of progranulin., Data Brief, PMID 27921079

PXD063970 no publication (from MassIVE)
Dataset title: Rapid photo-crosslinking in living cells reveals protein-nucleic acid dynamics on a timescale of minutes
Possible reference: Trendel, J. et al. (2026) Rapid photo-crosslinking in living cells reveals protein-nucleic acid dynamics on a timescale of minutes., Nucleic Acids Res, PMID 42011781

PXD063964 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic profiling of human cell lines using capillary and micro-pillar array column
Possible reference: Schroeter, CB. et al. (2025) Comparative Proteomic Profiling of Human Cell Lines Using Capillary and Micro-Pillar Array Columns., Proteomics, PMID 41055288

PXD063930 no publication (from MassIVE)
Dataset title: Tumor cell adipocyte gap junctions activate lipolysis and contribute to breast tumorigenesis
Possible reference: Williams, J. et al. (2025) Tumor cell-adipocyte gap junctions activate lipolysis and contribute to breast tumorigenesis., Nat Commun, PMID 40835606

PXD063924 no publication (from MassIVE)
Dataset title: Unveiling Proteomic and Peptide-Level Modifications in Cerebrospinal Fluid and Plasma in Normal Cognitive Aging
Possible reference: Kamalian, A. et al. (2025) Unveiling proteomic and peptide-level modifications in cerebrospinal fluid and plasma in normal cognitive aging., Commun Med (Lond), PMID 41254360

PXD063922 no publication (from MassIVE)
Dataset title: Eomesodermin interacting partners in mouse trophoblast stem cells
Possible reference: Bisia, AM. et al. (2025) Eomesodermin in conjunction with the BAF complex promotes expansion and invasion of the trophectoderm lineage., Nat Commun, PMID 40450029

PXD063907 no publication (from MassIVE)
Dataset title: Wu Combinatory Treatment to Alleviate Cellular Stress and Improve Skeletal Muscle Phenotype in Spinal Muscular Atrophy
Possible reference: Zeng, W. et al. (2025) Combinatory Treatment to Alleviate Cellular Stress and Improve Skeletal Muscle Phenotype in Spinal Muscular Atrophy., Circ Res, PMID 40654082

PXD063902 no publication (from MassIVE)
Dataset title: Beta-cell Galphas signaling is critical for physiological and pharmacological enhancement of insulin secretion
Possible reference: Capozzi, ME. et al. (2025) β Cell Gαs signaling is critical for physiological and pharmacological enhancement of insulin secretion., J Clin Invest, PMID 40526441

PXD063896 no publication (from MassIVE)
Dataset title: Revisiting the Venom Composition of the Black Judean Scorpion Hottentotta judaicus
Possible reference: Borges, A. et al. (2025) Proteomic characterization and lethality of the venom of the Black Judean scorpion, Hottentotta judaicus (Buthidae): expanded toxin diversity and revisited toxicological significance., Arch Toxicol, PMID 40928535

PXD063895 no publication (from MassIVE)
Dataset title: Revisiting the Venom Composition of the Black Judean Scorpion, Hottentotta judaicus (Buthidae): Lethality and Proteomic Evidence for Novel Components
Possible reference: Borges, A. et al. (2025) Proteomic characterization and lethality of the venom of the Black Judean scorpion, Hottentotta judaicus (Buthidae): expanded toxin diversity and revisited toxicological significance., Arch Toxicol, PMID 40928535

PXD063894 no publication (from MassIVE)
Dataset title: Extracellular Vesicles Mediate Cell Signaling and Systemic RNAi in Planarians
Possible reference: Sasidharan, V. et al. (2026) Extracellular vesicles mediate stem cell signaling and systemic RNAi in planarians., Sci Adv, PMID 41650266

PXD063893 no publication (from MassIVE)
Dataset title: Androgenic Effects of 11-oxyandrogens in Castration-Resistant Prostate Cancer
Possible reference: Lapointe-Belleau, A. et al. (2025) Androgenic effects of 11-oxyandrogens in castration-resistant prostate cancer., BMC Cancer, PMID 41257618

PXD063885 Dataset with its publication pending (from PRIDE)
Dataset title: PGC1-Î± drives Mfn2-linked Mitochondrial Fusion aiding Glioblastoma Cell Survival under TMZ stress
Possible reference: Sahu, AK. et al. (2026) PGC1-α drives MFN2-linked mitochondrial fusion aiding glioblastoma cell survival under TMZ stress., Int J Biol Macromol, PMID 41314582

PXD063865 Dataset with its publication pending (from PRIDE)
Dataset title: Proteostasis sustains T cell differentiation potential and tumor-infiltrating lymphocyte function
Possible reference: Scharping, NE. et al. (2026) Proteostasis sustains T cell differentiation potential and tumor-infiltrating lymphocyte function., bioRxiv, PMID 41727040

PXD063864 Dataset with its publication pending (from PRIDE)
Dataset title: ZDHHC11-mediated palmitoylation alleviates chondrocyte senescence and serves as a therapeutic target for osteoarthritis [III]
Possible reference: Wang, K. et al. (2025) ZDHHC11-mediated palmitoylation alleviates chondrocyte senescence and serves as a therapeutic target for osteoarthritis., Nat Aging, PMID 41028499

PXD063862 Dataset with its publication pending (from jPOST)
Dataset title: SIRT4 Controls Macrophage Function and Wound Healing through Control of Protein Itaconylation in Mice
Possible reference: Anderson, KA. et al. (2025) SIRT4 Controls Macrophage Function and Wound Healing through Control of Protein Itaconylation in Mice., bioRxiv, PMID 40463174

PXD063859 Dataset with its publication pending (from PRIDE)
Dataset title: ZDHHC11-mediated palmitoylation alleviates chondrocyte senescence and serves as a therapeutic target for osteoarthritis [II]
Possible reference: Wang, K. et al. (2025) ZDHHC11-mediated palmitoylation alleviates chondrocyte senescence and serves as a therapeutic target for osteoarthritis., Nat Aging, PMID 41028499

PXD063847 Dataset with its publication pending (from iProX)
Dataset title: Enrichment and Preservation of Urine Metabolites Using Styrene Divinylbenzene Reversed Phase Sulfonate (SDB-RPS) Disks for Enhanced Biomarker Discovery and Disease Monitoring
Possible reference: Wang, A. et al. (2026) Enrichment and Preservation of Urine Metabolites Using Styrene Divinylbenzene Reversed Phase Sulfonate (SDB-RPS) Disks for Enhanced Biomarker Discovery and Disease Monitoring., J Proteome Res, PMID 41744491

PXD063844 Dataset with its publication pending (from iProX)
Dataset title: Comparing and optimizing protein extraction methods for the analyses of human fecal microbiome via metaproteomics approach
Possible reference: Gao, S. et al. (2025) Comparing and optimizing protein extraction methods with different lysis buffers for the analyses of human fecal microbiome via metaproteomics approach., J Microbiol Methods, PMID 40886942

PXD063840 Dataset with its publication pending (from PRIDE)
Dataset title: ZDHHC11-mediated palmitoylation alleviates chondrocyte senescence and serves as a therapeutic target for osteoarthritis
Possible reference: Wang, K. et al. (2025) ZDHHC11-mediated palmitoylation alleviates chondrocyte senescence and serves as a therapeutic target for osteoarthritis., Nat Aging, PMID 41028499

PXD063817 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamic exchange of CRL4 regulated by CAND1 and CAND2
Possible reference: Reichermeier, KM. et al. (2020) PIKES Analysis Reveals Response to Degraders and Key Regulatory Mechanisms of the CRL4 Network., Mol Cell, PMID 31973889

PXD063797 Dataset with its publication pending (from PRIDE)
Dataset title: Transcriptomics-proteomics analysis reveals the role of SiNRX1 in regulating drought stress in foxtail millet (Setaria italica L.)
Possible reference: Chang, X. et al. (2025) Transcriptomics-proteomics analysis reveals the role of SiNRX1 in regulating drought stress in foxtail millet (Setaria italica L.)., BMC Genomics, PMID 41094417

PXD063792 Dataset with its publication pending (from iProX)
Dataset title: EGR2 O-GlcNAcylation Orchestrates the Development of Protumoral Macrophages to Limit CD8+ T Cell Antitumor Responses
Possible reference: Zhang, Y. et al. (2025) EGR2 O-GlcNAcylation orchestrates the development of protumoral macrophages to limit CD8+ T cell antitumor responses., Cell Chem Biol, PMID 40499546

PXD063787 Dataset with its publication pending (from jPOST)
Dataset title: TAG-PL: A Universal Proximity Labeling Platform for Mapping Mitochondrial Proteomes and Organelle Interactions Under Stress
Possible reference: Miao, E. et al. (2026) TAG-PL: A Universal Proximity Labeling Platform for Mapping Mitochondrial Proteomes and Organelle Interactions under Stress., J Proteome Res, PMID 41432230

PXD063756 Dataset with its publication pending (from iProX)
Dataset title: Genetically encoded activity-based ubiquitin and ubiquitin-like protein covalent probes
Possible reference: Pannala, NM. et al. (2025) Internal Ubiquitin Electrophiles for Covalent Trapping and Inhibition of Deubiquitinases., Chembiochem, PMID 40626928

PXD063754 Dataset with its publication pending (from iProX)
Dataset title: Quantitative Proteomic and Metabolomic Profiling Reveals Altered Purine Metabolism in Acute Kidney Injury after On-pump Coronary Artery Bypass Graft
Possible reference: Zhao, M. et al. (2025) Quantitative Proteomic and Metabolomic Profiling Reveals Altered Purine Metabolism in Acute Kidney Injury after On-Pump Coronary Artery Bypass Graft., J Proteome Res, PMID 40549498

PXD063732 Dataset with its publication pending (from PRIDE)
Dataset title: Insects evolved a monomeric histone-fold domain in the CENP-T protein family
Possible reference: Sankaranarayanan, SR. et al. (2025) Insects evolved a monomeric histone-fold domain in the CENP-T protein family., EMBO Rep, PMID 41162737

PXD063722 Dataset with its publication pending (from PRIDE)
Dataset title: Structural mechanisms of allosteric regulation in the human cis-prenyltransferase complex
Possible reference: Danley, DE. et al. (2015) Discovery and structural characterization of an allosteric inhibitor of bacterial cis-prenyltransferase., Protein Sci, PMID 25287857

PXD063714 Dataset with its publication pending (from PRIDE)
Dataset title: ABCF Protein-Mediated Resistance Shapes Bacterial Responses Based on Antibiotic Type and Concentration
Possible reference: Koběrská, M. et al. (2025) ABCF protein-mediated resistance shapes bacterial responses to antibiotics based on their type and concentration., mBio, PMID 40793774

PXD063702 Dataset with its publication pending (from iProX)
Dataset title: G1P promotes phase separation of glycogen and G6PD resulting in pentose phosphate pathway compartmentalization in CD8+ memory T cells
Possible reference: Zhou, Y. et al. (2025) Glucose-1-phosphate promotes compartmentalization of glycogen with the pentose phosphate pathway in CD8+ memory T cells., Mol Cell, PMID 40499549

PXD063693 Dataset with its publication pending (from iProX)
Dataset title: Deficiency of the UBE2C/F264 Axis Underlies Intrinsic Radioresistance in Cervical Carcinoma
Possible reference: Ni, M. et al. (2025) Deficiency of the UBE2C/F264 Axis Underlies Intrinsic Radioresistance in Cervical Carcinoma., J Proteome Res, PMID 40748296

PXD063690 Dataset with its publication pending (from iProX)
Dataset title: A Novel Strategy to Rapidly Profile and Quantify High-Risk Host Cell Proteins using Integrated DDA-PRM-dMRM Mode
Possible reference: Xu, X. et al. (2025) A Novel Strategy to Rapidly Profile and Quantify High-Risk Host Cell Proteins Using Integrated DDA-PRM-dMRM Mode., J Proteome Res, PMID 40562700

PXD063687 Dataset with its publication pending (from iProX)
Dataset title: Mild Tissue Extraction for Mass Spectrometry-based Proteomic Discovery of Biomarkers
Possible reference: Du, L. et al. (2025) Tissue Mild Extraction Enriches Membrane, Cytoplasmic, and Secreted Proteomes for Biomarker Discovery., J Proteome Res, PMID 40769942

PXD063686 Dataset with its publication pending (from iProX)
Dataset title: Deep Profiling of Oocyte Aging Enabled by Simple One-Step Vial-Based Pretreatment and Single-Cell Proteomics
Possible reference: Zhang, H. et al. (2025) Deep Profiling of Oocyte Aging Enabled by Simple One-Step Vial-Based Pretreatment and Single-Cell Proteomics., JACS Au, PMID 40443890

PXD063677 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-center multi-omics integration predicts individualized prognosis in medullary thyroid carcinoma
Possible reference: Zhou, Y. et al. (2026) Multi-center multi-omics integration predicts individualized prognosis in medullary thyroid carcinoma., Nat Commun, PMID 41535264

PXD063665 Dataset with its publication pending (from PRIDE)
Dataset title: The transcriptional landscape of metastatic hormone-na�ve prostate cancer
Possible reference: Asberry, AM. et al. (2022) Reprogramming landscape highlighted by dynamic transcriptomes in therapy-induced neuroendocrine differentiation., Comput Struct Biotechnol J, PMID 36382181

PXD063663 no publication (from MassIVE)
Dataset title: Specificity profiling of SARS-CoV-2 PLpro using proteome-derived libraries of linear peptides suggests secondary preference for basic motifs
Possible reference: Vogele, D. et al. (2026) Specificity profiling of SARS-CoV-2 PLpro using proteome-derived libraries of linear peptides suggests secondary preference for basic motifs., Arch Biochem Biophys, PMID 42214738

PXD063645 Dataset with its publication pending (from iProX)
Dataset title: A cationic polymer drives glycosaminoglycan assembly and secretion for preclinical osteoarthritis therapy
Possible reference: Chen, Y. et al. (2025) A cationic polymer drives glycosaminoglycan assembly and secretion for preclinical osteoarthritis therapy., Sci Transl Med, PMID 40561002

PXD063640 Dataset with its publication pending (from jPOST)
Dataset title: Therapeutic Potential of Red Bean (Phaseolus vulgaris) Peptides: Anticancer, Antihypertension, and Antioxidant Activities
Possible reference: Roytrakul, S. et al. (2025) Therapeutic potential of red bean (phaseolus vulgaris) peptides: anticancer, antihypertension, and antioxidant activities., Sci Rep, PMID 41198802

PXD063637 Dataset with its publication pending (from PRIDE)
Dataset title: UBE2J2 is essential for the progression of meiosis prophase I during spermatogenesis in mice
Possible reference: Yu, X. et al. (2025) UBE2J2 is essential for the progression of meiosis prophase I during spermatogenesis in mice., iScience, PMID 40686610

PXD063617 Dataset with its publication pending (from jPOST)
Dataset title: Quantitative Extracellular Vesicle Proteomics by Multiplexed Data-Independent Acquisition
Possible reference: Braga-Lagache, S. et al. (2016) Robust Label-free, Quantitative Profiling of Circulating Plasma Microparticle (MP) Associated Proteins., Mol Cell Proteomics, PMID 27738094

PXD063593 Dataset with its publication pending (from PRIDE)
Dataset title: Pre-analytical Sample Quality Determines Performance of Plasma Proteomics Workflows for Biomarker Discovery part02
Possible reference: Korff, K. et al. (2025) Pre-analytical drivers of bias in bead-enriched plasma proteomics., EMBO Mol Med, PMID 40940569

PXD063589 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic tracking extracellular vesicle RNA interactors through orthogonal labelings in recipient immune cells
Possible reference: Zhang, Z. et al. (2025) Proteomic Tracking Extracellular Vesicle RNA Interactors in Recipient Immune Cells through Orthogonal Labelings., J Am Chem Soc, PMID 40746261

PXD063585 Dataset with its publication pending (from PRIDE)
Dataset title: Dysregulated lipid metabolism and hypomyelination in postnatal peroxisome-deficient Pex2 knockout Zellweger mice
Possible reference: Eberhart, T. et al. (2026) Dysregulated lipid metabolism and hypomyelination in postnatal peroxisome-deficient Pex2 knockout Zellweger mice., Front Mol Neurosci, PMID 41815956

PXD063572 Dataset with its publication pending (from PRIDE)
Dataset title: Pre-analytical Sample Quality Determines Performance of Plasma Proteomics Workflows for Biomarker Discovery
Possible reference: Korff, K. et al. (2025) Pre-analytical drivers of bias in bead-enriched plasma proteomics., EMBO Mol Med, PMID 40940569

PXD063568 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Landscape of Porcine Induced Neural Stem Cell Reprogramming and Differentiation
Possible reference: Ploypetch, S. et al. (2025) Proteomic landscape of porcine induced neural stem cell reprogramming and differentiation., PeerJ, PMID 41059408

PXD063560 Dataset with its publication pending (from PRIDE)
Dataset title: Data-independent immunopeptidomics discovery of low-abundant bacterial epitopes
Possible reference: Willems, P. et al. (2025) Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes., J Proteome Res, PMID 41166551

PXD063550 Dataset with its publication pending (from PRIDE)
Dataset title: Selective ubiquitination of drug-like small molecules by the ubiquitin ligase HUWE1
Possible reference: Orth, B. et al. (2025) Selective ubiquitination of drug-like small molecules by the ubiquitin ligase HUWE1., Nat Commun, PMID 40897715

PXD063537 Dataset with its publication pending (from PRIDE)
Dataset title: ZDHHC11-mediated palmitoylation alleviates chondrocyte senescence
Possible reference: Wang, K. et al. (2025) ZDHHC11-mediated palmitoylation alleviates chondrocyte senescence and serves as a therapeutic target for osteoarthritis., Nat Aging, PMID 41028499

PXD063514 Dataset with its publication pending (from PRIDE)
Dataset title: Pex3 promotes formation of peroxisome-peroxisome and peroxisome-lipid droplet contact sites
Possible reference: Amado, L. et al. (2025) Pex3 promotes formation of peroxisome-peroxisome and peroxisome-lipid droplet contact sites., Sci Rep, PMID 40628847

PXD063513 no publication (from MassIVE)
Dataset title: Rapid elicitation of a new class of neutralizing N332-glycan independent V3-glycan antibodies against HIV-1 in nonhuman primates
Possible reference: Relano-Rodriguez, I. et al. (2025) Rapid elicitation of a new class of neutralizing N332-glycan independent V3-glycan antibodies against HIV-1 in nonhuman primates., bioRxiv, PMID 40964314

PXD063503 no publication (from MassIVE)
Dataset title: The ferroform and glycoform landscape of human milk lactoferrin dissected through hybrid mass spectrometric approaches
Possible reference: Zhu, J. et al. (2025) The ferroform and glycoform landscape of human milk lactoferrin dissected through hybrid mass spectrometric approaches., Front Nutr, PMID 41415843

PXD063497 Dataset with its publication pending (from PRIDE)
Dataset title: Endothelial cell Nrf2 controls neuroinflammation following a systemic insult
Possible reference: Zou, H. et al. (2025) Endothelial cell Nrf2 controls neuroinflammation following a systemic insult., iScience, PMID 40510127

PXD063475 Dataset with its publication pending (from iProX)
Dataset title: Multi-Omics Elucidation of KDM5C, KDM6A, and KMT2B Roles in Cancer Epigenetic Dysregulation and Transcriptional Reprogramming
Possible reference: Li, T. et al. (2025) Multi-omics elucidation of KDM5C, KDM6A, and KMT2B roles in cancer epigenetic dysregulation and transcriptional reprogramming., Commun Biol, PMID 41331063

PXD063446 no publication (from MassIVE)
Dataset title: Proteomics reveals substantial differences between in vitro matured abattoir-derived and in vivo matured oocytes in cattle
Possible reference: Herbicht, R. et al. (2025) Proteomics reveals substantial differences between in vitro matured abattoir-derived and in vivo matured oocytes in cattle., Anim Reprod Sci, PMID 41265306

PXD063443 Dataset with its publication pending (from PRIDE)
Dataset title: EP3 deletion in macrophages aggravates diet-induced obesity in mice by suppressing SPARC
Possible reference: Shang, W. et al. (2025) Deletion of EP3 prostaglandin receptor in murine macrophages aggravates diet-induced obesity by suppressing SPARC., EMBO J, PMID 40702315

PXD063433 Dataset with its publication pending (from PRIDE)
Dataset title: Vimentin network dysregulation mediates neurite deficits in SNCA duplication Parkinson’s patient-derived midbrain neurons
Possible reference: Schneider, Y. et al. (2025) Vimentin network dysregulation mediates neurite deficits in SNCA duplication Parkinson's patient-derived midbrain neurons., Sci Adv, PMID 40479066

PXD063379 Dataset with its publication pending (from jPOST)
Dataset title: Cross-linking mass spectrometry and integrative structural modelling identifies compact conformation of DENV NS2B to NS3
Possible reference: Ser, Z. et al. (2026) Cross-linking mass spectrometry and structural modeling identifies compact conformation of DENV NS2B cofactor region bound to NS3., Structure, PMID 41478287

PXD063369 Dataset with its publication pending (from jPOST)
Dataset title: Detecting protein higher-order structural changes using kinase as a phospho-labeler
Possible reference: Maeda, A. et al. (2026) Detecting protein higher-order structural changes using kinase as a phospho-labeler., Cell Rep Methods, PMID 42202787

PXD063362 Dataset with its publication pending (from iProX)
Dataset title: Dupilumab-Mediated Modulation of Skin Barrier Proteomics
Possible reference: Jha, MK. et al. (2025) Type 2 cytokines pleiotropically modulate sensory nerve architecture and neuroimmune interactions to mediate itch., J Allergy Clin Immunol, PMID 40436117

PXD063359 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated multi-omics analysis of liver metabolic dysregulation in ACE2 knockout mice
Possible reference: Xiao, S. et al. (2025) Integrated multi‑omics analysis of liver metabolic dysregulation in ACE2 knockout mice., Int J Mol Med, PMID 40613222

PXD063357 no publication (from MassIVE)
Dataset title: Increasing mass spectrometry throughput using time-encoded sample multiplexing
Possible reference: Derks, J. et al. (2025) Increasing mass spectrometry throughput using time-encoded sample multiplexing., bioRxiv, PMID 40501910

PXD063345 Dataset with its publication pending (from PRIDE)
Dataset title: A phosphorelay circuit drives extracellular alkalinization in receptor kinase-mediated immune and cell wall damage signaling
Possible reference: Zhai, K. et al. (2026) A phosphorelay circuit drives extracellular alkalinization in receptor kinase-mediated immune and cell-wall damage signaling., Mol Cell, PMID 42019498

PXD063342 Dataset with its publication pending (from PRIDE)
Dataset title: De Novo Pyrimidine Synthesis Is a Collateral Metabolic Vulnerability in NF2-deficient Mesothelioma
Possible reference: Xu, D. et al. (2025) De novo pyrimidine synthesis is a collateral metabolic vulnerability in NF2-deficient mesothelioma., EMBO Mol Med, PMID 40707702

PXD063336 Dataset with its publication pending (from PRIDE)
Dataset title: A histone methyltransferase-independent function of PRC2 controls small RNA dynamics during programmed DNA elimination in Paramecium
Possible reference: Mir�-Pina, C. et al. (2025) A histone methyltransferase-independent function of PRC2 controls small RNA dynamics during programmed DNA elimination in Paramecium., Nucleic Acids Res, PMID 41099712

PXD063304 Dataset with its publication pending (from PRIDE)
Dataset title: Post-translational modification of H2B C-terminal helix regulates nucleosome binding and chromatin signaling
Possible reference: Zhao, Y. et al. (2025) Post-translational modification of H2B C-terminal helix regulates nucleosome interactions and chromatin signaling., Nucleic Acids Res, PMID 40966523

PXD063298 Dataset with its publication pending (from PRIDE)
Dataset title: A programmed decline in ribosome levels governs human early neurodevelopment
Possible reference: Ni, C. et al. (2025) A programmed decline in ribosome levels governs human early neurodevelopment., Nat Cell Biol, PMID 40760247

PXD063286 no publication (from MassIVE)
Dataset title: Proliferative proteome induced by HPV 16E6 and NFX1-123 partnership in longitudinal keratinocyte cultures
Possible reference: Billingsley, CL. et al. (2025) Proliferative proteome induced by HPV 16E6 and NFX1-123 partnership in longitudinal keratinocyte cultures., J Virol, PMID 40801834

PXD063269 Dataset with its publication pending (from iProX)
Dataset title: Thermal proteome profiling reveals meltome upon NLRP3 inflammasome activation
Possible reference: Yang, C. et al. (2025) Thermal Proteome Profiling Reveals Meltome Upon NLRP3 Inflammasome Activation., Mol Cell Proteomics, PMID 40250624

PXD063230 no publication (from MassIVE)
Dataset title: Tissue-specific and sex-biased glycoproteomic landscape of Schistosoma mansoni
Possible reference: Chen, X. et al. (2026) Tissue-specific and sex-biased glycoproteomic landscape of Schistosoma mansoni., Nat Commun, PMID 41545360

PXD063225 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of Serine/Threonine Protein Phosphatase 6 Severely Impairs Sexual Stage Development in Malaria Parasite Plasmodium berghei
Possible reference: Feng, Y. et al. (2025) Loss of serine/threonine protein phosphatase 6 severely impairs sexual stage development in malaria parasite Plasmodium berghei., PLoS Pathog, PMID 40623036

PXD063219 Dataset with its publication pending (from PRIDE)
Dataset title: TAPBPR promotes editing of the HLA-B*44 peptide repertoire, increasing the presentation of peptides containing a C-terminal tryptophan
Possible reference: Aflalo, A. et al. (2025) TAPBPR promotes editing of the HLA-B44 peptide repertoire, increasing the presentation of peptides containing a C-terminal tryptophan., Front Immunol, PMID 41246309

PXD063210 no publication (from MassIVE)
Dataset title: Validation of antibodies suitable for flow cytometric analysis and immunopeptidomics of peptide-MHC complexes in the outbred Swiss albino mouse strain
Possible reference: Chung, S. et al. (2025) The Validation of Antibodies Suitable for Flow Cytometric Analysis and Immunopeptidomics of Peptide-MHC Complexes in the Outbred Swiss Albino Mouse Strain., Methods Protoc, PMID 40407470

PXD063209 no publication (from MassIVE)
Dataset title: Biodiversity library of protein acetylation in bacteria
Possible reference: Broering, EP. et al. (2013) Synthetic analogues of nickel superoxide dismutase: a new role for nickel in biology., Biochemistry, PMID 23240653

PXD063164 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of Serine/Threonine Protein Phosphatase 6 Severely Impairs Sexual Stage Development in Malaria Parasite Plasmodium berghei
Possible reference: Feng, Y. et al. (2025) Loss of serine/threonine protein phosphatase 6 severely impairs sexual stage development in malaria parasite Plasmodium berghei., PLoS Pathog, PMID 40623036

PXD063162 Dataset with its publication pending (from PRIDE)
Dataset title: Roles of the phosphorylated SF3B1 in the activated spliceosome - experiment 2
Possible reference: McGeoch, AJS. et al. (2026) Cryo-EM structures of the CDK11-cyclin L-SAP30BP complex reveal mechanisms of CDK11 regulation., Nat Commun, PMID 42034640

PXD063157 no publication (from MassIVE)
Dataset title: Assessment of venom variation of Micrurus dumerilii from three different regions of Colombia
Possible reference: Rey-Su�rez, P. et al. (2025) Assessment of venom variation and phylogenetic relationships of Micrurus dumerilii from three different regions of Colombia., Biochimie, PMID 40499610

PXD063146 Dataset with its publication pending (from iProX)
Dataset title: ERLIN1 downregulation promotes tumor progression
Possible reference: Ren, H. et al. (2022) Matrine impedes colorectal cancer proliferation and migration by downregulating endoplasmic reticulum lipid raft associated protein 1 expression., Bioengineered, PMID 35412433

PXD063136 Dataset with its publication pending (from iProX)
Dataset title: Scutellariae Radix and Atractylodis Macrocephalae Rhizoma pairs ameliorate preeclampsia via PI3K/AKT/eNOS pathway
Possible reference: Sun, S. et al. (2025) Scutellariae Radix and Atractylodis Macrocephalae Rhizoma pairs ameliorate preeclampsia via PI3K/AKT/eNOS pathway., Front Pharmacol, PMID 40717981

PXD063129 no publication (from PanoramaPublic)
Dataset title: Selective silencing of antibiotic--tethered ribosomes as resistance mechanism against aminoglycosides
Possible reference: Ghosh Dastidar, N. et al. (2025) Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides., Nat Commun, PMID 41162373

PXD063083 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular Vesicles from Candidozyma (Candida) auris inhibit proliferation of CD4 T cells by disrupting the IL-2 Axis
Possible reference: Botbol, Y. et al. (2026) Extracellular vesicles from Candidozyma (Candida) auris inhibit proliferation of CD4 T cells by disrupting the IL-2 axis., J Immunol, PMID 41351525

PXD063045 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of papillary thyroid carcinoma in the context of Hashimoto's thyroiditis
Possible reference: Zhou, H. et al. (2026) Proteomic analysis of papillary thyroid carcinoma in the context of Hashimoto's thyroiditis., Sci Rep, PMID 41896629

PXD063022 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-Omics and Machine Learning-Based Profiling of Severity Signatures in Mycoplasma Pneumoniae Infection in Children
Possible reference: Li, G. et al. (2026) Multi-omics and machine learning-based profiling of severity signatures in Mycoplasma pneumoniae infection in children., iScience, PMID 41732270

PXD063002 Dataset with its publication pending (from PRIDE)
Dataset title: Longitudinal Proteomic Changes in HCT 116 Colon Cancer Spheroids During Growth
Possible reference: Whitney, CB. et al. (2025) Longitudinal Proteomic Changes in HCT 116 Colon Cancer Spheroids During Growth., J Proteome Res, PMID 40622388

PXD062981 no publication (from MassIVE)
Dataset title: The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1
Possible reference: Gather, F. et al. (2025) The lincRNA Pantr1 is a�FOXG1 target gene conferring site-specific chromatin binding of FOXG1., Nucleic Acids Res, PMID 40548942

PXD062978 no publication (from MassIVE)
Dataset title: The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1
Possible reference: Gather, F. et al. (2025) The lincRNA Pantr1 is a�FOXG1 target gene conferring site-specific chromatin binding of FOXG1., Nucleic Acids Res, PMID 40548942

PXD062938 Dataset with its publication pending (from PRIDE)
Dataset title: A T-cell receptor targeting RUNX1 frameshift mutations in acute myeloid leukemia
Possible reference: Struckman, NE. et al. (2026) A T-cell receptor targeting RUNX1 frameshift mutations in acute myeloid leukemia., Leukemia, PMID 41388195

PXD062929 no publication (from MassIVE)
Dataset title: High-throughput chemical proteomics workflow for profiling protein citrullination dynamics
Possible reference: Meelker Gonz�lez, R. et al. (2026) High-throughput chemical proteomics workflow for profiling protein citrullination dynamics., Nat Commun, PMID 41723106

PXD062886 Dataset with its publication pending (from PRIDE)
Dataset title: The accessory type III secretion system effectors shape inflammatory infection outcome
Possible reference: Biswas, P. et al. (2025) The accessory type III secretion system effectors collectively shape intestinal inflammatory infection outcomes., Gut Microbes, PMID 40599135

PXD062883 Dataset with its publication pending (from jPOST)
Dataset title: cocotide affinity enrichment mass spectrometry
Possible reference: Loo, S. et al. (2025) Identification of Ginsentide-like Peptides from Cacao Beans with Oxidative Stress Protection., ACS Omega, PMID 40757324

PXD062870 Dataset with its publication pending (from PRIDE)
Dataset title: Directed evolution of the multicopper oxidase laccase for cell surface proximity labeling and electron microscopy
Possible reference: Lee, SY. et al. (2024) Directed evolution of the multicopper oxidase laccase for cell surface proximity labeling and electron microscopy., bioRxiv, PMID 39554088

PXD062869 Dataset with its publication pending (from PRIDE)
Dataset title: High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria
Possible reference: Li, K. et al. (2026) High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues and bacteria., Nat Struct Mol Biol, PMID 41193676

PXD062839 Dataset with its publication pending (from PRIDE)
Dataset title: Elaboration of molecular glues that target TRIM21 into TRIMTACs that degrade protein aggregates
Possible reference: Scemama de Gialluly, MA. et al. (2025) Elaboration of molecular glues that target TRIM21 into TRIMTACs that degrade protein aggregates., Nat Commun, PMID 40670348

PXD062827 Dataset with its publication pending (from iProX)
Dataset title: Nanoparticle-based Antigen Favors High Level of Humoral Immune Responses and Increases Antigenicity of Highly Glycosylated Protein
Possible reference: Zou, Y. et al. (2025) Nanoparticle-based antigen favors high level of humoral immune responses and increases antigenicity of highly glycosylated protein., Int J Biol Macromol, PMID 41022235

PXD062819 no publication (from MassIVE)
Dataset title: Omics Insights into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology
Possible reference: Zhong, H. et al. (2025) Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology., Proteomics, PMID 40913400

PXD062807 Dataset with its publication pending (from PRIDE)
Dataset title: Chaperone-mediated autophagy controls brown adipose tissue 2 thermogenic activity
Possible reference: Mestres-Arenas, A. et al. (2025) Chaperone-mediated autophagy controls brown adipose tissue thermogenic activity., Sci Adv, PMID 41160696

PXD062804 Dataset with its publication pending (from iProX)
Dataset title: Engineering yeast peroxisome assembly enables increased production of acetyl-CoA and derived 5-deoxyflavonoids
Possible reference: Li, Y. et al. (2025) Engineering yeast peroxisome assembly enables the increased production of acetyl-CoA and its derived 5-deoxyflavonoids., Nat Commun, PMID 41290603

PXD062790 no publication (from MassIVE)
Dataset title: Proteomic profiling of optogenetically activated mouse S1 microglia
Possible reference: Yi, MH. et al. (2025) Optogenetic activation of cortical microglia promotes neuronal activity and pain hypersensitivity., Cell Rep, PMID 40381194

PXD062780 Dataset with its publication pending (from PRIDE)
Dataset title: C8orf33 dictates DNA double-strand break repair choice by modulating KAT8-mediated H4K16 acetylation
Possible reference: Bishara, LA. et al. (2025) C8orf33 dictates DNA double-strand break repair choice by modulating KAT8-mediated H4K16 acetylation., Cell Death Dis, PMID 41249114

PXD062770 Dataset with its publication pending (from iProX)
Dataset title: Soybean inositol polyphosphate 5-phosphatase 8 confers salt tolerance by reducing sodium influx through inositol 1,4,5-trisphosphate signaling
Possible reference: Jia, Q. et al. (2026) Soybean Inositol Polyphosphate 5-Phosphatase 8 Confers Salt Tolerance by Reducing Sodium Influx Through Inositol 1,4,5-Trisphosphate Signalling., Plant Cell Environ, PMID 40735769

PXD062720 Dataset with its publication pending (from PRIDE)
Dataset title: Lactylome and proteomics analyses of bladder cancer
Possible reference: Xu, G. et al. (2025) HDAC2 as a therapeutic target in bladder cancer: insights into the altered epigenetic regulation and lysine lactylation., J Exp Clin Cancer Res, PMID 41408324

PXD062710 Dataset with its publication pending (from iProX)
Dataset title: Noscapine derivative 428 suppresses ferroptosis through targeting GPX4
Possible reference: Zhang, Y. et al. (2025) Noscapine derivative 428 suppresses ferroptosis through targeting GPX4., Redox Biol, PMID 40305884

PXD062695 Dataset with its publication pending (from PRIDE)
Dataset title: Identifying lncRNA-protein interactions in hematopoietic progenitor cells by hybridization capture and mass spectrometry
Possible reference: Dai, Y. et al. (2025) Identifying lncRNA-Protein Interactions in Hematopoietic Progenitor Cells by Hybridization Capture and Mass Spectrometry., J Proteome Res, PMID 40747827

PXD062678 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of potential salivary biomarkers and enriched protein domain/motif families for early detection and lymph node invasion in OSCC patients of the Indian population
Possible reference: Singh, A. et al. (2025) Identification of Potential Salivary Biomarkers and Enriched Protein Domain/Motif Families for Early Detection and Lymph Node Invasion in OSCC Patients of the Indian Population., J Proteome Res, PMID 40964852

PXD062672 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of human lung cancer and paracancer tissues
Possible reference: Wu, Y. et al. (2023) [Role of Eukaryotic Translation Elongation Factor 1 Family Members in the Tumorigenesis and Progression of Lung Adenocarcinoma]., Zhongguo Yi Xue Ke Xue Yuan Xue Bao, PMID 38173097

PXD062658 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of giant panda seminal plasma
Possible reference: Anel-L�pez, L. et al. (2017) Analysis of seminal plasma from brown bear (Ursus arctos) during the breeding season: Its relationship with testosterone levels., PLoS One, PMID 28771486

PXD062646 Dataset with its publication pending (from PRIDE)
Dataset title: Metabolic Reprogramming Driven by Ant2 Deficiency Augments T Cell Function and Anti-Tumor Immunity
Possible reference: Yosef, O. et al. (2025) Metabolic reprogramming driven by Ant2 deficiency augments T Cell function and anti-tumor immunity in mice., Nat Commun, PMID 40341170

PXD062635 Dataset with its publication pending (from PRIDE)
Dataset title: A genome-to-proteome map reveals how natural variants drive proteome diversity and shape fitness
Possible reference: Jakobson, CM. et al. (2025) A genome-to-proteome map reveals how natural variants drive proteome diversity and shape fitness., Science, PMID 41066569

PXD062623 Dataset with its publication pending (from PRIDE)
Dataset title: Changes in histone abundance and post-translational modifications in Rana [Lithobates] catesbeiana tissues during temperature-mediated thyroid hormone-induced metamorphosis
Possible reference: Kuecks-Winger, HN. et al. (2025) Changes in histone abundance and post-translational modifications in Rana [Lithobates] catesbeiana tissues during temperature-mediated thyroid hormone-induced metamorphosis., Comp Biochem Physiol Part D Genomics Proteomics, PMID 40262239

PXD062615 Dataset with its publication pending (from PRIDE)
Dataset title: Temporal changes in the protein cargo of extracellular vesicles and resultant immune reprogramming after severe burn injury in humans and mice.
Possible reference: Willis, ML. et al. (2025) Temporal changes in the protein cargo of extracellular vesicles and resultant immune reprogramming after severe burn injury in humans and mice., bioRxiv, PMID 40166336

PXD062594 no publication (from MassIVE)
Dataset title: O-mannose glycosylations influence E-cadherin protein interactions
Possible reference: Xie, S. et al. (2026) O-Mannose Glycosylations Influence E-Cadherin Functional Interactions., Mol Cell Proteomics, PMID 41887410

PXD062589 no publication (from MassIVE)
Dataset title: Improving cellular fitness of human stem cell-derived islets under hypoxia
Possible reference: Wang, X. et al. (2025) Improving cellular fitness of human stem cell-derived islets under hypoxia., Nat Commun, PMID 40404627

PXD062584 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles of Emergomyces africanus modulate immune responses and reflect metabolic adaptations to nutrient availability
Possible reference: Honorato, L. et al. (2026) Extracellular vesicles of Emergomyces africanus modulate host immune responses and reflect metabolic adaptations to nutrient availability., Infect Immun, PMID 41700888

PXD062583 Dataset with its publication pending (from PRIDE)
Dataset title: ER-tethering directs TREX1 penetration of a BAF-dependent barrier at micronuclei
Possible reference: Chen, Y. et al. (2026) ER-tethering directs TREX1 penetration of a BAF-dependent barrier at micronuclei., Mol Cell, PMID 41861785

PXD062566 Dataset with its publication pending (from PRIDE)
Dataset title: Protein CoAlation on TXNRD2 regulates mitochondrial thioredoxin system to protect against ferroptosis
Possible reference: Lin, CC. et al. (2025) Coenzyme A protects against ferroptosis via CoAlation of mitochondrial thioredoxin reductase., J Clin Invest, PMID 40694424

PXD062561 Dataset with its publication pending (from PRIDE)
Dataset title: The N-Myc MB0-MBI region interacts specifically and dynamically with the N-lobe of Aurora kinase A
Possible reference: Hultman, J. et al. (2026) The N-Myc MB0-MBI region interacts specifically and dynamically with the N-lobe of Aurora kinase A., Nat Commun, PMID 41735282

PXD062559 Dataset with its publication pending (from PRIDE)
Dataset title: Site-specific profiling of structure and function of IgM B cell receptor glycans
Possible reference: Holborough-Kerkvliet, MD. et al. (2026) Site-specific profiling of structure and function of Ig� B cell receptor glycans., Nat Commun, PMID 41786713

PXD062537 no publication (from MassIVE)
Dataset title: Worker honey bee heat stress proteomics
Possible reference: McAfee, A. et al. (2021) Queen honey bees exhibit variable resilience to temperature stress., PLoS One, PMID 34379669

PXD062530 no publication (from MassIVE)
Dataset title: Proteomic analysis of bone marrow CD138+ cells to identify proteins associated with the response of multiple myeloma patients to commonly used therapeutic regimens.
Possible reference: Paradeisi, F. et al. (2025) Proteomic Analysis of Bone Marrow CD138+ Cells to Identify Proteins Associated With the Response of Multiple Myeloma Patients to Commonly Used Therapeutic Regimens., Proteomics, PMID 40776449

PXD062518 Dataset with its publication pending (from PRIDE)
Dataset title: STN1 facilitates metastasis by promoting transcription of EMT-activator ZEB1 in pancreatic cancer
Possible reference: Dong, D. et al. (2025) STN1 facilitates metastasis by promoting transcription of EMT-activator ZEB1 in pancreatic cancer., Nat Commun, PMID 40841373

PXD062498 Dataset with its publication pending (from iProX)
Dataset title: Discovery of specific protein markers in multiple body fluids and their application in forensic science
Possible reference: Wang, Z. et al. (2025) Discovery of specific protein markers in multiple body fluids and their application in forensic science., Talanta, PMID 40187281

PXD062489 Dataset with its publication pending (from PRIDE)
Dataset title: Endogenous cathelicidin protects against Toxoplasma gondii- associated liver damage
Possible reference: Tan, YL. et al. (2026) Endogenous cathelicidin protects against Toxoplasma gondii-associated liver damage., Infect Immun, PMID 41728969

PXD062479 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping the Toxoplasma gondii cytosolic interactome by crosslinking mass spectrometry and machine learning
Possible reference: Tomita, T. et al. (2025) Mapping a Toxoplasma gondii interactome by crosslinking mass spectrometry and machine learning., mBio, PMID 40874616

PXD062467 no publication (from MassIVE)
Dataset title: H3.1K27M-induced misregulation of the TSK/TONSL-H3.1 pathway causes genomic instability
Possible reference: Yuan, W. et al. (2024) H3.1K27M-induced misregulation of the TSK/TONSL-H3.1 pathway causes genomic instability., bioRxiv, PMID 39713323

PXD062445 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of Salmonella infection-induced secretion of exosomes by macrophages
Possible reference: Qu, M. et al. (2025) The RNA binding protein hnRNP A/B controls exosomal miR-27a-5p loading during Salmonella infection., Poult Sci, PMID 40582159

PXD062437 Dataset with its publication pending (from PRIDE)
Dataset title: Divergent proteome tolerance against gain and loss of chromosome arms
Possible reference: Di, Y. et al. (2025) Divergent proteome tolerance against gain and loss of chromosome arms., Mol Cell, PMID 41270725

PXD062407 Dataset with its publication pending (from iProX)
Dataset title: Efficacy of a Postbiotic and its Components in Promoting Colonic Transit and Alleviating Chronic Constipation in Humans and Mice
Possible reference: Ma, T. et al. (2025) Efficacy of a postbiotic and its components in promoting colonic transit and alleviating chronic constipation in humans and mice., Cell Rep Med, PMID 40286792

PXD062399 Dataset with its publication pending (from PRIDE)
Dataset title: Integrating antigen capturing nanoparticles and type 1 conventional dendritic cell therapy for in situ cancer immunization
Possible reference: Chao, CJ. et al. (2025) Integrating antigen capturing nanoparticles and type 1 conventional dendritic cell therapy for in situ cancer immunization., Nat Commun, PMID 40379691

PXD062376 Dataset with its publication pending (from PRIDE)
Dataset title: Noncanonical Caspase 4/-5 Inflammasome Activation in Coronary Artery Endothelial Cells by Lipopolysaccharides Drives Extracellular Vesicle Secretion
Possible reference: Nurmi, K. et al. (2026) Lipopolysaccharides Drive Proinflammatory Extracellular Vesicle Secretion in Coronary Artery Endothelial Cells via Noncanonical Inflammasome Activation., Cell Mol Life Sci, PMID 42014472

PXD062370 Dataset with its publication pending (from PRIDE)
Dataset title: Distinct energetic blueprints diversify function of conserved protein folds
Possible reference: Wells, ML. et al. (2026) Distinct energetic blueprints diversify function of conserved protein folds., Nat Chem, PMID 42249116

PXD062350 Dataset with its publication pending (from PRIDE)
Dataset title: Mlycd deficiency in Dahl salt-sensitive rats
Possible reference: Kravtsova, O. et al. (2026) MCD enzyme deficiency drives early mortality and multiorgan metabolic disruption in Dahl salt-sensitive rats., iScience, PMID 41550752

PXD062347 Dataset with its publication pending (from PRIDE)
Dataset title: Deceptive Ceropegia sandersonii uses an arabinogalactan for trapping its fly pollinators
Possible reference: Feichtlbauer, P. et al. (2025) Deceptive Ceropegia sandersonii uses an arabinogalactan for trapping its fly pollinators., New Phytol, PMID 40254894

PXD062335 Dataset with its publication pending (from iProX)
Dataset title: Dynamic Changes in Antibodies and Proteomics in Breast Milk of Mothers Infected with Wild-type SARS-CoV-2 and Omicron
Possible reference: Guo, Y. et al. (2025) Dynamic Changes in Antibodies and Proteome in Breast Milk of Mothers Infected with Wild-Type SARS-CoV-2 and Omicron: A Longitudinal Study., Nutrients, PMID 40284260

PXD062324 Dataset with its publication pending (from PRIDE)
Dataset title: Split intein mdx skeletal muscle proteomics
Possible reference: Johnson, EE. et al. (2026) Proteomics-based evaluation of AAV dystrophin gene therapy outcomes in mdx skeletal muscle., JCI Insight, PMID 41307959

PXD062275 Dataset with its publication pending (from PRIDE)
Dataset title: A simplified perchloric acid workflow with neutralization (PCA N) for democratizing deep plasma proteomics at population scale - Submission02
Possible reference: Albrecht, V. et al. (2025) A Simplified Perchloric Acid Workflow With Neutralization (PCA N) for Democratizing Deep Plasma Proteomics at Population Scale., Mol Cell Proteomics, PMID 40976565

PXD062274 Dataset with its publication pending (from PRIDE)
Dataset title: A simplified perchloric acid workflow with neutralization (PCA N) for democratizing deep plasma proteomics at population scale - Submission01
Possible reference: Albrecht, V. et al. (2025) A Simplified Perchloric Acid Workflow With Neutralization (PCA N) for Democratizing Deep Plasma Proteomics at Population Scale., Mol Cell Proteomics, PMID 40976565

PXD062261 Dataset with its publication pending (from PRIDE)
Dataset title: Translational repression by 4E-T is crucial to maintain the prophase-I arrest in vertebrate oocytes
Possible reference: Heim, A. et al. (2025) Translational repression by 4E-T is crucial to maintain the prophase-I arrest in vertebrate oocytes., Nat Commun, PMID 40877279

PXD062254 Dataset with its publication pending (from PRIDE)
Dataset title: Deep palaeoproteomic profiling of archaeological human brains
Possible reference: Morton-Hayward, A. et al. (2025) Deep palaeoproteomic profiling of archaeological human brains., PLoS One, PMID 40435004

PXD062252 Dataset with its publication pending (from iProX)
Dataset title: FBXW7 Mutations Reprograms Glucose Metabolism by Activating the ETV6-GLUT Axis in Endometrial Cancer
Possible reference: Fei, S. et al. (2026) FBXW7 mutations reprogram glucose metabolism by activating the ETV6-GLUT1 axis., Mol Cancer, PMID 41691251

PXD062251 Dataset with its publication pending (from iProX)
Dataset title: Tumor Microenvironment-Associated Oxidative Stress Impairs SIRT1 Secretion to Suppress Anti-Tumor Immune Response
Possible reference: Wang, Z. et al. (2025) Tumor microenvironment-associated oxidative stress impairs SIRT1 secretion to suppress anti-tumor immune response., Cell Rep, PMID 40343797

PXD062247 Dataset with its publication pending (from iProX)
Dataset title: Testis-Specific Serine/Threonine Kinase dTSSK2 Regulates Sperm Motility and Male Fertility in Drosophila
Possible reference: Peng, J. et al. (2025) Testis-specific serine/threonine kinase dTSSK2 regulates sperm motility and male fertility in Drosophila., Commun Biol, PMID 40335644

PXD062231 Dataset with its publication pending (from PRIDE)
Dataset title: Single-cell spatial proteomics maps human liver zonation patterns and their vulnerability to disruption in tissue architecture
Possible reference: Weiss, CAM. et al. (2025) Single cell spatial proteomics maps human liver zonation patterns and their vulnerability to fibrosis., bioRxiv, PMID 40291651

PXD062227 Dataset with its publication pending (from PRIDE)
Dataset title: Covalent inhibitor design confers activity against both GDP- and GTP-bound forms of KRAS G12C
Possible reference: Condakes, ML. et al. (2026) Covalent inhibitor design confers activity against both GDP- and GTP-bound forms of KRAS G12C., Nat Commun, PMID 41620418

PXD062226 Dataset with its publication pending (from PRIDE)
Dataset title: SMARCB1 missense mutants disrupt SWI/SNF complex stability and remodeling activity
Possible reference: Cooper, GW. et al. (2025) SMARCB1 missense mutants disrupt SWI/SNF complex stability and remodeling activity., Res Sq, PMID 40196006

PXD062177 no publication (from MassIVE)
Dataset title: Structural Heterogeneity of Proteoform-Ligand Complexes in AMP-Activated Protein Kinase Uncovered by Integrated Top-Down Mass Spectrometry
Possible reference: Chan, HJ. et al. (2025) Structural Heterogeneity of Proteoform-Ligand Complexes in Adenosine Monophosphate-Activated Protein Kinase Uncovered by Integrated Top-Down Mass Spectrometry., J Am Chem Soc, PMID 40811720

PXD062168 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting the UFL1-AKT Cascade Suppresses Triple-Negative Breast Cancer Progression
Possible reference: Yang, X. et al. (2026) Targeting the UFL1-AKT cascade suppresses triple-negative breast cancer progression., Nat Commun, PMID 41559059

PXD062156 Dataset with its publication pending (from iProX)
Dataset title: Quantitative proteomics analysis of radiation-induced rectal injury in rectal cancer patients undergoing radiotherapy
Possible reference: Cai, H. et al. (2025) Quantitative proteomics analysis of radiation-induced rectal injury in rectal cancer patients undergoing radiotherapy., J Proteomics, PMID 40541928

PXD062078 Dataset with its publication pending (from PRIDE)
Dataset title: Talin force coupling underlies eukaryotic cell-substrate adhesion
Possible reference: Rangarajan, S. et al. (2025) Talin force coupling underlies eukaryotic cell-substrate adhesion., Nat Commun, PMID 41353402

PXD062073 Dataset with its publication pending (from PRIDE)
Dataset title: Capture and functional conversion of mitochondrial protein translocase by lipid metabolism enzyme
Possible reference: Heinen, S. et al. (2026) Mitochondria contact lipid droplets through the mitochondrial import complex binding to lipid metabolism enzyme Ayr1., Nat Cell Biol, PMID 41748941

PXD062053 Dataset with its publication pending (from PRIDE)
Dataset title: �Multi-omics identification of extracellular components of the fetal monkey and human neocortex
Possible reference: Vilicich, F. et al. (2024) Multi-omics identification of extracellular components of the fetal monkey and human neocortex., bioRxiv, PMID 39386730

PXD062007 Dataset with its publication pending (from iProX)
Dataset title: TM9SF3 is a Golgi-resident ATG8-binding protein essential for Golgi selective autophagy
Possible reference: Yang, J. et al. (2025) TM9SF3 is a Golgi-resident ATG8-binding protein essential for Golgi-selective autophagy., Dev Cell, PMID 40609542

PXD062005 no publication (from MassIVE)
Dataset title: Overexpression of ATase1 and ATase2 in the mouse disrupts the quality of the secretome and causes a progeria phenotype
Possible reference: Cheng, TL. et al. (2025) Overexpression of ATase1 and ATase2 disrupts the secretome and causes a progeria phenotype., Life Sci Alliance, PMID 40930841

PXD061996 Dataset with its publication pending (from PRIDE)
Dataset title: A Mass Spectrometry-based Multiplexed Targeted Assay for Detection of Hemoglobinopathies from Dried Blood Spots
Possible reference: Bellad, A. et al. (2025) A Mass Spectrometry-Based Multiplexed Targeted Assay for Detection of Hemoglobinopathies from Dried Blood Spots., J Mol Diagn, PMID 40998492

PXD061987 Dataset with its publication pending (from PRIDE)
Dataset title: Protein composition of the biofilm matrix and the outer membrane vesicles (OMVs) during iron-sufficient and iron-restricted growth.
Possible reference: Lee, Y-J. et al. (2025) Characterization of proteins present in the biofilm matrix and outer membrane vesicles of Histophilus somni during iron-sufficient and iron-restricted growth: identification of potential protective antigens through in silico analyses., mBio, PMID 40243366

PXD061975 no publication (from MassIVE)
Dataset title: Pilocarpine inhibits Candida albicans biofilm maturation by altering lipid, sphingolipid, and protein content
Possible reference: Ottaviano, E. et al. (2025) Pilocarpine inhibits Candida albicans SC5314 biofilm maturation by altering lipid, sphingolipid, and protein content., Microbiol Spectr, PMID 40111054

PXD061970 Dataset with its publication pending (from PRIDE)
Dataset title: The loss of Drosophila ribosomal protein S6 kinase II causes mitochondrial dysfunction and cell death
Possible reference: Deng, T. et al. (2025) Loss of Drosophila ribosomal protein S6 kinase II causes mitochondrial dysfunction and cell death., Dis Model Mech, PMID 40827382

PXD061965 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial surveillance activates the primary UPRmt
Possible reference: Deng, P. et al. (2019) Mitochondrial UPR repression during Pseudomonas aeruginosa infection requires the bZIP protein ZIP-3., Proc Natl Acad Sci U S A, PMID 30850535

PXD061962 Dataset with its publication pending (from jPOST)
Dataset title: Proteome analysis of FFPE samples from infantile hypertrophic pyloric stenosis patients
Possible reference: Shinohara, M. et al. (2025) Proteome analysis of preserved formalin-fixed and paraffin-embedded specimens to explore the pathogenesis of infantile hypertrophic pyloric stenosis., Pediatr Surg Int, PMID 40839121

PXD061949 Dataset with its publication pending (from iProX)
Dataset title: ILF3 mediates lipid metabolism to promote pancreatic cancer development by regulating CPT1A-activated PPARa signaling pathway
Possible reference: Zhan, T. et al. (2025) ILF3 mediates lipid metabolism to promote pancreatic cancer development by regulating CPT1A-activated PPARa signaling pathway., Biochim Biophys Acta Mol Basis Dis, PMID 40419169

PXD061946 Dataset with its publication pending (from iProX)
Dataset title: Global Methylation Profiling by Selective Release of Methylated Sites from Immobilized Tryptic Peptides
Possible reference: Sun, M. et al. (2025) Global Methylation Profiling by Selective Release of Methylated Sites from Immobilized Tryptic Peptides., Anal Chem, PMID 40309950

PXD061929 Dataset with its publication pending (from PRIDE)
Dataset title: Remodeling of RNA-Binding Proteome and RNA-mediated regulation as a new layer of control of sporulation
Possible reference: Kabor�, T. et al. (2025) Remodeling of RNA-binding proteome and RNA-mediated regulation as a new layer of control of sporulation., mSystems, PMID 40815471

PXD061909 Dataset with its publication pending (from iProX)
Dataset title: KIF26B regulates Bladder cancer progression through TRAF2
Possible reference: Wang, JM. et al. (2025) KIF26B promotes bladder cancer progression via activating Wnt/β-catenin signaling in a TRAF2-dependent pathway., Cell Rep, PMID 40253697

PXD061904 Dataset with its publication pending (from iProX)
Dataset title: NH4+ ——Regulation of nitrogen sources on manganese oxidation
Possible reference: Baek, S. et al. (2026) Intensified water column hypoxia drives disproportionate benthic P release and N:P imbalance via enhanced sedimentary sulfate reduction., Mar Pollut Bull, PMID 41763028

PXD061885 Dataset with its publication pending (from jPOST)
Dataset title: Characterizing lipoprotein profiles in coronary atherosclerosis development through quantitative lipidomics and proteomics approaches
Possible reference: Takeda, H. et al. (2025) Characterizing lipoprotein profiles in coronary atherosclerosis development through quantitative lipidomics and proteomics approaches., NPJ Cardiovasc Health, PMID 41776359

PXD061852 Dataset with its publication pending (from PRIDE)
Dataset title: Endogenous retrovirus-like proteins recruit UBQLN2 to stress granules and shape their functional biology
Possible reference: Mohan, HM. et al. (2025) Endogenous retrovirus-like proteins recruit UBQLN2 to stress granules and shape their functional biology., Sci Adv, PMID 40680123

PXD061835 Dataset with its publication pending (from iProX)
Dataset title: Pharmacological inhibition of PSPH reduces serine levels and epileptic seizures-Phosphoproteomics
Possible reference: Sha, L. et al. (2025) Pharmacological inhibition of PSPH reduces serine levels and epileptic seizures., Nat Chem Biol, PMID 40456963

PXD061834 Dataset with its publication pending (from iProX)
Dataset title: Pharmacological inhibition of PSPH reduces serine levels and epileptic seizures
Possible reference: Sha, L. et al. (2025) Pharmacological inhibition of PSPH reduces serine levels and epileptic seizures., Nat Chem Biol, PMID 40456963

PXD061820 no publication (from MassIVE)
Dataset title: Teredinibacter turnerae secretome highlights key enzymes for plant cell wall degradation
Possible reference: De Guzman, LIP. et al. (2025) Teredinibacter turnerae secretome highlights key enzymes for plant cell wall degradation., Bioresour Bioprocess, PMID 40327255

PXD061816 Dataset with its publication pending (from iProX)
Dataset title: Development of a Multiple Reaction Monitoring (MRM)-Based LC-MS/MS Method for the Quantification of Post-Translational Modifications on Histone H3 Variants in Arabidopsis thaliana
Possible reference: Hu, Y. et al. (2025) Development of a multiple reaction monitoring (MRM)-based LC-MS/MS method for the quantification of post-translational modifications on histone H3 variants in Arabidopsis thaliana., Analyst, PMID 40130344

PXD061815 Dataset with its publication pending (from iProX)
Dataset title: Midkine promotes lung cancer brain metastasis
Possible reference: Shin, DH. et al. (2020) Midkine Is a Potential Therapeutic Target of Tumorigenesis, Angiogenesis, and Metastasis in Non-Small Cell Lung Cancer., Cancers (Basel), PMID 32847073

PXD061812 Dataset with its publication pending (from PRIDE)
Dataset title: Global landscape of protein phosphorylation during plant regeneration initiation in cotton (Gossypium hirsutum L.)
Possible reference: Guo, H. et al. (2025) Global landscape of protein phosphorylation during plant regeneration initiation in cotton (Gossypium�hirsutum L.)., BMC Biol, PMID 40307803

PXD061811 Dataset with its publication pending (from PRIDE)
Dataset title: De novo lysine myristoylation mediates synaptic plasticity and long-term potentiation through membrane association of synaptic proteins
Possible reference: Matthews, B. et al. (2025) Lysine myristoylation mediates long-term potentiation via membrane enrichment of synaptic plasticity effectors., EMBO J, PMID 40528004

PXD061792 no publication (from MassIVE)
Dataset title: Proteome analysis of Corynebacterium diphtheriae - macrophage interaction
Possible reference: Musella, L. et al. (2025) Proteome Analysis of Corynebacterium diphtheriae-Macrophage Interaction., Proteomics, PMID 40211577

PXD061784 Dataset with its publication pending (from PRIDE)
Dataset title: The cardiac phospho-proteome during pressure overload in mice
Possible reference: Wardman, R. et al. (2025) The cardiac phospho-proteome during pressure overload in mice., Sci Data, PMID 40753091

PXD061751 Dataset with its publication pending (from PRIDE)
Dataset title: Changes in Sputum Viscoelastic Properties and Airway Inflammation in Primary Ciliary Dyskinesia are Comparable to Cystic Fibrosis on Elexacaftor/Tezacaftor/Ivacaftor Therapy
Possible reference: Nussstein, H. et al. (2026) Changes in sputum viscoelastic properties and airway inflammation in primary ciliary dyskinesia are comparable to cystic fibrosis on elexacaftor/tezacaftor/ivacaftor therapy., Eur Respir J, PMID 40967762

PXD061717 no publication (from MassIVE)
Dataset title: Identification of tofersen PD-response biomarkers in VALOR clinical trial CSF via multiplexed quantitative proteomics
Possible reference: Guise, AJ. et al. (2026) Identification of tofersen PD-response biomarkers in VALOR clinical trial CSF via multiplexed quantitative proteomics., Cell Rep Med, PMID 41850233

PXD061713 no publication (from MassIVE)
Dataset title: Glycosylation of serine/threonine-rich intrinsically disordered regions of membrane-associated proteins in streptococci
Possible reference: Rahman, MM. et al. (2025) Glycosylation of serine/threonine-rich intrinsically disordered regions of membrane-associated proteins in streptococci., bioRxiv, PMID 38746434

PXD061710 Dataset with its publication pending (from PRIDE)
Dataset title: Overcoming preservation challenges to enable single-cell proteomics of fixed cell and tissue samples with retained proteome integrity
Possible reference: Makar, AN. et al. (2025) Overcoming Preservation Challenges to Enable Single-Cell Proteomics of Fixed Cells and Tissue Samples with Retained Proteome Integrity., J Proteome Res, PMID 40534510

PXD061694 Dataset with its publication pending (from PRIDE)
Dataset title: Early NK-cell and T-cell dysfunction marks progression to severe dengue in patients with obesity and healthy weight
Possible reference: Gregorova, M. et al. (2025) Early NK-cell and T-cell dysfunction marks progression to severe dengue in patients with obesity and healthy weight., Nat Commun, PMID 40595657

PXD061693 Dataset with its publication pending (from PRIDE)
Dataset title: Cell-Surface RNA Forms Ternary Complex with RNA-Binding Protein and Heparan Sulfate to Recruit Immune Receptors Complex with RNA-Binding Protein and Heparan Sulfate to Recruit Immune Receptor
Possible reference: Li, Z. et al. (2025) Cell-surface RNA forms ternary complex with RNA-binding proteins and heparan sulfate to recruit immune receptors., Mol Cell, PMID 41418757

PXD061661 Dataset with its publication pending (from jPOST)
Dataset title: Mitochondrial cell-type-specific profiling: Differential function of mesophyll and guard cells is reflected by their mitochondrial proteome.
Possible reference: Hater, F. et al. (2025) Mitochondrial Cell-Type-Specific Profiling: Differential Function of Mesophyll and Guard Cells is Reflected by Their Mitochondrial Proteome., Physiol Plant, PMID 41178646

PXD061654 Dataset with its publication pending (from PRIDE)
Dataset title: The mammalian longevity associated acetylome
Possible reference: Feldman-Trabelsi, S. et al. (2025) The mammalian longevity associated acetylome., Nat Commun, PMID 40263264

PXD061652 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis for Cisplatin -induced mice spermatogenesis defects
Possible reference: Li, P. et al. (2026) Proteomic analysis of cisplatin-induced spermatogenesis defects in mice., Ann Med, PMID 41517957

PXD061650 Dataset with its publication pending (from PRIDE)
Dataset title: Optimizing PSC culture for generating neural organoids
Possible reference: Eguchi, N. et al. (2018) Self-organizing cortex generated from human iPSCs with combination of FGF2 and ambient oxygen., Biochem Biophys Res Commun, PMID 29524419

PXD061649 Dataset with its publication pending (from PRIDE)
Dataset title: Wnt signalosome assembly is governed by conformational flexibility of Axin and AP2 clathrin adaptor
Possible reference: Gammons, MV. et al. (2025) Wnt signalosome assembly is governed by conformational flexibility of Axin and by the AP2 clathrin adaptor., Nat Commun, PMID 40399324

PXD061645 Dataset with its publication pending (from PRIDE)
Dataset title: A systems-level insight into PHB-driven metabolic adaptation orchestrated by the PHB-binding transcriptional regulator AniA (PhaR)
Possible reference: Lagares, A. et al. (2025) A systems-level insight into PHB-driven metabolic adaptation orchestrated by the PHB-binding transcriptional regulator AniA (PhaR)., mSystems, PMID 40981414

PXD061644 Dataset with its publication pending (from PRIDE)
Dataset title: Clinicopathologic and Proteomic Characteristics of Low-Grade Undifferentiated Spindle Cell SarcomaClinicopathologic and Proteomic Characteristics of Low-Grade Undifferentiated Spindle Cell Sarcoma
Possible reference: Wei, Y. et al. (2025) Clinicopathologic and proteomic characteristics of low-grade undifferentiated spindle cell sarcoma., Front Mol Biosci, PMID 40666499

PXD061628 Dataset with its publication pending (from iProX)
Dataset title: CENPU promotes tumorigenesis and stem cell properties in triple-negative breast cancer by suppressing lysosomal furin degradation
Possible reference: Sun, S. et al. (2025) CENPU promotes tumorigenesis and stem cell properties in triple‑negative breast cancer by suppressing lysosomal furin degradation., Int J Mol Med, PMID 41041859

PXD061623 Dataset with its publication pending (from PRIDE)
Dataset title: LGI3 promotes the progression of TFE3-rearranged renal cell carcinoma through GEMIN6/AURKB axis
Possible reference: Liu, J. et al. (2025) LGI3 promotes the progression of TFE3-rearranged renal cell carcinoma through GEMIN6/AURKB axis., Oncogene, PMID 40849584

PXD061615 Dataset with its publication pending (from jPOST)
Dataset title: Proteogenomic profiling of urine extracellular vesicles
Possible reference: Hakozaki, Y. et al. (2026) Proteogenomic detection of tumor-specific somatic mutant proteins in urinary extracellular vesicles for non-invasive monitoring of bladder cancer., Front Oncol, PMID 42063735

PXD061598 Dataset with its publication pending (from PRIDE)
Dataset title: PP1/PNUTS phosphatase binds the restrictor complex and stimulates RNA pol II transcription termination
Possible reference: Erickson, B. et al. (2025) PP1/PNUTS phosphatase binds the restrictor complex and stimulates RNA Pol II transcription termination., Cell Rep, PMID 40244850

PXD061583 Dataset with its publication pending (from PRIDE)
Dataset title: Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides
Possible reference: Ghosh Dastidar, N. et al. (2025) Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides., Nat Commun, PMID 41162373

PXD061581 Dataset with its publication pending (from PRIDE)
Dataset title: Conserved role of the SERK‒BIR module in development and immunity across land plants
Possible reference: Yan, Y. et al. (2025) Conserved role of the SERK-BIR module in development and immunity across land plants., Curr Biol, PMID 40250435

PXD061547 Dataset with its publication pending (from PRIDE)
Dataset title: An Isoprenol Biosensor for Combinatorial High Throughput Strain Engineering in Pseudomonas putida
Possible reference: Menasalvas, J. et al. (2025) Biosensor-driven strain engineering reveals key cellular processes for maximizing isoprenol production in Pseudomonas putida., Sci Adv, PMID 41134890

PXD061529 Dataset with its publication pending (from PRIDE)
Dataset title: Convergent evolutionary adaption of spider venom from predation to defense
Possible reference: L�ddecke, T. et al. (2025) Comparative venomics suggests an evolutionary adaption of spider venom from predation to defense., Commun Biol, PMID 41131346

PXD061505 no publication (from MassIVE)
Dataset title: Theropod: Tools to Analyze Externally Collected Selective Temporal Overview of Resonant Ions
Possible reference: Cleland, TP. et al. (2026) Theropod: Software Tools to Analyze Externally Collected Selective Temporal Overview of Resonant Ions., J Am Soc Mass Spectrom, PMID 41543977

PXD061479 Dataset with its publication pending (from PRIDE)
Dataset title: Cardiomyocyte OTUD1 drives diabetic cardiomyopathy via directly deubiquitinating AMPKÎ±2 to inhibit AMPK activity and induce mitochondrial dysfunctionCardiomyocyte OTUD1 drives diabetic cardiomyopathy via directly deubiquitinating AMPKÎ±2 to inhibit AMPK
Possible reference: Han, X. et al. (2025) Cardiomyocyte OTUD1 drives diabetic cardiomyopathy via directly deubiquitinating AMPKα2 and inducing mitochondrial dysfunction., Nat Commun, PMID 40683882

PXD061478 no publication (from MassIVE)
Dataset title: Affinity-based protein profiling of benzodiazepine targets in rat synaptosomes
Possible reference: Griggs, LH. et al. (2026) Combined Quantitative and Qualitative Statistical Analyses Improve Benzodiazepine Target Discovery in Label-free Affinity-Based Protein Profiling Data., J Proteome Res, PMID 41830962

PXD061475 Dataset with its publication pending (from jPOST)
Dataset title: Phosphoproteomic profiling of feline mammary carcinoma: insights into tumor grading and potential therapeutic targets
Possible reference: Aruvornlop, P. et al. (2025) Phosphoproteomic profiling of feline mammary carcinoma: Insights into tumor grading and potential therapeutic targets., PLoS One, PMID 40839607

PXD061463 Dataset with its publication pending (from PRIDE)
Dataset title: USP37 prevents unscheduled replisome unloading through MCM complex deubiquitination
Possible reference: Bolhuis, DL. et al. (2024) USP37 prevents unscheduled replisome unloading through MCM complex deubiquitination., bioRxiv, PMID 39282338

PXD061422 Dataset with its publication pending (from iProX)
Dataset title: Post-translational modifications orchestrate the intrinsic signaling bias of orphan receptor GPR52
Possible reference: Zhang, B. et al. (2025) Post-translational modifications orchestrate the intrinsic signaling bias of GPR52., Nat Chem Biol, PMID 40087539

PXD061393 Dataset with its publication pending (from PRIDE)
Dataset title: Zombosomes are anucleated cell couriers that spread Î±-synuclein pathology
Possible reference: Dakhel, A. et al. (2026) Zombosomes are anucleated cell couriers that spread α-synuclein pathology., Cell Rep, PMID 41538327

PXD061359 Dataset with its publication pending (from jPOST)
Dataset title: Establishment of a simple, efficient, and scalable method to generate oocyte-like cells in vitro
Possible reference: Banno, A. et al. (2026) A simple, efficient, and scalable method to generate oocyte-like cells in vitro., Life Sci Alliance, PMID 41271398

PXD061317 Dataset with its publication pending (from PRIDE)
Dataset title: Unveiling Cellular Communications through Rapid Pan-Membrane-Protein Labeling
Possible reference: Gunasekara, H. et al. (2025) Unveiling cellular communications through rapid pan-membrane-protein labeling., Nat Commun, PMID 40234465

PXD061275 Dataset with its publication pending (from PRIDE)
Dataset title: Human adipose tissue diurnal proteomics during MASLD
Possible reference: Marjot, T. et al. (2026) Human MASLD is a diurnal disease driven by multisystem insulin resistance and reduced insulin availability at night., Cell Metab, PMID 41529695

PXD061256 Dataset with its publication pending (from PRIDE)
Dataset title: A multi-omics analysis identifies retinol metabolism in fibroblasts as a key pathway in wound healing
Possible reference: W�stemann, T. et al. (2025) A multiomics analysis identifies retinol metabolism in fibroblasts as a key pathway in wound healing., JCI Insight, PMID 41100455

PXD061240 Dataset with its publication pending (from iProX)
Dataset title: Mucin proteomics of haliotis discus hannai
Possible reference: Di, G. et al. (2025) 4D-FastDIA proteomic analysis of pedal mucus in Pacific abalone Haliotis discus hannai heat-resistance group., Comp Biochem Physiol Part D Genomics Proteomics, PMID 40199049

PXD061239 Dataset with its publication pending (from PRIDE)
Dataset title: An H3K4me3 reader recruits the positive transcription elongation factor B complex to facilitate transcription elongation
Possible reference: Yu, X. et al. (2026) An H3K4me3 reader recruits the positive transcription elongation factor B complex to facilitate transcription elongation in Arabidopsis., Dev Cell, PMID 41785857

PXD061225 Dataset with its publication pending (from PRIDE)
Dataset title: Rehydration rescues Il22-/- mice from lethal Citrobacter rodentium infection
Possible reference: Mishra, V. et al. (2025) Rehydration rescues Il22-/- mice from lethal Citrobacter rodentium infection., Nat Commun, PMID 41361166

PXD061210 Dataset with its publication pending (from jPOST)
Dataset title: Retention of DLK1 in the endoplasmic reticulum identifies roles for EGF domain-specific O-glycans in the secretory pathway
Possible reference: Tashima, Y. et al. (2025) Retention of DLK1 in the endoplasmic reticulum identifies roles for EGF-like-domain-specific O-glycans in the secretory pathway., FEBS J, PMID 40637009

PXD061189 no publication (from MassIVE)
Dataset title: Survey of megadalton protein assemblies from Dictyostelium discoideum
Possible reference: McCafferty, CL. et al. (2025) The CAGE complex: a hollow, megadalton, protein assembly in prokaryotic and eukaryotic microbes., bioRxiv, PMID 41040395

PXD061184 Dataset with its publication pending (from PRIDE)
Dataset title: A bipartite motif of Mrx6 binds the Lon protease Pim1 N-terminal domain to confer substrates specificity and regulate mtDNA copy number
Possible reference: Schrott, S. et al. (2026) Mrx6 binds the Lon protease Pim1�N-terminal domain to confer selective substrate specificity and regulate mtDNA copy number., Nucleic Acids Res, PMID 41533588

PXD061178 Dataset with its publication pending (from PRIDE)
Dataset title: TCR targeting of KRAS G12V/C neoantigens is enhanced by lymphodepleting chemotherapy
Possible reference: Sagie, S. et al. (2025) Lymphodepleting chemotherapy potentiates neoantigen-directed T cell therapy by enhancing antigen presentation., Cell Rep Med, PMID 41406943

PXD061167 Dataset with its publication pending (from PRIDE)
Dataset title: A multi-omics analysis identifies retinol metabolism in fibroblasts as a key pathway in wound healing
Possible reference: W�stemann, T. et al. (2025) A multiomics analysis identifies retinol metabolism in fibroblasts as a key pathway in wound healing., JCI Insight, PMID 41100455

PXD061143 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic Analysis of Tityus obscurus Venom: Novel Ion Channel-Targeting Peptides Identified
Possible reference: Panchera, KC. et al. (2025) Molecular Diversity and Isoform Evolution in Tityus obscurus Venom: Insights from Proteomic Analysis., Toxins (Basel), PMID 40423293

PXD061099 no publication (from MassIVE)
Dataset title: Native Top-Down Proteomics of Endogenous Protein Complexes Enabled by Online Two-Dimensional Liquid Chromatography
Possible reference: Fischer, MS. et al. (2025) Native Top-Down Proteomics of Endogenous Protein Complexes Enabled by Online Two-Dimensional Liquid Chromatography., bioRxiv, PMID 40236213

PXD061094 no publication (from MassIVE)
Dataset title: Proteomics of bacterial and ovarian cancer ascites extracellular vesicles
Possible reference: Asano-Inami, E. et al. (2025) Proteomic Profiling of Bacterial Extracellular Vesicles for Exploring Ovarian Cancer Biomarkers., J Extracell Biol, PMID 41078591

PXD061088 no publication (from MassIVE)
Dataset title: An Unbiased Proteomic Platform for ATE1-based Arginylation Profiling-Sciex7600
Possible reference: Lin, Z. et al. (2025) An Unbiased Proteomic Platform for ATE1-based Arginylation Profiling., bioRxiv, PMID 38854050

PXD061071 Dataset with its publication pending (from PRIDE)
Dataset title: NASP modulates histone turnover to drive PARP inhibitor resistance
Possible reference: Moser, SC. et al. (2025) NASP modulates histone turnover to drive PARP inhibitor resistance., Nature, PMID 40804522

PXD061052 Dataset with its publication pending (from PRIDE)
Dataset title: Human neutrophil glioblastoma mini-bulk proteomes
Possible reference: Sadiku, P. et al. (2025) Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma., Nat Commun, PMID 41397978

PXD061044 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of ascidian metamorphosis
Possible reference: Liberti, A. et al. (2023) Transcriptional and proteomic analysis of the innate immune response to microbial stimuli in a model invertebrate chordate., Front Immunol, PMID 37600818

PXD061038 Dataset with its publication pending (from PRIDE)
Dataset title: Riboflavin metabolism shapes FSP1-driven ferroptosis resistance
Possible reference: Skafar, V. et al. (2026) Riboflavin metabolism shapes FSP1-driven ferroptosis resistance., Nat Cell Biol, PMID 41826699

PXD061030 Dataset with its publication pending (from iProX)
Dataset title: TMEM63B Regulates Nucleocytoplasmic Transport and Placental Development
Possible reference: Cai, M. et al. (2026) TMEM63B regulates nucleocytoplasmic transport and placental development., Nat Commun, PMID 42259794

PXD060997 Dataset with its publication pending (from PRIDE)
Dataset title: An atypical Arp2/3 complex is required for Plasmodium DNA segregation and transmission of malaria.
Possible reference: Hentzschel, F. et al. (2025) An atypical Arp2/3 complex is required for Plasmodium DNA segregation and malaria transmission., Nat Microbiol, PMID 40514561

PXD060993 no publication (from MassIVE)
Dataset title: Dissection of Vitronectin-Regulated Secretome in Hepatocellular Carcinoma
Possible reference: Han, SB. et al. (2026) Dissection of Vitronectin-Regulated Secretome in Hepatocellular Carcinoma., J Proteome Res, PMID 41616260

PXD060981 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial NADPH fuels mitochondrial fatty acid synthesis and lipoylation to power oxidative metabolism
Possible reference: Kim, D. et al. (2025) Mitochondrial NADPH fuels mitochondrial fatty acid synthesis and lipoylation to power oxidative metabolism., Nat Cell Biol, PMID 40258949

PXD060971 Dataset with its publication pending (from PRIDE)
Dataset title: ANXA11 biomolecular condensates facilitate protein-lipid phase coupling on lysosomal membranes
Possible reference: Nixon-Abell, J. et al. (2023) ANXA11 biomolecular condensates facilitate protein-lipid phase coupling on lysosomal membranes., bioRxiv, PMID 36993242

PXD060956 no publication (from MassIVE)
Dataset title: MSP-MS of mice wound fluid from day 5 at pH 5
Possible reference: Barbosa da Silva, E. et al. (2025) The impact of pH on proteolytic activity in wound fluid: Implications for acid therapy., J Biol Chem, PMID 40962052

PXD060949 Dataset with its publication pending (from PRIDE)
Dataset title: Protein disulfide isomerase is essential for osteoblast differentiation in mice
Possible reference: Wang, Y. et al. (2014) Impaired bone formation in Pdia3 deficient mice., PLoS One, PMID 25405762

PXD060944 Dataset with its publication pending (from iProX)
Dataset title: The cancer-testis lncRNA LINC01940 contributes to gastric cancer progression and chemosensitivity through NOL11-dependent ribosome biogenesis
Possible reference: Zang, W. et al. (2025) The cancer-testis lncRNA LINC01940 promotes gastric cancer malignant progression and chemoresistance by enhancing ribosome biogenesis via TAF15-mediated NOL11 SUMOylation., Cell Mol Biol Lett, PMID 41402710

PXD060943 Dataset with its publication pending (from iProX)
Dataset title: Resveratrol exerts antiviral activity against pseudorabies virus through regulation of the OPN-ERK/JNK-IL-1Î² signaling axis
Possible reference: Luan, H. et al. (2025) Resveratrol exerts antiviral activity against pseudorabies virus through regulation of the OPN-ERK/JNK-IL-1β signaling axis., J Proteomics, PMID 40274095

PXD060940 Dataset with its publication pending (from iProX)
Dataset title: Cocktail Chemical Labeling for In-Depth Surfaceome Profiling
Possible reference: Sun, S. et al. (2025) Cocktail Chemical Labeling for In-Depth Surfaceome Profiling of Bone-Marrow-Derived Dendritic Cells., Anal Chem, PMID 41043136

PXD060934 Dataset with its publication pending (from PRIDE)
Dataset title: DNA-PKcs governs LAT-dependent signaling in CD4+ and CD8+ T cells
Possible reference: Rainwater, RR. et al. (2025) DNA-PKcs governs LAT-dependent signaling in CD4 + and CD8 + T cells., bioRxiv, PMID 40161607

PXD060926 Dataset with its publication pending (from PRIDE)
Dataset title: Defining the cardiac fibroblast secretome - in vitro stimulation
Possible reference: Goltseva, Y. et al. (2026) uPAR deficiency triggers TGFβ1-mediated fibrotic remodeling in a cardiac perivascular-like microenvironment., Stem Cell Res Ther, PMID 41689076

PXD060902 Schertzer, M.D., Stirn, A., Isaev, K. et al. Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox. Nat Commun 16, 6948 (2025). (from PanoramaPublic)
Dataset title: Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox
Possible reference: Schertzer, MD. et al. (2023) Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox., bioRxiv, PMID 37745416

PXD060891 Dataset with its publication pending (from jPOST)
Dataset title: A Comparison of SWATH-MS Methods for Measurement of Residual Host Cell Proteins in Adeno-Associated Virus Preparations
Possible reference: Leibiger, TM. et al. (2025) A comparison of SWATH-MS methods for measurement of residual host cell proteins in adeno-associated virus preparations., Front Bioeng Biotechnol, PMID 40386465

PXD060890 Dataset with its publication pending (from PRIDE)
Dataset title: Dysregulated pathways and potential biomarkers in dermatomyositis plasma-derived extracellular vesicles
Possible reference: Baniel, A. et al. (2026) Dysregulated Pathways and Potential Biomarkers in Dermatomyositis Plasma-Derived Extracellular Vesicles: A Pilot Study., J Invest Dermatol, PMID 40716701

PXD060857 Dataset with its publication pending (from iProX)
Dataset title: Efficient fabrication of human corneal stromal cell spheroids and promoting cell stemness based on 3D-printed derived PDMS microwell platform
Possible reference: Chen, Y. et al. (2025) Efficient Fabrication of Human Corneal Stromal Cell Spheroids and Promoting Cell Stemness Based on 3D-Printed Derived PDMS Microwell Platform., Biomolecules, PMID 40149974

PXD060853 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of ANK3-knockdown 786-O cells
Possible reference: Somsuan, K. et al. (2025) Downregulation of ankyrin 3 (ANK3) promotes malignant behaviors associated with altered adhesion dynamics and actin cytoskeleton remodeling in renal cell carcinoma., Cell Tissue Res, PMID 41186628

PXD060850 Dataset with its publication pending (from PRIDE)
Dataset title: A nowhere-to-hide mechanism ensures complete piRNA-directed LINE1 methylation
Possible reference: Chowdhury, T. et al. (2026) A nowhere-to-hide mechanism ensures complete piRNA-directed DNA methylation., Nature, PMID 41535457

PXD060835 no publication (from MassIVE)
Dataset title: Analysis of a cancer-associated mutation in the budding yeast Nuf2 kinetochore protein
Possible reference: Andrade Latino, A. et al. (2025) Analysis of a cancer-associated mutation in the budding yeast Nuf2 kinetochore protein., MicroPubl Biol, PMID 40161439

PXD060833 no publication (from MassIVE)
Dataset title: The immune NIK1 RPL10 LIMYB signaling module regulates photosynthesis and translation under biotic and abiotic stresses
Possible reference: Ferreira, MA. et al. (2025) The immune NIK1/RPL10/LIMYB signaling module regulates photosynthesis and translation under biotic and abiotic stresses., Nat Commun, PMID 40360515

PXD060829 Dataset with its publication pending (from PRIDE)
Dataset title: Combination of in vivo and in vitro phosphoproteomics determines the PP2A target repertoire on proteome scale
Possible reference: Brunner, M. et al. (2025) Combination of in vivo and in vitro phosphoproteomics determines the PP2A target repertoire on proteome scale., Cell Rep Methods, PMID 40541179

PXD060825 Dataset with its publication pending (from PRIDE)
Dataset title: Interaction of Human Cytomegalovirus pUL52 with major components of the viral DNA encapsidation network underlines its essential role in genome cleavage-packaging
Possible reference: Harmening, S. et al. (2025) Interaction of human cytomegalovirus pUL52 with major components of the viral DNA encapsidation network underlines its essential role in genome cleavage-packaging., J Virol, PMID 40062846

PXD060810 Dataset with its publication pending (from PRIDE)
Dataset title: Unveiling Diagnostic Biomarkers in Autism: Comparative Proteome Analysis of CNTNAP2 Knockout Mice and Human ASD Patients
Possible reference: Kim, A. et al. (2026) Unveiling Diagnostic Biomarkers in Autism: A Comparative Proteome Analysis of CNTNAP2 Knockout Mice and Human ASD Patients., Biomolecules, PMID 41897278

PXD060800 Dataset with its publication pending (from iProX)
Dataset title: The proteome profiles of psoas major muscle (PMM), longissimus dorsi muscle (LDM) and semimembranosus (SM) in Saba pig
Possible reference: Yang, Y. et al. (2025) Integrative transcriptomic and proteomic analyses of different muscles reveal the molecular mechanism of pig psoas major muscle as a high eating and nutritional quality meat., BMC Genomics, PMID 41120854

PXD060797 Dataset with its publication pending (from iProX)
Dataset title: Proteomic profiling of lactylation and acetylation modifications in Streptococcus mutans
Possible reference: Ma 马其钊, Q. et al. (2025) Crosstalk Between Lysine Lactylation and Acetylation Regulates Lactate Dehydrogenase in Streptococcus mutans., Genomics Proteomics Bioinformatics, PMID 40845146

PXD060783 Dataset with its publication pending (from PRIDE)
Dataset title: Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii)
Possible reference: Mochales-Ria�o, G. et al. (2025) Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii)., Gigascience, PMID 40478730

PXD060777 Dataset with its publication pending (from PRIDE)
Dataset title: Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii)
Possible reference: Mochales-Ria�o, G. et al. (2025) Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii)., Gigascience, PMID 40478730

PXD060751 Dataset with its publication pending (from iProX)
Dataset title: DISC1 Protects Against Zika Virus Infection and Long-Term Neurological Damage Through AMPK-mTOR-Mediated Autophagy
Possible reference: Zhang, S. et al. (2025) DISC1 Protects Against Zika Virus Infection and Long-Term Neurological Damage Through AMPK-mTOR-Mediated Autophagy., Nat Commun, PMID 41203603

PXD060741 Dataset with its publication pending (from PRIDE)
Dataset title: Engineering controllable alteration of malonyl-CoA levels to enhance polyketide production
Possible reference: Klass, SH. et al. (2025) Engineering controllable alteration of malonyl-CoA levels to enhance polyketide production., Nat Chem Biol, PMID 40500421

PXD060699 Dataset with its publication pending (from PRIDE)
Dataset title: Continuous and prolonged breastfeeding in wild Bornean orangutans verified with fecal proteomics
Possible reference: Makbul, NS. et al. (2026) Continuous and prolonged breastfeeding in wild Bornean orangutans verified with fecal proteomics., Commun Biol, PMID 42185501

PXD060698 Dataset with its publication pending (from PRIDE)
Dataset title: Predictive chemoproteomics and functional validation reveal Coeae6g mediated insecticide cross-resistance in the malaria vector Anopheles gambiae
Possible reference: Balaska, S. et al. (2025) Predictive chemoproteomics and functional validation reveal Coeae6g-mediated insecticide cross-resistance in the malaria vector Anopheles gambiae., Nat Commun, PMID 41315252

PXD060688 Dataset with its publication pending (from PRIDE)
Dataset title: DdiA, an XRE family transcriptional regulator, regulates a LexA-independent DNA damage response in Myxococcus xanthus
Possible reference: Jung, J. et al. (2025) DdiA, an XRE family transcriptional regulator, is a co-regulator of the DNA damage response in Myxococcus xanthus., J Bacteriol, PMID 40608330

PXD060668 no publication (from MassIVE)
Dataset title: Elodie Mailler_Carlos Guardia_ATG9A_12LFQ
Possible reference: Mailler, E. et al. (2021) The autophagy protein ATG9A enables lipid mobilization from lipid droplets., Nat Commun, PMID 34799570

PXD060662 Dataset with its publication pending (from iProX)
Dataset title: Deletion of the PtrDJ1C Gene Leads to Increased Branching in Poplar
Possible reference: Du, J. et al. (2025) Deletion of the PtrDJ1C gene leads to increased branching in poplar., Plant Physiol Biochem, PMID 40118012

PXD060661 Dataset with its publication pending (from iProX)
Dataset title: Proteomic data of DIA in flag and -2nd leaves of wheat
Possible reference: Li, W. et al. (2025) Proteomic profiling reveals important regulators of photosynthate accumulation in wheat leaves during grain development., BMC Plant Biol, PMID 40604394

PXD060658 Dataset with its publication pending (from iProX)
Dataset title: Proteomic and Metabolomic Insights into the Impact of Topping Treatment on Cigar Tobacco
Possible reference: Guo, D. et al. (2024) Proteomic and metabolomic insights into the impact of topping treatment on cigar tobacco., Front Plant Sci, PMID 40052119

PXD060655 Dataset with its publication pending (from jPOST)
Dataset title: Peritoneal fluid proteome in horses with colic
Possible reference: Bardell, D. et al. (2019) Differences in plasma and peritoneal fluid proteomes identifies potential biomarkers associated with survival following strangulating small intestinal disease., Equine Vet J, PMID 30854696

PXD060648 Dataset with its publication pending (from PRIDE)
Dataset title: Integrator loss leads to dsRNA formation that triggers the Integrated Stress Response
Possible reference: Baluapuri, A. et al. (2025) Integrator loss leads to dsRNA formation that triggers the integrated stress response., Cell, PMID 40233738

PXD060644 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive Nucleoside Analysis of Archaeal RNA Modification Profiles Reveals a m7G in the Conserved P-loop of 23S rRNA
Possible reference: Tsai, YL. et al. (2025) Comprehensive nucleoside analysis of archaeal RNA modification profiles reveals an m7G in the conserved P loop of 23S rRNA., Cell Rep, PMID 40131932

PXD060623 no publication (from MassIVE)
Dataset title: SDF2 and SDF2L1 are essential co-factors of DNAJB11 for Polycystin-1 processing
Possible reference: Busch, T. et al. (2025) SDF2 and SDF2L1 are essential co-factors of DNAJB11 for Polycystin-1 processing., J Biol Chem, PMID 41109348

PXD060607 Dataset with its publication pending (from PRIDE)
Dataset title: Malonyl-CoA Promotes Prostate Cancer Progression and Castration Resistance by Enhancing Lipogenesis and Ran Activation
Possible reference: Dai, Y. et al. (2025) Malonyl-CoA Promotes Prostate Cancer Progression and Castration Resistance by Enhancing Lipogenesis and Ran Activation., Cancer Res, PMID 40865048

PXD060606 Dataset with its publication pending (from jPOST)
Dataset title: Leveraging complementary ion activation methods with proton transfer charge reduction reactions for comprehensive characterization of monoclonal antibody heavy chain subunits
Possible reference: Dunham, SD. et al. (2025) Leveraging Complementary Ion Activation Methods with Proton Transfer Charge Reduction Reactions for Comprehensive Characterization of Monoclonal Antibody Heavy Chain Subunits., Anal Chem, PMID 40607953

PXD060605 no publication (from MassIVE)
Dataset title: Nunziata Maio_Tracey Rouault_8LFQ_nsp14
Possible reference: Maio, N. et al. (2025) Iron-sulfur clusters in SARS-CoV-2 exoribonuclease and methyltransferase complexes: relevance for viral genome proofreading and capping., Nat Commun, PMID 40817372

PXD060597 Chevenier A, Fanuel M, Sokolova E, Latorre DM, Jouanneau D, Jeudy A, et al. Structure, function and catalytic mechanism of the carrageenan-sulfatases from the marine bacterium Zobellia galactanivorans DsijT. Carbohydr Polym. 2025;358:123487 (from PanoramaPublic)
Dataset title: Carrageenan-sulfatases from the marine bacterium Zobellia galactanivorans Dsij
Possible reference: Chevenier, A. et al. (2025) Structure, function and catalytic mechanism of the carrageenan-sulfatases from the marine bacterium Zobellia galactanivorans DsijT., Carbohydr Polym, PMID 40383559

PXD060588 no publication (from MassIVE)
Dataset title: EGFR inhibitor-resistant lung cancers exhibit collateral sensitivity to a covalent, cysteine-independentKEAP1 oligomerizing molecular bridge
Possible reference: Bassil, CF. et al. (2026) EGFR inhibitor-resistant lung cancers exhibit collateral sensitivity to a covalent, cysteine-independent KEAP1 oligomerizing molecular bridge., Nat Commun, PMID 41535280

PXD060584 Dataset with its publication pending (from PRIDE)
Dataset title: Biphasic in vitro maturation (CAPA-IVM) on equine oocytes
Possible reference: Fakhar-I-Adil, M. et al. (2025) Biphasic CAPA-IVM Improves Equine Oocyte Quality and Subsequent Embryo Development Without Inducing Genetic Aberrations., Int J Mol Sci, PMID 40564960

PXD060582 Dataset with its publication pending (from PRIDE)
Dataset title: Cryo-EM structure of the CDK11-cyclin L-SAP30BP complex reveals mechanisms of CDK11 regulation
Possible reference: McGeoch, AJS. et al. (2026) Cryo-EM structures of the CDK11-cyclin L-SAP30BP complex reveal mechanisms of CDK11 regulation., Nat Commun, PMID 42034640

PXD060567 Dataset with its publication pending (from iProX)
Dataset title: Pentraxin3 exacerbates acute pancreatitis injury by inhibiting oxidative phosphorylation pathway
Possible reference: Wang, W. et al. (2025) Pentraxin3 exacerbates acute pancreatitis injury by inhibiting oxidative phosphorylation pathway., Sci Rep, PMID 40011615

PXD060558 Dataset with its publication pending (from PRIDE)
Dataset title: Global Spinal Cord Peptidome Profiling in Response to Osteoarthritis in Rats
Possible reference: Lu, G. et al. (2025) Global spinal cord peptidome profiling in response to osteoarthritis in rats., Mol Omics, PMID 41159712

PXD060539 Dataset with its publication pending (from iProX)
Dataset title: Identification of crucial genes sustaining the curled leaf phenotype in perennial transgenic poplar via advanced proteomic and phosphoproteomic analyses
Possible reference: Wu, ZQ. et al. (2025) Identification of crucial genes sustaining the curled leaf phenotype in perennial transgenic poplar via advanced proteomic and phosphoproteomic analyses., J Proteomics, PMID 40472892

PXD060524 Dataset with its publication pending (from PRIDE)
Dataset title: A non-coding role for trypanosome VSG transcripts in allelic exclusion
Possible reference: Escrivani, DO. et al. (2025) A non-coding role for trypanosome VSG transcripts in allelic exclusion., Nucleic Acids Res, PMID 41118571

PXD060491 Dataset with its publication pending (from iProX)
Dataset title: Integrated proteomics and metabolomics revealed the regulatory pathways of quality between wild and cultivated Ophiocordyceps sinensis
Possible reference: Tang, C. et al. (2025) Integrated Proteomics and Metabolomics Reveal Regulatory Pathways Underlying Quality Differences Between Wild and Cultivated Ophiocordyceps sinensis., J Fungi (Basel), PMID 40985417

PXD060464 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting chaperone-mediated autophagy inhibits properties of glioblastoma stem cells and restores anti-tumor immunity
Possible reference: Li, Y. et al. (2025) Targeting chaperone-mediated autophagy inhibits properties of glioblastoma stem cells and restores anti-tumor immunity., Nat Commun, PMID 41390755

PXD060457 Dataset with its publication pending (from PRIDE)
Dataset title: TBC1D22B Regulates ER-to-Golgi Trafficking via RAB1B Inactivation and Promotes Oncogenic Programs in Breast Cancer
Possible reference: Martino, F. et al. (2025) TBC1D22B Regulates ER-to-Golgi Trafficking via RAB1B Inactivation and Promotes Oncogenic Programs in Breast Cancer., Adv Sci (Weinh), PMID 40878439

PXD060429 Dataset with its publication pending (from PRIDE)
Dataset title: Cross-organelle Coordination to Advance Plant Cytochrome P450 Functionality in Yeast
Possible reference: Xu, S. et al. (2025) Enhancing cross-organelle coordination to advance plant cytochrome P450 functionality in yeast., Sci Adv, PMID 41134884

PXD060411 no publication (from MassIVE)
Dataset title: A functional map of phosphoprotein phosphatase regulation identifies an evolutionary conserved reductase for the active site
Possible reference: Meeusen, B. et al. (2025) A functional map of phosphoprotein phosphatase regulation identifies an evolutionary conserved reductase for the catalytic metal ions., bioRxiv, PMID 39990307

PXD060391 Dataset with its publication pending (from PRIDE)
Dataset title: Architecture of the human KICSTOR and GATOR1-KICSTOR complexes
Possible reference: Teng, F. et al. (2025) Architecture of the human KICSTOR and GATOR1-KICSTOR complexes., Nat Struct Mol Biol, PMID 41198956

PXD060389 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic characterisation of Aspergillus fumigatus – host interactions using the ex-vivo pig lung model (EVPL)
Possible reference: Curtis, A. et al. (2025) Proteomic characterization of Aspergillus fumigatus - host interactions using the ex-vivo pig lung (EVPL) model., Virulence, PMID 40665229

PXD060380 no publication (from MassIVE)
Dataset title: VIPER-TACs leverage viral E3 ligases for disease-specific targeted protein degradation
Possible reference: Mangano, K. et al. (2025) VIPER-TACs leverage viral E3 ligases for disease-specific targeted protein degradation., Cell Chem Biol, PMID 40049166

PXD060335 Dataset with its publication pending (from PRIDE)
Dataset title: Critical Assessment of MetaProteome Investigation 2 (CAMPI-2)
Possible reference: Tanca, A. et al. (2025) Critical Assessment of MetaProteome Investigation 2 (CAMPI-2): multi-laboratory assessment of sample processing methods to stabilize fecal microbiome for functional analysis., Microbiome, PMID 41310812

PXD060327 Dataset with its publication pending (from PRIDE)
Dataset title: Systems acclimation to osmotic stress in zygnematophyte cells
Possible reference: Zegers, JMS. et al. (2026) Systems acclimation to osmotic stress in zygnematophyte cells., Nat Commun, PMID 41545391

PXD060316 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of nasal epithelial cells infected with Bordetella pertussis B1917
Possible reference: Zmuda, M. et al. (2025) Limited response of primary nasal epithelial cells to Bordetella pertussis infection., Microbiol Spectr, PMID 40757824

PXD060311 Dataset with its publication pending (from PRIDE)
Dataset title: A boundary-defining protein facilitates megabase-scale regulatory chromosomal loop formation in Drosophila neurons
Possible reference: Mouginot, M. et al. (2025) A boundary-defining protein facilitates megabase-scale regulatory chromosomal loop formation in Drosophila neurons., Genes Dev, PMID 40240144

PXD060300 Dataset with its publication pending (from PRIDE)
Dataset title: ARAP2 regulates the Interferon-gamma response by restricting SOCS1
Possible reference: Keating, N. et al. (2025) ARAP2 regulates responses to interferon-gamma by restricting SOCS1., Cell Rep, PMID 41401070

PXD060284 Dataset with its publication pending (from PRIDE)
Dataset title: An inherited mtDNA mutation remodels inflammatory cytokine responses in macrophages and in vivo
Possible reference: Marques, E. et al. (2025) An inherited mitochondrial DNA mutation remodels inflammatory cytokine responses in macrophages and in vivo in mice., Nat Commun, PMID 41266309

PXD060281 no publication (from MassIVE)
Dataset title: Immunoglobulin A Carries Sulfated and O-acetylated N-glycans Primarily at the Tailpiece Site
Possible reference: Zuniga-Banuelos, FJ. et al. (2025) Immunoglobulin A carries sulfated and O-acetylated N-glycans primarily at the tailpiece site - strategies for site-specific N-glycan identification., Front Mol Biosci, PMID 40821702

PXD060266 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis reveals the alleviation of follicular development defects in offspring mice under DEHP exposure by melatonin
Possible reference: Liu, JC. et al. (2025) Proteomic analysis reveals the alleviation of follicular development defects in offspring mice under DEHP exposure by melatonin., BMC Biol, PMID 40022026

PXD060265 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanical confinement governs phenotypic plasticity in melanoma
Possible reference: Hunter, MV. et al. (2025) Mechanical confinement governs phenotypic plasticity in melanoma., Nature, PMID 40866703

PXD060257 Dataset with its publication pending (from PRIDE)
Dataset title: Metaproteomics on PET degrading bacterial biofilms from wastewater
Possible reference: Vijande, C. et al. (2026) Multi-omics reveals wastewater sludge bacteria with genomic potential to degrade poly(ethylene terephthalate)., Bioresour Technol, PMID 41539626

PXD060234 Dataset with its publication pending (from iProX)
Dataset title: Protective Effects of Bone Marrow Mesenchymal Stem Cell-Derived Exosomes Loaded Cerium Dioxide Nanoparticle Against Deoxynivalenol-Induced Liver Damage
Possible reference: Meng, Z. et al. (2025) Protective effects of bone marrow mesenchymal stem cell-derived exosomes loaded cerium dioxide nanoparticle against deoxynivalenol-induced liver damage., J Nanobiotechnology, PMID 40098176

PXD060215 Dataset with its publication pending (from PRIDE)
Dataset title: Dietary carbohydrates alter immune-modulatory functionalities and DNA inversions in Bacteroides thetaiotaomicron
Possible reference: Gal-Mandelbaum, N. et al. (2025) Dietary carbohydrates alter immune-modulatory functionalities and DNA inversions in Bacteroides thetaiotaomicron., Nat Commun, PMID 40436824

PXD060214 Dataset with its publication pending (from jPOST)
Dataset title: Identification of Serum Metabolite Biomarkers and Metabolic Reprogramming Mechanisms to Predict Recurrence in Cholangiocarcinoma
Possible reference: Prajumwongs, P. et al. (2025) Identification of serum metabolite biomarkers and metabolic reprogramming mechanisms to predict recurrence in cholangiocarcinoma., Sci Rep, PMID 40229491

PXD060212 Dataset with its publication pending (from PRIDE)
Dataset title: CAV2-expressing Nerves induce Metabolic Switch toward Mitochondrial Oxidative Phosphorylation to Promote Cancer Stemness
Possible reference: Zhang, Z. et al. (2025) CAV2-expressing nerves induce metabolic switch toward mitochondrial oxidative phosphorylation to promote cancer stemness., Nat Commun, PMID 41330921

PXD060210 no publication (from MassIVE)
Dataset title: Micrurus ephippifer snake venom proteomics data
Possible reference: Zarzosa, V. et al. (2025) Integrative transcriptomic, proteomic, biochemical and neutralization studies on the venom of Micrurus ephippifer., J Proteomics, PMID 40023277

PXD060204 no publication (from MassIVE)
Dataset title: Pseudomonas putida produces two distinct populations of membrane vesicles during growth on lignin
Possible reference: Werner, AZ. et al. (2025) A distinct subpopulation of membrane vesicles in Pseudomonas putida is enriched in enzymes for lignin catabolism., Appl Environ Microbiol, PMID 41031834

PXD060187 Dataset with its publication pending (from iProX)
Dataset title: Multi-proteomics investigation of the early response to X-rays and carbon ion irradiation of HeLa cells
Possible reference: Ben Diouf, O. et al. (2025) Multi-proteomics investigation of the early response to X-rays and carbon ion irradiations of HeLa cells., Integr Biol (Camb), PMID 40532120

PXD060183 Dataset with its publication pending (from iProX)
Dataset title: The molecular mechanism of AP-2 complex degradation of LLO secreted by Listeria in the cytoplasm
Possible reference: Chen, C. et al. (2018) The Listeriolysin O PEST-like Sequence Co-opts AP-2-Mediated Endocytosis to Prevent Plasma Membrane Damage during Listeria Infection., Cell Host Microbe, PMID 29902442

PXD060162 Dataset with its publication pending (from PRIDE)
Dataset title: Acetyl-phosphate dependent protein acetylation in Neisseria gonorrhoeae
Possible reference: Post, DMB. et al. (2017) Identification and characterization of AckA-dependent protein acetylation in Neisseria gonorrhoeae., PLoS One, PMID 28654654

PXD060161 no publication (from MassIVE)
Dataset title: Comparative Proteomic Profiling of Receptor Kinase Signaling Reveals Key Trafficking Components Enforcing Plant Stomatal Development
Possible reference: Bai, P. et al. (2025) Comparative Proteomic Profiling of Receptor Kinase Signaling Reveals Key Trafficking Components Enforcing Plant Stomatal Development., bioRxiv, PMID 40777324

PXD060159 no publication (from MassIVE)
Dataset title: Proteomic characterization of checkpoint inhibitor-induced liver injury
Possible reference: Ji, C. et al. (2025) Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury., Cancer Immunol Immunother, PMID 40317333

PXD060146 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted Translation Inhibition of Chloroplast and Mitochondrial mRNAs by Designer Pentatricopeptide Repeat Proteins
Possible reference: Manavski, N. et al. (2025) Targeted translation inhibition of chloroplast and mitochondrial mRNAs by designer pentatricopeptide repeat proteins., Nucleic Acids Res, PMID 40138717

PXD060140 no publication (from MassIVE)
Dataset title: SWAPS: a modular deep-learning empowered peptide identity propagation framework beyond match-between-run
Possible reference: Xiao, Z. et al. (2025) SWAPS: A Modular Deep-Learning Empowered Peptide Identity Propagation Framework Beyond Match-Between-Run., J Proteome Res, PMID 40052690

PXD060137 Dataset with its publication pending (from jPOST)
Dataset title: Unveiling IRF4-steered regulation of context-dependent effector programs in CD4+ T cells under Th17- and Treg-skewing conditions
Possible reference: Gabele, A. et al. (2025) Unveiling IRF4-steered regulation of context-dependent effector programs in CD4+ T cells under Th17- and Treg-skewing conditions., Cell Rep, PMID 40067830

PXD060128 Dataset with its publication pending (from jPOST)
Dataset title: Predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation
Possible reference: Na, S. et al. (2022) Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation., Bioinformatics, PMID 35441674

PXD060108 Dataset with its publication pending (from PRIDE)
Dataset title: Mass spectrometry of co-immunoprecipitation using Arabidopsis MKIP1-YFP as bait
Possible reference: Kriechbaumer, V. et al. (2015) Reticulomics: Protein-Protein Interaction Studies with Two Plasmodesmata-Localized Reticulon Family Proteins Identify Binding Partners Enriched at Plasmodesmata, Endoplasmic Reticulum, and the Plasma Membrane., Plant Physiol, PMID 26353761

PXD060084 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic surveys of the mouse heart unveil cardiovascular responses to nitric oxide/cGMP signaling deficiencies.
Possible reference: Mohanty, I. et al. (2025) Proteomic surveys of the mouse heart unveil cardiovascular responses to nitric oxide/cGMP signaling deficiencies., Commun Biol, PMID 40425728

PXD060069 no publication (from MassIVE)
Dataset title: Oxidation of Retromer Complex controls Mitochondrial Translation
Possible reference: Salminen, A. et al. (2013) Impaired autophagy and APP processing in Alzheimer's disease: The potential role of Beclin 1 interactome., Prog Neurobiol, PMID 23827971

PXD060028 Dataset with its publication pending (from PRIDE)
Dataset title: Recommendations for Automating Hydrogen/Deuterium Exchange Mass Spectrometry Measurements using Data-Independent Acquisition Methods
Possible reference: Filandr, F. et al. (2025) Examining Instrumental Factors Influencing the Performance of Data-Independent Acquisition Methods in Hydrogen/Deuterium Exchange Mass Spectrometry., Anal Chem, PMID 40165489

PXD060017 Dataset with its publication pending (from PRIDE)
Dataset title: Explainable Machine Learning Identifies Factors for Dosage Compensation in Aneuploid Human Cancer Cells
Possible reference: Heller, EM. et al. (2025) Explainable Machine Learning Identifies Factors for Dosage Compensation in Aneuploid Human Cancer Cells., bioRxiv, PMID 40463217

PXD060004 Dataset with its publication pending (from iProX)
Dataset title: CRISPR-edited iPSCs reveal BSN gene mutations induce neuronal hyperexcitability via astrocyte lipid accumulation
Possible reference: Chen, H. et al. (2025) CRISPR-edited iPSCs reveal BSN gene mutations induce neuronal hyperexcitability via astrocyte lipid accumulation., Neurotherapeutics, PMID 40962686

PXD060001 Dataset with its publication pending (from iProX)
Dataset title: Linker-free PROTACs efficiently induce the degradation of oncoproteins
Possible reference: Zhang, J. et al. (2025) Linker-free PROTACs efficiently induce the degradation of oncoproteins., Nat Commun, PMID 40410168

PXD059986 Huwa, N., Sch�nenberger, R., & Groh, K. J. (2025). Development and application of a targeted phosphoproteomics method for analysing the mTOR pathway dynamics in zebrafish PAC2 cell line. Journal of Proteomics, 319, 105469. (from PanoramaPublic)
Dataset title: Development and Application of a Targeted Phosphoproteomics Method for Analysing the mTOR Pathway Dynamics in Zebrafish PAC2 Cell Line
Possible reference: Huwa, N. et al. (2025) Development and application of a targeted phosphoproteomics method for analysing the mTOR pathway dynamics in zebrafish PAC2 cell line., J Proteomics, PMID 40466985

PXD059968 Dataset with its publication pending (from PRIDE)
Dataset title: Leishmania regulates host YY1: comparative proteomic analysis identifies infection modulated YY1 dependent proteinsLeishmania regulates host YY1: comparative proteomic analysis identifies infection modulated YY1 dependent proteins
Possible reference: Brar, HK. et al. (2025) Leishmania regulates host YY1: Comparative proteomic analysis identifies infection modulated YY1 dependent proteins., PLoS One, PMID 40373059

PXD059966 Dataset with its publication pending (from PRIDE)
Dataset title: Chaperone-mediated autophagy sustains muscle stem cell regenerative function
Possible reference: Ram�rez-Pardo, I. et al. (2025) Chaperone-mediated autophagy sustains muscle stem cell regenerative functions but declines with age., Nat Metab, PMID 41339968

PXD059955 Dataset with its publication pending (from iProX)
Dataset title: Heat shock chaperone HSPB1 mitigates poly-glycine-induced neurodegeneration via restoration of autophagic flux
Possible reference: Ding, N. et al. (2025) Heat-shock chaperone HSPB1 mitigates poly-glycine-induced neurodegeneration via restoration of autophagic flux., Autophagy, PMID 39936620

PXD059924 Dataset with its publication pending (from PRIDE)
Dataset title: Stressosome-independent but RsbT-dependent environmental stress sensing in Bacillus subtilis
Possible reference: Khadka, R. et al. (2025) Stressosome-independent but RsbT-dependent environmental stress sensing in Bacillus subtilis., Nat Commun, PMID 39939311

PXD059910 Dataset with its publication pending (from PRIDE)
Dataset title: The role of USP7 in TNBC proteomes
Possible reference: Kim, A. et al. (2026) USP7 inhibition perturbs proteostasis and tumorigenesis in triple-negative breast cancer., NPJ Breast Cancer, PMID 42177192

PXD059901 Dataset with its publication pending (from iProX)
Dataset title: proteomics of 293T treated with lipid
Possible reference: Lv, X. et al. (2026) The ovarian tumor domain-containing protein 4 (OTUD4)-targeted ferroptosis inhibitor Maclekarpine E attenuates ulcerative colitis., Phytomedicine, PMID 41759427

PXD059898 no publication (from MassIVE)
Dataset title: Disulfide bonds are required for cell division, cell envelope biogenesis and antibiotic resistance proteins in mycobacteria
Possible reference: Mejia-Santana, A. et al. (2025) Disulfide bonds are required for cell division, cell envelope biogenesis and antibiotic resistance proteins in mycobacteria., bioRxiv, PMID 39975046

PXD059894 Dataset with its publication pending (from PRIDE)
Dataset title: FIbromyalgia diagnosis from a multiomics approach: a gut feeling
Possible reference: Dur�n-Gonz�lez, E. et al. (2025) Fibromyalgia diagnosis from a multi-omics approach: a gut feeling., Front Microbiol, PMID 41113645

PXD059871 no publication (from MassIVE)
Dataset title: Quantitative proteomic analysis reveals JMJD6 and DNAJB11 as endogenous substrates of E3 ligase RFFL
Possible reference: Narendradev, ND. et al. (2025) Quantitative Proteomic Analysis Reveals JMJD6 and DNAJB11 as Endogenous Substrates of E3 Ligase RFFL., J Proteome Res, PMID 40568870

PXD059866 Dataset with its publication pending (from iProX)
Dataset title: Aspirin inhibits proteasomal degradation and promotes Î±-synuclein aggregate clearance through K63 ubiquitination
Possible reference: Gao, J. et al. (2025) Aspirin inhibits proteasomal degradation and promotes α-synuclein aggregate clearance through K63 ubiquitination., Nat Commun, PMID 39920137

PXD059856 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of Sternaspis chinensis to understand phosphate biomineralization in annelids
Possible reference: Ge, M. et al. (2025) Proteomics of Sternaspis chinensis to understand phosphate biomineralization in annelids., J Proteomics, PMID 40090575

PXD059848 no publication (from MassIVE)
Dataset title: Quantitative proteomic analysis reveals JMJD6 and DNAJB11 as endogenous substrates of E3 ligase RFFL
Possible reference: Narendradev, ND. et al. (2025) Quantitative Proteomic Analysis Reveals JMJD6 and DNAJB11 as Endogenous Substrates of E3 Ligase RFFL., J Proteome Res, PMID 40568870

PXD059839 no publication (from MassIVE)
Dataset title: Brain-wide measurement of synaptic protein turnover reveals localized plasticity during learning
Possible reference: Mohar, B. et al. (2025) DELTA: a method for brain-wide measurement of synaptic protein turnover reveals localized plasticity during learning., Nat Neurosci, PMID 40164741

PXD059825 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting the mitochondrial recycling dysfunction in systemic lupus erythematosus (SLE) patients NK cells with Hydroxychloroquine (HCQ)
Possible reference: Fluder, NW. et al. (2025) Mitochondrial dysfunction drives natural killer cell dysfunction in systemic lupus erythematosus., medRxiv, PMID 39973995

PXD059824 Dataset with its publication pending (from PRIDE)
Dataset title: Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics
Possible reference: Shapiro, IE. et al. (2025) Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics., Nat Commun, PMID 40775223

PXD059809 Dataset with its publication pending (from jPOST)
Dataset title: Saliva and silk proteins in spider mites: dual roles in feeding and silk fiber coating
Possible reference: Arai, Y. et al. (2025) Dual roles of salivary proteins in feeding and silk fiber coating in the spider mite Tetranychus urticae., Commun Biol, PMID 41107479

PXD059802 Dataset with its publication pending (from PRIDE)
Dataset title: A stabilized MERS-CoV spike ferritin nanoparticle vaccine elicits robust and protective neutralizing antibody responses
Possible reference: Powell, AE. et al. (2026) A stabilized MERS-CoV spike ferritin nanoparticle vaccine elicits robust and protective neutralizing antibody responses., Nat Commun, PMID 41644950

PXD059780 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics data of extracellular vesicles, which are specifically derived from Leydig cells or testicular macrophage cells respectively within the mouse testis, offer detailed and comprehensive insights into the unique biochemical compositions and potenti
Possible reference: O'Donnell, L. et al. (2023) Sertoli cell-enriched proteins in mouse and human testicular interstitial fluid., PLoS One, PMID 37656709

PXD059752 Dataset with its publication pending (from PRIDE)
Dataset title: Micropillar-induced changes in cell nucleus morphology enhance bone regeneration by modulating the secretome
Possible reference: Wang, X. et al. (2025) Micropillar-induced changes in cell nucleus morphology enhance bone regeneration by modulating the secretome., Res Sq, PMID 39866882

PXD059748 Dataset with its publication pending (from iProX)
Dataset title: Proteomic Analysis of Biofilm Formation in Aeromonas hydrophila LP-2: Impact of orf-2341 Deletion
Possible reference: Xu, Q. et al. (2025) Proteomics reveals the role of the EamB transporter from Aeromonas hydrophila LP-2 in biofilm formation., J Proteomics, PMID 40744271

PXD059744 Dataset with its publication pending (from iProX)
Dataset title: Phosphorylated proteomics of yellowing broccoli
Possible reference: He, MJ. et al. (2023) Transcriptomic and Proteomic Analyses of Myzus persicae Carrying Brassica Yellows Virus., Biology (Basel), PMID 37508340

PXD059737 Dataset with its publication pending (from PRIDE)
Dataset title: Endogenous RALF peptide function is required for powdery mildew host colonization
Possible reference: Leicher, H. et al. (2026) Endogenous RALF peptide function is required for powdery mildew host colonization., New Phytol, PMID 42203759

PXD059731 no publication (from MassIVE)
Dataset title: Structural obstruction to full DNA replication in the chromatin of terminally differentiated skeletal muscle cells
Possible reference: Zribi, S. et al. (2025) Structural obstruction to full DNA replication in terminally differentiated skeletal muscle cells., EMBO Rep, PMID 40859015

PXD059727 no publication (from MassIVE)
Dataset title: A universal peptide and any peptidoform spectrum annotator for mass spectrometry-based proteomics
Possible reference: Schulte, D. et al. (2025) A Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics., Anal Chem, PMID 41085411

PXD059712 Dataset with its publication pending (from iProX)
Dataset title: lnc-FAM72D-3 augments the affinity of the E3 ubiquitin ligase HECTD3 for MBNL1, inciting lysine 48-linked ubiquitination and subsequent degradation of MBNL1
Possible reference: Cao, M. et al. (2025) Exosome-derived lnc-FAM72D-3 promotes lenvatinib resistance by remodeling hepatocellular carcinoma cytoskeleton via MBNL1/FAK axis., Drug Resist Updat, PMID 40517686

PXD059707 Dataset with its publication pending (from iProX)
Dataset title: Exosome-derived lnc-FAM72D-3 promotes lenvatinib resistance by remodeling hepatocellular carcinoma cytoskeleton via MBNL1/FAK axis
Possible reference: Cao, M. et al. (2025) Exosome-derived lnc-FAM72D-3 promotes lenvatinib resistance by remodeling hepatocellular carcinoma cytoskeleton via MBNL1/FAK axis., Drug Resist Updat, PMID 40517686

PXD059704 Dataset with its publication pending (from iProX)
Dataset title: DMLL alleviates ulcerative colitis in mice
Possible reference: Cheng, Y. et al. (2025) Integrated Metabolomics and Gut Microbiome Analysis Reveal the Role of Demethylzeylasteral in Alleviating Ulcerative Colitis in Mice., J Proteome Res, PMID 40653681

PXD059683 Dataset with its publication pending (from PRIDE)
Dataset title: SpLICE: A reference database enabling in depth proteome and PTM analysis of mouse immune cells
Possible reference: Siemes, D. et al. (2025) A reference database enabling in-depth proteome and PTM analysis of mouse immune cells., Sci Data, PMID 40210874

PXD059630 Dataset with its publication pending (from PRIDE)
Dataset title: ABCF Protein-Mediated Resistance Shapes Bacterial Responses Based on Antibiotic Type and Concentration
Possible reference: Koběrská, M. et al. (2025) ABCF protein-mediated resistance shapes bacterial responses to antibiotics based on their type and concentration., mBio, PMID 40793774

PXD059624 Dataset with its publication pending (from PRIDE)
Dataset title: Cooking methods affect Advanced Glycation End products and lipid profiles: a randomized cross-over study in healthy subjects
Possible reference: Wellens, J. et al. (2025) Cooking methods affect advanced glycation end products and lipid profiles: A randomized cross-over study in healthy subjects., Cell Rep Med, PMID 40280130

PXD059605 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive single cell transcriptomics analysis of murine osteosarcoma uncovers Skp2 function in metastasis, genomic instability and immune activation and reveals additional target pathways
Possible reference: Ferrena, A. et al. (2024) Comprehensive single cell transcriptomics analysis of murine osteosarcoma uncovers Skp2 function in metastasis, genomic instability and immune activation and reveals additional target pathways., bioRxiv, PMID 38895216

PXD059596 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibition of tumor-intrinsic NAT10 enhances antitumor immunity by triggering type I interferon responses via MYC/CDK2/DNMT1 pathway
Possible reference: Liu, WC. et al. (2025) Inhibition of tumor-intrinsic NAT10 enhances antitumor immunity by triggering type I interferon response via MYC/CDK2/DNMT1 pathway., Nat Commun, PMID 40461504

PXD059595 no publication (from MassIVE)
Dataset title: Differential protein expression analysis of western flower thrips +/- TSWV
Possible reference: Khan, F. et al. (2025) Binding Specificity and Oligomerization of TSWV N Protein in the Western Flower Thrips, Frankliniella occidentalis., Viruses, PMID 40573417

PXD059572 Dataset with its publication pending (from iProX)
Dataset title: Discovery of novel potent triple IKZF1/2/3 degraders for the treatment of hematological cancers
Possible reference: Wei, T. et al. (2025) Discovery of Novel Potent Triple IKZF1/2/3 Degraders for the Treatment of Hematological Cancers., J Med Chem, PMID 40747902

PXD059569 Dataset with its publication pending (from jPOST)
Dataset title: Bacterial proteins encapsulated in extracellular membrane vesicles of Escherichia coli-infected macrophages
Possible reference: Imamiya, R. et al. (2025) Bacterial proteins encapsulate in extracellular membrane vesicles from Escherichia coli-infected macrophages., Microbiol Resour Announc, PMID 40488506

PXD059561 no publication (from MassIVE)
Dataset title: Local growth hormone facilitates the aging colon epithelial microenvironment
Possible reference: Chesnokova, V. et al. (2021) Local non-pituitary growth hormone is induced with aging and facilitates epithelial damage., Cell Rep, PMID 34910915

PXD059539 Dataset with its publication pending (from PRIDE)
Dataset title: FMNL2/SRC-mediated androgen receptor translocation into the nucleus promotes enzalutamide resistance of prostate cancer
Possible reference: Yu, J. et al. (2025) FMNL2/SRC-mediated androgen receptor translocation into the nucleus promotes enzalutamide resistance of prostate cancer., iScience, PMID 40212590

PXD059531 Dataset with its publication pending (from iProX)
Dataset title: Host proteins interacting with EV71-VP1 were identified by mass spectrometry
Possible reference: Tian, L. et al. (2025) ZYG11B suppresses multiple enteroviruses by triggering viral VP1 degradation., J Virol, PMID 40135890

PXD059519 Dataset with its publication pending (from PRIDE)
Dataset title: Pluripotent stem cell-based screening uncovers sildenafil as a mitochondrial disease therapy
Possible reference: Zink, A. et al. (2026) Pluripotent stem-cell-based screening uncovers sildenafil as a mitochondrial disease therapy., Cell, PMID 41819105

PXD059516 Dataset with its publication pending (from jPOST)
Dataset title: Comparative Proteomics of mHippoE-18 Cells Treated with Peptide Fraction from Naja mandalayensis Snake Venom
Possible reference: Silva, BR. et al. (2025) Peptide Fraction from Naja mandalayensis Snake Venom Showed Neuroprotection Against Oxidative Stress in Hippocampal mHippoE-18 Cells but Not in Neuronal PC12 Cells., Antioxidants (Basel), PMID 40227273

PXD059506 no publication (from MassIVE)
Dataset title: Direct histone proteoform profiling of the unannotated, endangered coral Acropora cervicornis
Possible reference: Fuller, CN. et al. (2025) Direct histone proteoform profiling of the unannotated,�endangered coral Acropora cervicornis., Nucleic Acids Res, PMID 40744498

PXD059504 Dataset with its publication pending (from jPOST)
Dataset title: Drug Repurposing Identifies Proteasome Inhibitors as Antiproliferative Agents Counteracting Inflammation-Driven Chemoresistance in Triple-Negative Breast Cancer Organoids
Possible reference: Sari, AIP. et al. (2025) Drug repurposing identifies proteasome inhibitors as antiproliferative agents counteracting inflammation-driven chemoresistance in triple-negative breast cancer organoids., Biomed Pharmacother, PMID 40695045

PXD059487 Dataset with its publication pending (from iProX)
Dataset title: Integrative Transcriptomic and Proteomic profiling reveals carbon metabolism and complement systems are mainly affected in Bovine Coronavirus infection in MDBK cells
Possible reference: Zhang, H. et al. (2025) Integrative transcriptomic and proteomic analyses reveal that carbon metabolism and complement system of Madin Darby Bovine Kidney cells are affected by bovine coronavirus infection., BMC Vet Res, PMID 40457360

PXD059475 no publication (from MassIVE)
Dataset title: Global Proteoform Alterations Across Multiple Cellular Compartments Underlie Obstructive Hypertrophic Cardiomyopathy
Possible reference: Gao, Z. et al. (2025) Global Proteoform Alterations Across Multiple Cellular Compartments Underlie Obstructive Hypertrophic Cardiomyopathy., Circ Heart Fail, PMID 41277423

PXD059464 Dataset with its publication pending (from PRIDE)
Dataset title: Nuclear-localized HKDC1 promotes hepatocellular carcinoma through phosphorylating RBBP5 to upregulate H3K4me3
Possible reference: Ye, L. et al. (2025) Nuclear-localized HKDC1 promotes hepatocellular carcinoma through phosphorylating RBBP5 to upregulate H3K4me3., Cell Rep, PMID 39891906

PXD059463 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibition of tumor-intrinsic NAT10 enhances antitumor immunity by triggering type I interferon responses via MYC/CDK2/DNMT1 pathway
Possible reference: Liu, WC. et al. (2025) Inhibition of tumor-intrinsic NAT10 enhances antitumor immunity by triggering type I interferon response via MYC/CDK2/DNMT1 pathway., Nat Commun, PMID 40461504

PXD059457 no publication (from MassIVE)
Dataset title: Dual Roles of hABCB1 in Drug Resistance and Immune Evasion: Implications for Lung Cancer Therapy
Possible reference: Min, JY. et al. (2026) Dual Roles of hABCB1 in Drug Resistance and Immune Evasion: Implications for Lung Cancer Therapy., ACS Omega, PMID 42222820

PXD059455 Dataset with its publication pending (from PRIDE)
Dataset title: Wastewater metaproteomics: tracking microbial and human protein biomarkers
Possible reference: Tugui, CG. et al. (2026) Wastewater metaproteomics: tracking microbial and human protein biomarkers., ISME Commun, PMID 41561306

PXD059451 Dataset with its publication pending (from PRIDE)
Dataset title: Data for Cross-platform Construction of Comprehensive Proteomic Database for Human Corneal Epithelial Cell
Possible reference: Chan, KK. et al. (2025) A Comprehensive Proteome of Human Corneal Epithelial Cells Constructed by Cross-platform DIA-Mass Spectrometry., Sci Data, PMID 40410165

PXD059447 Dataset with its publication pending (from iProX)
Dataset title: Novel kethoxal derivatives-assisted identification of single-stranded RNA-binding proteins
Possible reference: Zhao, R. et al. (2023) Transcriptome-wide identification of single-stranded RNA binding proteins., Chem Sci, PMID 37063799

PXD059440 no publication (from MassIVE)
Dataset title: Identification of disulfide bond-linking sites in biosynthesized platelet factor 4 by establishing a partial reduction method without alkylation
Possible reference: Hu, W. et al. (2025) Identification of disulfide bond-linking sites in biosynthesized platelet factor 4 by establishing a partial reduction method without alkylation., Anal Methods, PMID 39865791

PXD059425 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Profile of multidrug- resistant Serratia marcescens under meropenem challenge
Possible reference: Ferreira, RL. et al. (2025) Proteomic profile of multidrug-resistant Serratia marcescens under meropenem challenge., Microb Pathog, PMID 40222567

PXD059395 Dataset with its publication pending (from PRIDE)
Dataset title: Liquid crystal monomers induce placental development and progesterone release dysregulation through transplacental transportation
Possible reference: Zhang, S. et al. (2025) Liquid crystal monomers induce placental development and progesterone release dysregulation through transplacental transportation., Nat Commun, PMID 39885209

PXD059392 Dataset with its publication pending (from PRIDE)
Dataset title: G3BP1 Ribonucleoprotein Complexes Regulate Focal Adhesion Protein Mobility and Cell Migration
Possible reference: Boraas, LC. et al. (2025) G3BP1 ribonucleoprotein complexes regulate focal adhesion protein mobility and cell migration., Cell Rep, PMID 39883578

PXD059357 Dataset with its publication pending (from iProX)
Dataset title: A Novel Î±-Conotoxin [D1G, Q14] LvIC Decreased Mouse Locomotor Activity
Possible reference: Wang, W. et al. (2024) A novel α-conotoxin [D1G, ΔQ14] LvIC decreased mouse locomotor activity., Front Pharmacol, PMID 39906393

PXD059328 Dataset with its publication pending (from iProX)
Dataset title: Global Profiling of Protein Lysine Malonylation In Goat
Possible reference: Yang, C. et al. (2025) Global profiling of protein lysine Malonylation during goat intramuscular Preadipocyte differentiation., J Proteomics, PMID 40812545

PXD059316 Dataset with its publication pending (from PRIDE)
Dataset title: Mavacamten inhibits myosin activity by stabilising the myosin interacting-heads motif and stalling motor force generation
Possible reference: McMillan, SN. et al. (2025) Mavacamten inhibits myosin activity by stabilising the myosin interacting-heads motif and stalling motor force generation., bioRxiv, PMID 39990378

PXD059301 Dataset with its publication pending (from iProX)
Dataset title: Targeting the ATM-TRMT10A-BRCA1 Axis Confers Synthetic Lethality to PARP Inhibition in Metastatic Castration-Resistant Prostate Cancer
Possible reference: Yang, Y. et al. (2025) Targeting the ATM-TRMT10A-BRCA1 axis confers synthetic lethality to PARP inhibition in metastatic castration-resistant prostate cancer., Sci Adv, PMID 41071892

PXD059299 Dataset with its publication pending (from iProX)
Dataset title: Plasma metabolome alterations in cardiac surgery-associated acute kidney injury
Possible reference: Bai, Y. et al. (2023) Metabolomic interplay between gut microbiome and plasma metabolome in cardiac surgery-associated acute kidney injury., Rapid Commun Mass Spectrom, PMID 36918294

PXD059280 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated Structural and Glycoproteomic Profiling Reveals Protein Conformational Remodeling and Biomarkers Across Alzheimer’s Disease Progression
Possible reference: Lu, H. et al. (2026) Integrated Structural and Glycoproteomic Profiling Reveals Protein Conformational Remodeling and Biomarkers Across Alzheimer's Disease Progression., ACS Cent Sci, PMID 41625220

PXD059272 Dataset with its publication pending (from jPOST)
Dataset title: Structural Insights into the Role of Eukaryotic Translation Initiation Factor 3 (eIF3) in Translation Mediated by the Hepatitis C Virus IRES
Possible reference: Cate, JH. et al. (2017) Human eIF3: from 'blobology' to biological insight., Philos Trans R Soc Lond B Biol Sci, PMID 28138064

PXD059269 no publication (from MassIVE)
Dataset title: Enhancing photosynthesis under salt stress via directed evolution in cyanobacteria
Possible reference: Jiang, Z. et al. (2025) Enhancing photosynthesis under salt stress via directed evolution in cyanobacteria., Plant Physiol, PMID 40397698

PXD059237 no publication (from MassIVE)
Dataset title: Multi-omic Signatures of Host Response Associated with Presence, Type, and Outcome of Enterococcal Bacteremia proteomics data
Possible reference: Bayne, C. et al. (2025) Multi-omic signatures of host response associated with presence, type, and outcome of enterococcal bacteremia., mSystems, PMID 39835799

PXD059234 Dataset with its publication pending (from iProX)
Dataset title: Analysis of O-glycans by oxidative release combined with 3-nitrophenylhydrazine derivatization
Possible reference: Min, Z. et al. (2025) Analysis of O-Glycans by Oxidative Release Combined with 3-Nitrophenylhydrazine Derivatization., ACS Omega, PMID 40256550

PXD059224 Dataset with its publication pending (from PanoramaPublic)
Dataset title: Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding
Possible reference: Feldman, D. et al. (2025) Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding., bioRxiv, PMID 40060547

PXD059214 Dataset with its publication pending (from jPOST)
Dataset title: The proteomic differences and expression of fatty acid-binding protein 6 (FABP6) associated with gastrointestinal injury in horses with oral administration of a clinical dose of phenylbutazone
Possible reference: Vinijkumthorn, R. et al. (2026) The proteomic differences and expression of fatty acid-binding protein 6 (FABP6) associated with gastrointestinal injury in horses with oral administration of a clinical dose of phenylbutazone., Equine Vet J, PMID 40405508

PXD059207 Dataset with its publication pending (from iProX)
Dataset title: Integrated analysis of proteome and transcriptome profiling reveals pan-cancer-associated pathways and molecular biomarkers
Possible reference: Hu, GS. et al. (2025) Integrated Analysis of Proteome and Transcriptome Profiling Reveals Pan-Cancer-Associated Pathways and Molecular Biomarkers., Mol Cell Proteomics, PMID 39884577

PXD059190 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics of cytokine-induced memory-like (CIML) NK cells
Possible reference: Carreira-Santos, S. et al. (2025) Phenotypic, proteomic, and functional analyses of cytokine-induced memory-like NK cells show two distinct subsets based on CD16 expression., Sci Rep, PMID 41131029

PXD059180 Dataset with its publication pending (from PRIDE)
Dataset title: Temporal photoproximity labeling of ligand-activated EGFR neighborhoods using MultiMap
Possible reference: Lin, Z. et al. (2026) Temporal photoproximity labeling of ligand-activated EGFR neighborhoods using MultiMap., Nat Chem Biol, PMID 41254216

PXD059172 Dataset with its publication pending (from PRIDE)
Dataset title: A Proteogenomic View of Synchronous Endometrioid Endometrial and Ovarian Cancer
Possible reference: Coscia, F. et al. (2025) A Proteogenomic View of Synchronous Endometrioid Endometrial and Ovarian Cancer., Clin Cancer Res, PMID 40145935

PXD059118 Dataset with its publication pending (from PRIDE)
Dataset title: Click-linking: a cell-compatible protein crosslinking method based on click chemistry
Possible reference: Amaral, BC. et al. (2025) Click-linking: a cell-compatible protein crosslinking method based on click chemistry., Nat Commun, PMID 41198667

PXD059111 no publication (from MassIVE)
Dataset title: Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics
Possible reference: Steger, M. et al. (2025) Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics., Nat Commun, PMID 40835825

PXD059092 Dataset with its publication pending (from PRIDE)
Dataset title: Temporal Proteomic Profiling of Pheromone-Induced Cell Cycle Re-Entry in Saccharomyces cerevisiae
Possible reference: Parmar, S. et al. (2025) Temporal Proteomic Profiling of Pheromone-Induced Cell Cycle Re-Entry in Saccharomyces cerevisiae., Proteomics, PMID 40259487

PXD059088 Dataset with its publication pending (from PRIDE)
Dataset title: TORC1 autonomously controls its spatial partitioning via the Rag GTPase tether Tco89
Possible reference: Nicastro, R. et al. (2025) TORC1 autonomously controls its spatial partitioning via the Rag GTPase tether Tco89., Cell Rep, PMID 40359108

PXD059083 Dataset with its publication pending (from PRIDE)
Dataset title: Meta-unstable mRNAs in activated CD8+ T cells are defined by interlinked AU-rich elements and m6A mRNA methylation
Possible reference: Gameiro, PA. et al. (2026) Meta-unstable mRNAs in activated CD8+ T cells are defined by interlinked AU-rich elements and m6A mRNA methylation., Nat Commun, PMID 41571642

PXD059029 Dataset with its publication pending (from jPOST)
Dataset title: Protein expression in warmed human lens epithelium cells using shotgun proteomics
Possible reference: Otake, H. et al. (2025) Changes in Protein Expression in Warmed Human Lens Epithelium Cells Using Shotgun Proteomics., Medicina (Kaunas), PMID 40005403

PXD059018 Dataset with its publication pending (from iProX)
Dataset title: YKT6 is essential for male fertility by stabilizing intercellular bridges in meiosis during spermatogenesis of mice
Possible reference: Cen, J. et al. (2026) YKT6 Is Essential for Male Fertility by Promoting Meiosis Progression During Spermatogenesis of Mice., Cell Prolif, PMID 40528727

PXD059010 Dataset with its publication pending (from PRIDE)
Dataset title: PLAA/UFD-3 regulates P-bodies through its intrinsic disordered domain
Possible reference: Das, A. et al. (2025) PLAA/UFD-3 regulates P-bodies through its intrinsic disordered domain., Proc Natl Acad Sci U S A, PMID 40560612

PXD059007 no publication (from MassIVE)
Dataset title: PHOSPHORYLATION-DEPENDENT ASSOCIATION OF WRN WITH RPA IS REQUIRED FOR RECOVERY OF REPLICATION FORKS STALLED AT SECONDARY DNA STRUCTURES
Possible reference: Noto, A. et al. (2023) PHOSPHORYLATION-DEPENDENT ASSOCIATION OF WRN WITH RPA IS REQUIRED FOR RECOVERY OF REPLICATION FORKS STALLED AT SECONDARY DNA STRUCTURES., bioRxiv, PMID 37609214

PXD058960 Dataset with its publication pending (from PRIDE)
Dataset title: Ontology-guided clustering enables proteomic analysis of rare pediatric disorders
Possible reference: Itang, ECM. et al. (2025) Ontology-guided clustering enables proteomic analysis of rare pediatric disorders., EMBO Mol Med, PMID 40425748

PXD058954 Dataset with its publication pending (from PRIDE)
Dataset title: PSKH1 kinase activity is differentially modulated via allosteric binding of Ca2+ sensor proteins
Possible reference: Horne, CR. et al. (2025) PSKH1 kinase activity is differentially modulated via allosteric binding of Ca2+ sensor proteins., Proc Natl Acad Sci U S A, PMID 39964718

PXD058951 Kegley, N. R., Ito, A., Williamson, D. B., McArdle, C. C., and Haltiwanger, R. S. Marfan syndrome variation of the POGLUT2 and POGLUT3 consensus sequence can produce aberrant fibrillin-1 O-glucosylation. Journal of Biological Chemistry (from PanoramaPublic)
Dataset title: Marfan syndrome variation of the POGLUT2 and POGLUT3 consensus sequence can produce aberrant fibrillin-1 O-glucosylation
Possible reference: Kegley, NR. et al. (2025) Marfan syndrome variation of the POGLUT2 and POGLUT3 consensus sequence can produce aberrant fibrillin-1 O-glucosylation., J Biol Chem, PMID 40107616

PXD058936 Dataset with its publication pending (from PRIDE)
Dataset title: DNA Damage in Macrophages Drives Immune Autoreactivity via Nuclear Antigen Presentation
Possible reference: Niotis, G. et al. (2026) DNA damage in macrophages drives immune autoreactivity via nuclear antigen presentation., Nat Aging, PMID 41540279

PXD058930 Dataset with its publication pending (from iProX)
Dataset title: Dissecting the anti-pancreatic cancer mechanism of gold nanorods mediate photothermal therapy through quantitative proteomics analysis
Possible reference: Sun, Z. et al. (2025) Dissecting the anti-pancreatic cancer mechanism of gold nanorods mediate photothermal therapy through quantitative proteomics analysis., Biochem Biophys Res Commun, PMID 39798534

PXD058917 no publication (from MassIVE)
Dataset title: Dynamic Expression of the Zebrafish (Danio rerio) Proteome Across Early Larval Development
Possible reference: Henke, AN. et al. (2025) Dynamic expression of the zebrafish (Danio rerio) proteome across early larval development., Comp Biochem Physiol Part D Genomics Proteomics, PMID 41092632

PXD058914 Dataset with its publication pending (from PRIDE)
Dataset title: TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination
Possible reference: Eickhoff, N. et al. (2025) TRIM33 loss reduces androgen receptor transcriptional output and H2BK120 ubiquitination., Commun Biol, PMID 40646276

PXD058884 Dataset with its publication pending (from iProX)
Dataset title: Chlamydomonas reinhardtii cc125 co-fractionation mass spectrometry (CF-MS) data
Possible reference: Yao, S. et al. (2025) Analysis of Protein-Protein Interactions in Chlamydomonas reinhardtii CC125 by Co-Fractionation Mass Spectrometry., J Proteome Res, PMID 40641464

PXD058862 no publication (from MassIVE)
Dataset title: Reproductive Adaptation of Astyanax mexicanus Under Nutrient Limitation
Possible reference: Xia, F. et al. (2025) Reproductive Adaptation of Astyanax mexicanus Under Nutrient Limitation., bioRxiv, PMID 40027826

PXD058858 Dataset with its publication pending (from PRIDE)
Dataset title: Serine ADP-ribosylation on histones and PARP1 is a cellular target for ester-linked ubiquitylation
Possible reference: Kolvenbach, A. et al. (2025) Serine ADPr on histones and PARP1 is a cellular target of ester-linked ubiquitylation., Nat Chem Biol, PMID 40634527

PXD058845 Dataset with its publication pending (from PRIDE)
Dataset title: The SPFH complex HflK-HflC regulates aerobic respiration in bacteria
Possible reference: P�rez-L�pez, MI. et al. (2025) The SPFH complex HflK-HflC regulates aerobic respiration in bacteria., PLoS Biol, PMID 40193326

PXD058811 Dataset with its publication pending (from PRIDE)
Dataset title: BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1
Possible reference: Monziani, A. et al. (2025) BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1., Nucleic Acids Res, PMID 40682820

PXD058810 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of Tie2 as a sensor for reactive oxygen species and its therapeutic implication
Possible reference: Pham, AVQ. et al. (2025) Identification of Tie2 as a sensor for reactive oxygen species and its therapeutic implication., Redox Biol, PMID 39993340

PXD058807 Dataset with its publication pending (from PRIDE)
Dataset title: Early innate immune response and evolution of a SARS-CoV-2 furin cleavage site inactive variant in bat cells
Possible reference: Baid, K. et al. (2025) Early innate immune response and evolution of a SARS-CoV-2 furin cleavage site inactive variant in bat cells., Cell Rep, PMID 40608518

PXD058804 Dataset with its publication pending (from jPOST)
Dataset title: Development of non-targeted proteome analysis of dried blood spots using an automated protein extraction system
Possible reference: Nakajima, D. et al. (2025) Toward the Development of a Novel Newborn Screening Modality: In-Depth Nontargeted Proteome Analysis of Dried Blood Spots with a Robotic Pipeline Using Low-Cost Iron Powders., Anal Chem, PMID 40790917

PXD058795 Dataset with its publication pending (from iProX)
Dataset title: The Impact of Lysine Succinylation Modifications of Hfq Protein at K56 site on the Biological Functions of Aeromonas hydrophila
Possible reference: Lian, L. et al. (2025) The impact of lysine succinylation modification of host factor for RNA phage Qβ replicase at K56 site on the biological functions of Aeromonas hydrophila., Int J Biol Macromol, PMID 40239779

PXD058793 Dataset with its publication pending (from PRIDE)
Dataset title: RNA N6-Methyladenosine (m6A) regulates cell cycle progression in Diffuse Midline Glioma (DMG) and confers sensitivity to FTO inhibition
Possible reference: Ross, SE. et al. (2026) RNA N6-methyladenosine (m6A) regulates cell cycle progression in diffuse midline glioma (DMG) and confers sensitivity to FTO inhibition., Cell Death Dis, PMID 41888518

PXD058788 no publication (from MassIVE)
Dataset title: A ubiquitin ligase protects lysosomes from CLN4 mutant-induced membrane damages
Possible reference: Lee, J. et al. (2025) CHIP protects lysosomes from CLN4 mutant-induced membrane damages., bioRxiv, PMID 40027688

PXD058775 Dataset with its publication pending (from PRIDE)
Dataset title: DNA Damage in Macrophages Drives Immune Autoreactivity via Nuclear Antigen Presentation
Possible reference: Niotis, G. et al. (2026) DNA damage in macrophages drives immune autoreactivity via nuclear antigen presentation., Nat Aging, PMID 41540279

PXD058768 Dataset with its publication pending (from PRIDE)
Dataset title: Integrating Protein Language Models and Automatic Biofoundry for Enhanced Protein Evolution
Possible reference: Zhang, Q. et al. (2025) Integrating protein language models and automatic biofoundry for enhanced protein evolution., Nat Commun, PMID 39934638

PXD058752 Dataset with its publication pending (from PRIDE)
Dataset title: Impact of Tau Overexpression on DNA Replication Dynamics in Centromeres of Human Neural Progenitor Cells
Possible reference: Balzano, E. et al. (2026) Impact of Tau overexpression on DNA replication dynamics in centromeres of human neural progenitor cells., iScience, PMID 41660240

PXD058750 no publication (from MassIVE)
Dataset title: Structural and Functional Insights into the Evolution of SARS-CoV-2 KP.3.1.1 Spike Protein
Possible reference: Feng, Z. et al. (2024) Structural and Functional Insights into the Evolution of SARS-CoV-2 KP.3.1.1 Spike Protein., bioRxiv, PMID 39713475

PXD058728 Dataset with its publication pending (from PRIDE)
Dataset title: Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies
Possible reference: K�ry, S. et al. (2024) Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies., medRxiv, PMID 38293138

PXD058725 no publication (from MassIVE)
Dataset title: Embedding a ribonuclease in the spore crust couples gene expression to spore development in Bacillus subtilis
Possible reference: D'Halluin, A. et al. (2025) Embedding a ribonuclease in the spore crust couples gene expression to spore development in Bacillus subtilis., Nucleic Acids Res, PMID 39817517

PXD058713 Dataset with its publication pending (from iProX)
Dataset title: Model of rat rhabdomyolysis-induced acute kidney injury Proteomics
Possible reference: Zhang, Y. et al. (2024) Proteomic analysis of multiple organ dysfunction induced by rhabdomyolysis., J Proteomics, PMID 38403185

PXD058711 Dataset with its publication pending (from iProX)
Dataset title: Î±-1,2 glycosyltransferase plays an essential role in maintaining leaf margin shape in kale
Possible reference: Feng, X. et al. (2022) BoALG10, an α-1,2 glycosyltransferase, plays an essential role in maintaining leaf margin shape in ornamental kale., Hortic Res, PMID 36072832

PXD058709 Dataset with its publication pending (from PRIDE)
Dataset title: PP2A-B56alpha is a key determinant of cardiac protein phosphorylation and functional responses to beta-adrenergic signalling
Possible reference: Güran, A. et al. (2025) PP2A-B56α is a key determinant of cardiac protein phosphorylation and functional responses to β-adrenergic signalling., J Mol Cell Cardiol Plus, PMID 40485773

PXD058703 no publication (from MassIVE)
Dataset title: In-depth Characterization of S-Glutathionylation of Ventricular Myosin Light Chain 1 Across Species by Top-Down Proteomics
Possible reference: Chapman, EA. et al. (2024) In-depth Characterization of S-Glutathionylation in Ventricular Myosin Light Chain 1 Across Species by Top-Down Proteomics., bioRxiv, PMID 39713419

PXD058669 Dataset with its publication pending (from jPOST)
Dataset title: Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation
Possible reference: Kubinski, HC. et al. (2024) Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation., bioRxiv, PMID 38559000

PXD058668 Dataset with its publication pending (from PRIDE)
Dataset title: A subcellular map of translational machinery composition and regulation at the single-molecule level
Possible reference: Zhang, Z. et al. (2025) A subcellular map of translational machinery composition and regulation at the single-molecule level., Science, PMID 40048539

PXD058656 Dataset with its publication pending (from PRIDE)
Dataset title: A BAG-1-inhibitory peptide, GO-Pep, suppresses c-Raf activity in cancer
Possible reference: Tatli, O. et al. (2025) A BAG-1-inhibitory peptide, GO-Pep, suppresses c-Raf activity in cancer., Commun Biol, PMID 40021821

PXD058631 Dataset with its publication pending (from iProX)
Dataset title: Pre-established ATF4 occupancy and chromatin organization instruct selective transcription activation during integrated stress response
Possible reference: Jiang, P. et al. (2025) Pre-established ATF4 occupancy and chromatin organization instruct selective transcription activation during integrated stress response., Nat Commun, PMID 41152234

PXD058629 Dataset with its publication pending (from PRIDE)
Dataset title: Pervasive divergence in protein thermostability is mediated by both structural changes and cellular environments
Possible reference: Walunjkar, N. et al. (2025) Pervasive Divergence in Protein Thermostability is Mediated by Both Structural Changes and Cellular Environments., Mol Biol Evol, PMID 40476605

PXD058602 Dataset with its publication pending (from iProX)
Dataset title: ERK- and USP9X-coupled regulation of thymidine kinase 1 promotes both its enzyme activity-dependent and enzyme activity-independent functions for tumor growth
Possible reference: Tao, J. et al. (2025) ERK-USP9X-coupled regulation of thymidine kinase 1 promotes both its enzyme activity-dependent and its enzyme activity-independent functions for tumor growth., Nat Struct Mol Biol, PMID 39824978

PXD058591 no publication (from MassIVE)
Dataset title: SPE-CZE-MS Quantifies Zeptomole Amounts of Phosphorylated Peptides
Possible reference: Serrano, LR. et al. (2025) SPE-CZE-MS Quantifies Zeptomole Amounts of Phosphorylated Peptides., J Proteome Res, PMID 40293921

PXD058588 Dataset with its publication pending (from PRIDE)
Dataset title: Wolbachia-mediated reduction in the glutamate receptor mGluR promotes female promiscuity and bacterial spread
Possible reference: Warecki, B. et al. (2025) Wolbachia-mediated reduction in the glutamate receptor mGluR promotes female promiscuity and bacterial spread., Cell Rep, PMID 40347951

PXD058571 Dataset with its publication pending (from PRIDE)
Dataset title: The SPFH complex HflK-HflC regulates aerobic respiration in bacteria
Possible reference: P�rez-L�pez, MI. et al. (2025) The SPFH complex HflK-HflC regulates aerobic respiration in bacteria., PLoS Biol, PMID 40193326

PXD058557 Dataset with its publication pending (from iProX)
Dataset title: Yellow catfish brain exposure to hypoxia
Possible reference: Pei, X. et al. (2021) Effects of acute hypoxia and reoxygenation on oxygen sensors, respiratory metabolism, oxidative stress, and apoptosis in hybrid yellow catfish "Huangyou-1"., Fish Physiol Biochem, PMID 34313912

PXD058556 Dataset with its publication pending (from iProX)
Dataset title: The maternal vitamin D level regulates the metabolic rearrangement of offspring-CD4+ T cells in response to intestinal inflammation
Possible reference: Zhu, B. et al. (2025) Maternal vitamin D regulates the metabolic rearrangement of offspring CD4+ T cells in response to intestinal inflammation., Cell Rep, PMID 40512616

PXD058554 Dataset with its publication pending (from iProX)
Dataset title: Proteomic profiling of serum-derived extracellular vesicles in diffuse idiopathic skeletal hyperostosis patients
Possible reference: Zhou, H. et al. (2025) Proteomic Profiling of Serum-Derived Extracellular Vesicles in Diffuse Idiopathic Skeletal Hyperostosis Patients., J Proteome Res, PMID 40387066

PXD058545 Dataset with its publication pending (from PRIDE)
Dataset title: GRK-biased adrenergic agonists for the treatment of type II diabetes and obesity
Possible reference: Motso, A. et al. (2025) GRK-biased adrenergic agonists for the treatment of type 2 diabetes and obesity., Cell, PMID 40555230

PXD058541 Dataset with its publication pending (from PRIDE)
Dataset title: The phosphoproteomics study of Chk1 and ATR inhibitors regulation on cells
Possible reference: Cheng, AN. et al. (2017) Cdc7-Dbf4-mediated phosphorylation of HSP90-S164 stabilizes HSP90-HCLK2-MRN complex to enhance ATR/ATM signaling that overcomes replication stress in cancer., Sci Rep, PMID 29209046

PXD058540 Dataset with its publication pending (from PRIDE)
Dataset title: BRD9 functions as a methylarginine reader to regulate AKT-EZH2 signaling
Possible reference: Yin, S. et al. (2025) BRD9 functions as a methylarginine reader to regulate AKT-EZH2 signaling., Sci Adv, PMID 40279411

PXD058535 Dataset with its publication pending (from PRIDE)
Dataset title: Ubiquitination proteome profiling of Candida albicans
Possible reference: Sandai, D. et al. (2012) The evolutionary rewiring of ubiquitination targets has reprogrammed the regulation of carbon assimilation in the pathogenic yeast Candida albicans., mBio, PMID 23232717

PXD058534 Dataset with its publication pending (from PRIDE)
Dataset title: The lactylome data of renal tubular epithelial cells
Possible reference: Chen, J. et al. (2024) ACSF2 and lysine lactylation contribute to renal tubule injury in diabetes., Diabetologia, PMID 38676722

PXD058530 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Analysis of Kidney Tissues Following Ischemia-Reperfusion Injury in Male Mice
Possible reference: Song, T. et al. (2018) miR-17-92 ameliorates renal ischemia reperfusion injury., Kaohsiung J Med Sci, PMID 29699633

PXD058477 no publication (from MassIVE)
Dataset title: Urolithin A protects hepatocytes from palmitic acid-induced ER stress by regulating calcium homeostasis in the MAM
Possible reference: Ryu, G. et al. (2024) Urolithin A Protects Hepatocytes from Palmitic Acid-Induced ER Stress by Regulating Calcium Homeostasis in the MAM., Biomolecules, PMID 39766212

PXD058458 Dataset with its publication pending (from iProX)
Dataset title: IEC-TMT for pTyr protein complex analysis
Possible reference: Liu, W. et al. (2024) Unraveling of Phosphotyrosine Signaling Complexes Associated with T Cell Exhaustion Using Multiplex Co-Fractionation/Mass Spectrometry., Anal Chem, PMID 39661755

PXD058454 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of Escherichia coli Nissle 1917 derived outer membrane vesicles (EcN-derived OMVs) and the EcN-derived OMVs of three specific sizes
Possible reference: Li, N. et al. (2025) Separation and Characterization of Heterogeneity Among Various Sizes of Outer Membrane Vesicles Derived from the Probiotic Escherichia coli Nissle 1917., Membranes (Basel), PMID 40422751

PXD058451 Dataset with its publication pending (from iProX)
Dataset title: Mitochondrial ROS triggers mitophagy through activating DNA damage response signaling pathway
Possible reference: Guo, QQ. et al. (2025) Mitochondrial ROS triggers mitophagy through activating the DNA damage response signaling pathway., Proc Natl Acad Sci U S A, PMID 41026812

PXD058427 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics of infected macrophages reveals novel Leishmania virulence factors
Possible reference: Hagedorn, N. et al. (2026) Quantitative proteomics of infected macrophages reveals novel Leishmania virulence factors., PLoS Pathog, PMID 41666232

PXD058398 Dataset with its publication pending (from iProX)
Dataset title: Modulation of Ferroptosis via YY1-SLC7A11 Axis in Hepatic Ischemia-Reperfusion Injury Pathogenesis
Possible reference: Wang, S. et al. (2025) Modulation of ferroptosis via YY1-SLC7A11 axis in hepatic ischemia-reperfusion injury pathogenesis., Acta Biochim Biophys Sin (Shanghai), PMID 40589411

PXD058385 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Profiling Reveals Differentially Expressed Proteins in TAMs
Possible reference: Yang, Y. et al. (2014) CDK2 and CDK4 play important roles in promoting the proliferation of SKOV3 ovarian carcinoma cells induced by tumor-associated macrophages., Oncol Rep, PMID 24700371

PXD058384 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of phosphatases that dephosphorylate Tom6 using synthetic trap-peptides
Possible reference: Scheinost, L. et al. (2026) Synthetic trap-peptides identify a TOM complex phosphatase - PP2A dephosphorylates Tom6., FEBS J, PMID 40891445

PXD058381 Dataset with its publication pending (from PRIDE)
Dataset title: Typhoid toxin of Salmonella Typhi elicits host antimicrobial response during acute typhoid fever
Possible reference: Srour, S. et al. (2026) Typhoid toxin of Salmonella Typhi elicits host antimicrobial response during acute typhoid fever., EMBO Mol Med, PMID 41326716

PXD058359 Dataset with its publication pending (from iProX)
Dataset title: System-wide discovery of functional protein modifications by Refined-TPP
Possible reference: Wang, G. et al. (2025) A Chemoproteomic Approach for System-Wide and Site-Specific Uncovering of Functional Protein N-Glycosylation., J Am Chem Soc, PMID 40574371

PXD058358 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of enriched fungal proteins during hydrolysis of polyurethane and polyethylene terephthalate by Fusarium vanettenii
Possible reference: Okal, EJ. et al. (2025) Elucidation of the biodegradation pathways of polyurethane and polyethylene terephthalate by a Fusarium strain enriched from soil-plant systems., Bioresour Technol, PMID 40848955

PXD058342 Dataset with its publication pending (from PRIDE)
Dataset title: The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma’s information flow
Possible reference: Zhong, Z. et al. (2025) The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma's information flow., Genome Biol, PMID 41024265

PXD058327 Dataset with its publication pending (from PRIDE)
Dataset title: The PRC1 and PRC2 proximal interactome
Possible reference: Zijlmans, DW. et al. (2025) PRC1 and PRC2 proximal interactome in mouse embryonic stem cells., Cell Rep, PMID 40053453

PXD058286 Dataset with its publication pending (from PRIDE)
Dataset title: The Histone Acetyltransferase MOZ is a Molecular Dependency and Therapeutic Target in NUP98-Rearranged Acute Myeloid Leukemia
Possible reference: Michmerhuizen, NL. et al. (2025) KAT6A and KAT7 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia., Cancer Discov, PMID 40536430

PXD058268 Dataset with its publication pending (from jPOST)
Dataset title: Synergistic enhancement of anticancer effects by periodontal ligament stem cell exosomes and oxaliplatin via apoptosis induction and protein modulation
Possible reference: Ngamkham, J. et al. (2025) Synergistic enhancement of anticancer effects by periodontal ligament stem cell exosomes and oxaliplatin via apoptosis induction and protein modulation., Biomed Pharmacother, PMID 40834748

PXD058247 Dataset with its publication pending (from PRIDE)
Dataset title: Chronic inflammation drives epididymal tertiary lymphoid structure formation and autoimmune fertility disorders
Possible reference: Elizagaray, ML. et al. (2024) Chronic inflammation drives epididymal tertiary lymphoid structure formation and autoimmune fertility disorders., bioRxiv, PMID 39605691

PXD058245 Dataset with its publication pending (from PRIDE)
Dataset title: p53 isoforms have a high aggregation propensity, interact with chaperones and lack binding to p53 interaction partners
Possible reference: Brdar, A. et al. (2025) p53 isoforms have a high aggregation propensity, interact with chaperones and lack binding to p53 interaction partners., Elife, PMID 40928972

PXD058242 no publication (from MassIVE)
Dataset title: Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines
Possible reference: Gonz�lez, A. et al. (2025) Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines., Sci Data, PMID 40885748

PXD058239 Dataset with its publication pending (from PRIDE)
Dataset title: Ependymoma instructs cranial haematopoiesis and immunotolerance
Possible reference: Cooper, E. et al. (2026) Childhood brain tumors instruct cranial hematopoiesis and immunotolerance., Nat Genet, PMID 41634415

PXD058227 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of EcpK, a bacterial tyrosine pseudokinase important for exopolysaccharide biosynthesis in Myxococcus xanthus
Possible reference: Bl�cher, L. et al. (2025) Identification of EcpK, a bacterial tyrosine pseudokinase important for exopolysaccharide biosynthesis in Myxococcus xanthus., J Bacteriol, PMID 40067014

PXD058218 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic and phosphoproteomic analyses for HT-29
Possible reference: Abe, Y. et al. (2017) Deep Phospho- and Phosphotyrosine Proteomics Identified Active Kinases and Phosphorylation Networks in Colorectal Cancer Cell Lines Resistant to Cetuximab., Sci Rep, PMID 28874695

PXD058212 Dataset with its publication pending (from iProX)
Dataset title: Expression data of IgG antibodies based on the SARS-CoV-2 proteome
Possible reference: Curtis, NC. et al. (2023) Characterization of SARS-CoV-2 Convalescent Patients' Serological Repertoire Reveals High Prevalence of Iso-RBD Antibodies., bioRxiv, PMID 37745524

PXD058209 Dataset with its publication pending (from iProX)
Dataset title: Paricalcitol and hydroxychloroquine modulates extracellular matrix and enhance chemotherapy efficacy in pancreatic cancer
Possible reference: El-Rayes, B. et al. (2025) Paricalcitol and hydroxychloroquine modulates extracellular matrix and enhance chemotherapy efficacy in pancreatic cancer., Res Sq, PMID 40386428

PXD058206 Dataset with its publication pending (from iProX)
Dataset title: Rab32 is a key protein for controlling bacterial infections
Possible reference: Li, Y. et al. (2016) Analysis of the Rab GTPase Interactome in Dendritic Cells Reveals Anti-microbial Functions of the Rab32 Complex in Bacterial Containment., Immunity, PMID 26885862

PXD058204 Dataset with its publication pending (from iProX)
Dataset title: Integrating multi-omics to reveal and validate key proteins, metabolites, and pathways of ASB14 affecting mitochondrial function in cardiomyocytes AC16
Possible reference: Wang, C. et al. (2025) Integrating Multiomics to Reveal and Validate Key Proteins, Metabolites, and Pathways of ASB14 Affecting Mitochondrial Function in Cardiomyocytes AC16., FASEB J, PMID 40417864

PXD058197 Dataset with its publication pending (from PRIDE)
Dataset title: Structural dynamics and immunogenicity of the recombinant and outer membrane vesicle-embedded Meningococcal antigen NadA
Possible reference: Calvaresi, V. et al. (2026) Structural dynamics and immunogenicity of the recombinant and outer membrane vesicle-embedded Meningococcal antigen NadA., Nat Commun, PMID 41807399

PXD058194 Dataset with its publication pending (from PRIDE)
Dataset title: The adaptor protein AP-3Î² disassembles heat-induced stress granules via 19S RP-associated deubiquitylation in Arabidopsis
Possible reference: Pang, L. et al. (2025) The adaptor protein AP-3β disassembles heat-induced stress granules via 19S regulatory particle in Arabidopsis., Nat Commun, PMID 40016204

PXD058168 Dataset with its publication pending (from PRIDE)
Dataset title: DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts
Possible reference: Kuś, K. et al. (2025) DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts., Nat Commun, PMID 39746995

PXD058157 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis reveals changes in protein expression in oocytes at different meiosis stages
Possible reference: Shen, X. et al. (2021) Quantitative proteomic analysis of chicken serum reveals key proteins affecting follicle development during reproductive phase transitions., Poult Sci, PMID 33357697

PXD058152 no publication (from MassIVE)
Dataset title: Mitochondrial Calcium Signaling Regulates Branched-Chain Amino Acid Catabolism in Fibrolamellar Carcinoma
Possible reference: Marsh, NM. et al. (2024) Mitochondrial Calcium Signaling Regulates Branched-Chain Amino Acid Catabolism in Fibrolamellar Carcinoma., bioRxiv, PMID 38853984

PXD058151 no publication (from MassIVE)
Dataset title: Mechanosensor-mediated Hsp70 phosphorylation orchestrates the landscape of the heat shock response
Possible reference: Omkar, S. et al. (2025) Mechanosensor-mediated Hsp70 phosphorylation orchestrates the landscape of the heat shock response., Nat Commun, PMID 41390490

PXD058150 Dataset with its publication pending (from PRIDE)
Dataset title: Putative PINK1/Parkin activators cause mitochondrial stress and lower the threshold for mitophagy
Possible reference: Rosencrans, WM. et al. (2025) Putative PINK1/Parkin activators lower the threshold for mitophagy by sensitizing cells to mitochondrial stress., Sci Adv, PMID 40864725

PXD058137 no publication (from MassIVE)
Dataset title: Ontogeny independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis
Possible reference: Dey, S. et al. (2026) Ontogeny independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis., Commun Biol, PMID 41862629

PXD058134 Dataset with its publication pending (from PRIDE)
Dataset title: Rank signaling drives basal cell-lineage infidelity leading to mammary tumorigenesis
Possible reference: Redondo-Pedraza, J. et al. (2026) Rank signaling drives basal cell-lineage infidelity leading to mammary tumorigenesis., Nat Commun, PMID 41760656

PXD058127 no publication (from MassIVE)
Dataset title: Polystyrene Microplastics effects on human gingival fibroblasts
Possible reference: Di Cintio, F. et al. (2025) Polystyrene microplastics are internalized by human gingival fibroblasts, enhance cell motility and induce molecular changes revealed through proteomic analysis., Sci Rep, PMID 41062560

PXD058112 Dataset with its publication pending (from iProX)
Dataset title: Flutamide untargeted metabolomics data
Possible reference: Yamazaki, M. et al. (2013) Perturbation of bile acid homeostasis is an early pathogenesis event of drug induced liver injury in rats., Toxicol Appl Pharmacol, PMID 23360887

PXD058111 Dataset with its publication pending (from iProX)
Dataset title: Molecular insights into oocyte development and sperm storage in black rockfish (Sebastes schlegelii): proteomic changes across reproductive stages
Possible reference: Chen, Y. et al. (2025) Molecular insights into oocyte development and sperm storage in black rockfish (Sebastes schlegelii): Proteomic changes across reproductive stages., Comp Biochem Physiol Part D Genomics Proteomics, PMID 39612540

PXD058023 Dataset with its publication pending (from PRIDE)
Dataset title: Protein lactylation promotes AKI–CKD transition in mice
Possible reference: Yu, F. et al. (2025) Protein lactylation of citrate synthase promotes the AKI-CKD transition by activating the NLRP3 inflammasome., Cell Rep, PMID 40748753

PXD058017 Dataset with its publication pending (from iProX)
Dataset title: E2-Ub-R74G strategy reveals E2-specific ubiquitin conjugation profiles in live cells
Possible reference: Shen, S. et al. (2025) E2-Ub-R74G strategy reveals E2-specific ubiquitin conjugation profiles in live cells., Nat Chem Biol, PMID 39762535

PXD058010 no publication (from MassIVE)
Dataset title: TYMS expression regulates AMPK-mTOR signaling in pancreatic neuroendocrine tumors
Possible reference: Vijayakurup, V. et al. (2025) Integrated proteomic analysis identifies TYMS-dependent AMPK-mTOR signaling in pancreatic neuroendocrine tumors., iScience, PMID 41362763

PXD058003 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative single-cell and spatial transcriptomics illuminate bat immunity and barrier tissue evolution
Possible reference: Levinger, R. et al. (2025) Single-cell and Spatial Transcriptomics Illuminate Bat Immunity and Barrier Tissue Evolution., Mol Biol Evol, PMID 39836373

PXD057997 no publication (from MassIVE)
Dataset title: Schistosomiasis Metabolites Mining by SPME Dataset
Possible reference: Tawana-Ndolo, SM. et al. (2025) MS-DIAL pre-processing for mining schistosomiasis metabolites in urine samples from the Okavango Delta of Botswana from a GC-MS dataset., Bioanalysis, PMID 41170651

PXD057969 Dataset with its publication pending (from PRIDE)
Dataset title: KDM3A catalysed formation of hydroxyacetyl-lysine on histone H3K9
Possible reference: Belle, R. et al. (2026) KDM3A catalyses the oxidation of acetyl-lysine to hydroxyacetyl-lysine on histone H3K9., Nat Chem, PMID 41986689

PXD057961 Dataset with its publication pending (from PRIDE)
Dataset title: Angiostrongylus cantonensis extracellular vesicles (EVs) proteomes
Possible reference: Cheng, C-J. et al. (2025) Extracellular vesicles from fifth-stage larval Angiostrongylus cantonensis upregulate cholesterol biosynthesis and suppress NLRP2-associated inflammatory responses in mouse astrocytes., mSystems, PMID 39636121

PXD057955 no publication (from MassIVE)
Dataset title: Global Protein-Ligand Binding Affinity Profiling via Photocatalytic Labeling
Possible reference: Warren, CD. et al. (2025) Global Protein-Ligand Binding Affinity Profiling via Photocatalytic Labeling., bioRxiv, PMID 40631297

PXD057949 no publication (from MassIVE)
Dataset title: MEF2A, MEF2C, and MEF2D Interactomes in Mouse MA-10 Leydig Cells
Possible reference: de Mattos, K. et al. (2025) Identification of MEF2A, MEF2C, and MEF2D interactomes in basal and Fsk-stimulated mouse MA-10 Leydig cells., Andrology, PMID 40277654

PXD057934 no publication (from MassIVE)
Dataset title: Distinct Gene Regulatory Dynamics Drive Skeletogenic Cell Fate Convergence During Vertebrate Embryogenesis
Possible reference: Wang, M. et al. (2025) Distinct gene regulatory dynamics drive skeletogenic cell fate convergence during vertebrate embryogenesis., Nat Commun, PMID 40038298

PXD057927 Dataset with its publication pending (from iProX)
Dataset title: IMPDH2 dephosphorylation mediated by PPP2R1A promotes S-phase progression
Possible reference: Zhou, B. et al. (2025) IMPDH2 dephosphorylation under FGFR signaling promotes S-phase progression and tumor growth., Cell Rep, PMID 39739531

PXD057926 Dataset with its publication pending (from PRIDE)
Dataset title: The epigenetic reader Phf2 is positioned in the genome by cohesin
Possible reference: Tang, W. et al. (2025) Cohesin positions the epigenetic reader Phf2 within the genome., EMBO J, PMID 39748119

PXD057906 Dataset with its publication pending (from PRIDE)
Dataset title: Stress granule phase separation in stress-responsive cytosolic extract-in-oil droplets
Possible reference: Lieber, A. et al. (2026) Stress granule phase separation in stress-responsive cytosolic extract-in-oil droplets., Nat Commun, PMID 42248842

PXD057902 Dataset with its publication pending (from PRIDE)
Dataset title: Test HDX experiment on cytochrome C
Possible reference: Donohoe, GC. et al. (2015) Ion mobility spectrometry-hydrogen deuterium exchange mass spectrometry of anions: part 1. Peptides to proteins., J Am Soc Mass Spectrom, PMID 25510931

PXD057898 Dataset with its publication pending (from PRIDE)
Dataset title: PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites
Possible reference: Dimond, A. et al. (2025) PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites., Nat Commun, PMID 40987773

PXD057894 Dataset with its publication pending (from PRIDE)
Dataset title: PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites
Possible reference: Dimond, A. et al. (2025) PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites., Nat Commun, PMID 40987773

PXD057873 Dataset with its publication pending (from iProX)
Dataset title: Shigella infection is facilitated by interaction of human enteric Î±-defensin 5 with colonic epithelial receptor P2Y11
Possible reference: Xu, D. et al. (2025) Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11., Nat Microbiol, PMID 39901059

PXD057858 no publication (from MassIVE)
Dataset title: HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy
Possible reference: Jiang, Q. et al. (2025) HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy., Cell, PMID 40023154

PXD057852 no publication (from MassIVE)
Dataset title: Characterization of site-specific O- and N-glycopeptides from recombinant spike and ACE2 glycoproteins using LC-MS/MS analysis
Possible reference: Song, JH. et al. (2024) Characterization of Site-Specific N- and O-Glycopeptides from Recombinant Spike and ACE2 Glycoproteins Using LC-MS/MS Analysis., Int J Mol Sci, PMID 39769415

PXD057850 no publication (from MassIVE)
Dataset title: Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms
Possible reference: Frankenfield, AM. et al. (2025) Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms., Mol Cell Proteomics, PMID 40315959

PXD057839 Dataset with its publication pending (from PRIDE)
Dataset title: Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells
Possible reference: Kowar, A. et al. (2025) Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells., Nat Commun, PMID 40866359

PXD057837 Dataset with its publication pending (from jPOST)
Dataset title: Salt stress activates CDK8-AHL10-SUVH2/9 module to dynamically regulate salt tolerance in Arabidopsis
Possible reference: Guo, P. et al. (2025) Salt stress activates the CDK8-AHL10-SUVH2/9 module to dynamically regulate salt tolerance in Arabidopsis., Nat Commun, PMID 40074748

PXD057820 Dataset with its publication pending (from iProX)
Dataset title: Proteomic and Acetylation Profiling of Stemness Induced by Soft Matrix in Breast Cancer Repopulating Cells
Possible reference: Han, R. et al. (2025) Dynamic Proteomic and Acetylomic Profiling of Mechanically Induced Cancer Stemness in Breast Cancer Cells., Proteomics, PMID 39981796

PXD057817 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of meninges from autoimmune encephalitis (mouse model)
Possible reference: Lesec, L. et al. (2024) Specific and Polyfunctional T Cell Response Against N-Methyl-d-aspartate Receptor in an Autoantibody-Mediated Encephalitis Model., Biomedicines, PMID 39595024

PXD057814 no publication (from MassIVE)
Dataset title: Plasma proteomics for novel biomarker discovery in childhood tuberculosis
Possible reference: Fossati, A. et al. (2025) Plasma proteomics for novel biomarker discovery in childhood tuberculosis., medRxiv, PMID 39677468

PXD057797 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanisms of recalcitrant fucoidan breakdown in marine Planctomycetota
Possible reference: P�rez-Cruz, C. et al. (2024) Mechanisms of recalcitrant fucoidan breakdown in marine Planctomycetota., Nat Commun, PMID 39738071

PXD057796 no publication (from MassIVE)
Dataset title: Rare SNP in the HELB gene interferes with RPA interaction and cellular function of HELB
Possible reference: Osei, B. et al. (2024) Rare SNP in the HELB gene interferes with RPA interaction and cellular function of HELB., bioRxiv, PMID 38464108

PXD057785 no publication (from MassIVE)
Dataset title: M1-linked Ubiquitination by LUBAC Regulates AMPK Activity and the Response to Energetic Stress
Possible reference: Elb�k, CR. et al. (2026) M1-linked ubiquitination by LUBAC regulates AMPK signalling and the response to energetic stress., Cell Death Differ, PMID 41688728

PXD057767 Dataset with its publication pending (from iProX)
Dataset title: Nascent proteomics profiling reveals NNMT as a regulator to promote drug resistance in lung cancer
Possible reference: Hou, Z. et al. (2026) Nicotinamide N-methyltransferase promotes drug resistance in lung cancer, as revealed by nascent proteomic profiling., Mol Oncol, PMID 40679940

PXD057757 no publication (from MassIVE)
Dataset title: diaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling
Possible reference: Woods, K. et al. (2024) diaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling., bioRxiv, PMID 39605566

PXD057743 Dataset with its publication pending (from PRIDE)
Dataset title: FGF13 in septic lung injury: A regulator of the ERK/aerobic glycolysis axis in the inflammatory state
Possible reference: Zhu, J. et al. (2026) FGF 13 functions as a regulator of the ERK/aerobic glycolysis axis in the inflammatory state during septic lung injury., Nat Commun, PMID 41644549

PXD057732 Dataset with its publication pending (from iProX)
Dataset title: Proteomic and phosphoproteomic analyses reveal the biological perturbations caused by capsaicin
Possible reference: Li, Z. et al. (2025) Proteomic and phosphoproteomic analyses reveal the biological perturbations caused by capsaicin treatment., Food Res Int, PMID 40022394

PXD057722 Dataset with its publication pending (from iProX)
Dataset title: Effects of obesity on kidney complications in mice and precise prevention and treatment
Possible reference: Larkin, BP. et al. (2022) Low-dose hydralazine reduces albuminuria and glomerulosclerosis in a mouse model of obesity-related chronic kidney disease., Diabetes Obes Metab, PMID 35635331

PXD057716 Dataset with its publication pending (from iProX)
Dataset title: Clec16a Regulates the Emergence of Hematopoietic Stem and Progenitor Cells via Mitophagy in Zebrafish
Possible reference: Cai, S. et al. (2026) Clec16a maintains definitive hematopoietic stem and progenitor cells via mitophagy., Cell Rep, PMID 41719124

PXD057710 Dataset with its publication pending (from PRIDE)
Dataset title: Fine-tuning regulation of (p)ppGpp-driven outer membrane vesicle formation in Acinetobacter baumannii
Possible reference: Han, S. et al. (2025) Fine-tuning regulation of (p)ppGpp-driven outer membrane vesicle formation in Acinetobacter baumannii., FEBS J, PMID 40172085

PXD057707 Dataset with its publication pending (from PRIDE)
Dataset title: AMPylation Regulates 5'-3' Exonuclease PLD3 processing
Possible reference: Hoffmann, L. et al. (2025) AMPylation Regulates 5'-3' Exonuclease PLD3 Processing., Mol Cell Proteomics, PMID 40816421

PXD057657 no publication (from MassIVE)
Dataset title: MGAT3 and MGAT5 overexpression alters the protein cargo of extracellular vesicles released by metastatic melanoma cells
Possible reference: Wilczak, M. et al. (2025) MGAT3 and MGAT5 overexpression alters the protein cargo of extracellular vesicles released by metastatic melanoma cells., Biochem Biophys Res Commun, PMID 40199132

PXD057656 Dataset with its publication pending (from PRIDE)
Dataset title: Caspase-8’s non-apoptotic role is critical for orchestrating exaggerated inflammation during severe SARS-CoV-2 infection.
Possible reference: M Bader, S. et al. (2025) Non-apoptotic caspase-8 is critical for orchestrating exaggerated inflammation during severe SARS-CoV-2 infection., Nat Commun, PMID 41233351

PXD057649 Dataset with its publication pending (from iProX)
Dataset title: Glial UDP-glycosyltransferase Ugt35b regulates longevity by maintaining lipid homeostasis in Drosophila
Possible reference: Sheng, L. et al. (2025) The glial UDP-glycosyltransferase Ugt35b regulates longevity by maintaining lipid homeostasis in Drosophila., Cell Rep, PMID 39723892

PXD057642 Dataset with its publication pending (from iProX)
Dataset title: Phospho-proteomics analysis of early-response of U251 cells to X-ray irradiation
Possible reference: Ben Diouf, O. et al. (2024) Phospho-Proteomics Analysis of Early Response to X-Ray Irradiation Reveals Molecular Mechanism Potentially Related to U251 Cell Radioresistance., Proteomes, PMID 39846632

PXD057632 Dataset with its publication pending (from PRIDE)
Dataset title: A Robust Multiplex-DIA Workflow Profiles Protein Turnover Regulations Associated with Cisplatin Resistance and Aneuploidy
Possible reference: Salovska, B. et al. (2024) A Comprehensive and Robust Multiplex-DIA Workflow Profiles Protein Turnover Regulations Associated with Cisplatin Resistance., bioRxiv, PMID 39554001

PXD057626 no publication (from MassIVE)
Dataset title: Nanobody-thioesterase chimeras to specifically target protein palmitoylation
Possible reference: Kuo, CW. et al. (2025) Nanobody-thioesterase chimeras to specifically target protein palmitoylation., Nat Commun, PMID 39920166

PXD057613 no publication (from MassIVE)
Dataset title: Enhancing the bothropic antivenom through a reverse antivenomics approach
Possible reference: Sousa, LF. et al. (2017) Functional proteomic analyses of Bothrops atrox venom reveals phenotypes associated with habitat variation in the Amazon., J Proteomics, PMID 28274896

PXD057602 Dataset with its publication pending (from PRIDE)
Dataset title: Protein modification by a eukaryotic-like ubiquitin-related modifier in the hyperthermophilic archaeon Saccharolobus islandicus
Possible reference: Cao, J. et al. (2025) Protein modification by a eukaryotic-like ubiquitin-related modifier in the hyperthermophilic archaeon Saccharolobus islandicus., mSystems, PMID 41114577

PXD057596 Dataset with its publication pending (from PRIDE)
Dataset title: A0913 interacts with CP47 of PSII
Possible reference: Zheng, Z. et al. (2025) Molecular glue for phycobilisome attachment to photosystem II in Synechococcus sp. PCC 7002., Proc Natl Acad Sci U S A, PMID 39847327

PXD057589 no publication (from MassIVE)
Dataset title: Baculoviral IAP repeat-containing protein 6 Ubiquitinates KRAS4A
Possible reference: Kochen Rossi, J. et al. (2025) The differential interactomes of the KRAS splice variants identify BIRC6 as a ubiquitin ligase for KRAS4A., Cell Rep, PMID 39705142

PXD057583 no publication (from MassIVE)
Dataset title: Mass Spectrometry-Based Proteomics of Extracellular Vesicle Proteins (EVPs)
Possible reference: Kenari, AN. et al. (2023) Protocol for Plasma Extracellular Vesicle and Particle Isolation and Mass Spectrometry-Based Proteomic Identification., Methods Mol Biol, PMID 36781793

PXD057580 doi: https://doi.org/10.1101/2024.11.05.622109 (from PanoramaPublic)
Dataset title: SysQuan: repurposing SILAC mice for the affordable absolute quantitation of the human proteome
Possible reference: Mohammed, Y. et al. (2025) SysQuan: Repurposing SILAC Mice for the Cost-Effective Absolute Quantitation of the Human Proteome., Mol Cell Proteomics, PMID 40254065

PXD057552 no publication (from MassIVE)
Dataset title: Human coronavirus-229E infection alters the structure of host RNA processing complexes
Possible reference: Sarkar, S. et al. (2025) Human Coronavirus-229E Hijacks Key Host-Cell RNA-Processing Complexes for Replication., J Proteome Res, PMID 40938355

PXD057540 Dataset with its publication pending (from PRIDE)
Dataset title: Mouse hepatocyte conditioned media LC-MS/MS.
Possible reference: Temnov, AA. et al. (2019) Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure., Mol Biol Rep, PMID 30977085

PXD057537 Dataset with its publication pending (from PRIDE)
Dataset title: Microbial metabolite Indole-3-propionic acid drives mitochondrial respiration in CD4+ T cells to confer protection against intestinal inflammation
Possible reference: Li, Q. et al. (2025) Microbial metabolite indole-3-propionic acid drives mitochondrial respiration in CD4+ T cells to confer protection against intestinal inflammation., Nat Metab, PMID 41120706

PXD057484 Dataset with its publication pending (from jPOST)
Dataset title: Proteomics Unveils Chemical Modifications on Protein Side Chains in Raw Chicken Meat Affected with Growth-Related Myopathies
Possible reference: Malila, Y. et al. (2025) Proteomics unveils chemical modifications on protein side chains in raw breast meat of broilers (Gallus gallus) affected with growth-related myopathies., Anim Biosci, PMID 40302679

PXD057472 Dataset with its publication pending (from PRIDE)
Dataset title: Quantification profiles of enzyme activity, secretion and psychosine levels of�Krabbe disease galactosylceramidase�missense variants
Possible reference: Peng, H. et al. (2024) Expression study of Krabbe Disease GALC missense variants - Insights from quantification profiles of residual enzyme activity, secretion and psychosine levels., bioRxiv, PMID 39464077

PXD057444 Dataset with its publication pending (from PRIDE)
Dataset title: Ionizable polymeric micelles (IPMs) for efficient siRNA delivery
Possible reference: Zhou, Z. et al. (2025) Ionizable polymeric micelles (IPMs) for efficient siRNA delivery., Nat Commun, PMID 39753560

PXD057435 no publication (from MassIVE)
Dataset title: Unrecognized bacterial catalyst for N2O reduction
Possible reference: He, G. et al. (2025) A novel bacterial protein family that catalyses nitrous oxide reduction., Nature, PMID 40836093

PXD057415 Dataset with its publication pending (from PRIDE)
Dataset title: Lon Protease-Mediated Secretome Profiling in Klebsiella pneumoniae
Possible reference: Reitzel, C. et al. (2026) Lon protease-mediated secretome profiling in Klebsiella pneumoniae., Microbiol Resour Announc, PMID 41778832

PXD057412 Dataset with its publication pending (from jPOST)
Dataset title: Profiling Protein Post-Translational Modifications in Plasma-derived Extracellular Vesicles as Fingerprints for Breast Cancer Subtypes
Possible reference: Hadisurya, M. et al. (2025) Profiling Protein Post-Translational Modifications in Plasma-derived Extracellular Vesicles as Fingerprints for Breast Cancer Subtypes., Res Sq, PMID 40894036

PXD057408 no publication (from MassIVE)
Dataset title: Human coronavirus-229E infection alters the structure of host RNA processing complexes
Possible reference: Sarkar, S. et al. (2025) Human Coronavirus-229E Hijacks Key Host-Cell RNA-Processing Complexes for Replication., J Proteome Res, PMID 40938355

PXD057403 Dataset with its publication pending (from PRIDE)
Dataset title: A viral protein activates the MAPK pathway to promote viral infection by downregulating callose deposition in plants
Possible reference: Feng, L. et al. (2024) A viral protein activates the MAPK pathway to promote viral infection by downregulating callose deposition in plants., Nat Commun, PMID 39632828

PXD057400 no publication (from MassIVE)
Dataset title: Self-priming of Plk1 binding to BubR1 ensures accurate mitotic progression
Possible reference: Song, C. et al. (2024) Self-priming of Plk1 binding to BubR1 ensures accurate mitotic progression., Commun Biol, PMID 39516273

PXD057397 Dataset with its publication pending (from jPOST)
Dataset title: Serum Proteomics Analysis of Cats with Effusive Feline Infectious Peritonitis
Possible reference: Moyadee, W. et al. (2025) Serum proteomic approach to identifying differentially expressed proteins in effusive feline infectious peritonitis., Sci Rep, PMID 40442209

PXD057394 Dataset with its publication pending (from PRIDE)
Dataset title: A mass spectrometry-based proteomics strategy to detect long-chain S-acylated peptides
Possible reference: Sardana, S. et al. (2025) A mass spectrometry-based proteomics strategy to detect long-chain S-acylated peptides., Analyst, PMID 40878156

PXD057380 Dataset with its publication pending (from jPOST)
Dataset title: The ER Thioredoxin-Related Transmembrane Protein TMX2 Controls Redox-Mediated Tethering of ER-Mitochondria Contacts (ERMCS)
Possible reference: Chen, J. et al. (2025) The ER thioredoxin-related transmembrane protein TMX2 controls redox-mediated tethering of ER-mitochondria contacts., Cell Rep, PMID 41175374

PXD057372 Dataset with its publication pending (from PRIDE)
Dataset title: PLD3 and PLD4 synthesize lysosomal S,S-BMP
Possible reference: Singh, S. et al. (2024) PLD3 and PLD4 synthesize S,S-BMP, a key phospholipid enabling lipid degradation in lysosomes., bioRxiv, PMID 38562702

PXD057369 no publication (from MassIVE)
Dataset title: Development of subunit-selective proteasome substrates for Schistosoma species by MSP-MS
Possible reference: Jiang, Z. et al. (2024) Development of subunit selective proteasome substrates for Schistosoma species., bioRxiv, PMID 38405969

PXD057361 Dataset with its publication pending (from PRIDE)
Dataset title: Urine proteomics as a source of biological information and outcome predictor in living kidney transplantation
Possible reference: Hoyer-Allo, KJR. et al. (2026) Urine Proteomics as a Source of Biological Information and Outcome Predictor in Living Kidney Transplantation., Mol Cell Proteomics, PMID 41825594

PXD057360 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Profiling of Kidney Organoids in Extended Culture Conditions
Possible reference: Lass�, M. et al. (2023) An integrated organoid omics map extends modeling potential of kidney disease., Nat Commun, PMID 37580326

PXD057349 Dataset with its publication pending (from PRIDE)
Dataset title: A SET domain-containing protein and HCF-1 maintain transgenerational epigenetic memory
Possible reference: Zeng, C. et al. (2026) A SET domain-containing protein and HCF-1 maintain transgenerational epigenetic memory., Nat Commun, PMID 41513691

PXD057335 Dataset with its publication pending (from PRIDE)
Dataset title: ClpC1-targeting peptide natural products differentially dysregulate the proteome of Mycobacterium tuberculosis
Possible reference: Barter, IK. et al. (2026) ClpC1-targeting peptide natural products differentially dysregulate the proteome of Mycobacterium tuberculosis., Nat Commun, PMID 41611701

PXD057333 no publication (from MassIVE)
Dataset title: Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation
Possible reference: Devlin, KL. et al. (2024) Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation., bioRxiv, PMID 39605331

PXD057332 Dataset with its publication pending (from iProX)
Dataset title: Proteomic Insights into the Regulatory Mechanisms of Freezing Response in the Alpine Subnivale Plant Chorispora bungeana
Possible reference: Hu, H. et al. (2024) Proteomic Insights into the Regulatory Mechanisms of the Freezing Response in the Alpine Subnivale Plant Chorispora bungeana., Int J Mol Sci, PMID 39769146

PXD057331 Dataset with its publication pending (from iProX)
Dataset title: A Full Window Data Independent Acquisition Method for Deeper Top-down Proteomics
Possible reference: Sun, C. et al. (2025) Full Window Data-Independent Acquisition Method for Deeper Top-Down Proteomics., Anal Chem, PMID 40119838

PXD057292 Dataset with its publication pending (from PRIDE)
Dataset title: Plasma proteomics in epilepsy: network-based identification of proteins associated with seizures
Possible reference: Ashtiani, SH. et al. (2025) Plasma proteomics in epilepsy: Network-based identification of proteins associated with seizures., Epilepsy Res, PMID 39626528

PXD057286 Dataset with its publication pending (from PRIDE)
Dataset title: ADSL promotes autophagy and liver tumor growth through fumarate-mediated Beclin1 dimethylation
Possible reference: Wang, L. et al. (2025) ADSL promotes autophagy and tumor growth through fumarate-mediated Beclin1 dimethylation., Nat Chem Biol, PMID 39881212

PXD057265 Dataset with its publication pending (from PRIDE)
Dataset title: Lysosomal sequestration of PARP inhibitors drives heterogeneous accumulation in ovarian cancer to increase efficacy
Possible reference: R Moncayo, C. et al. (2026) Multimodal imaging reveals a lysosomal drug reservoir that drives heterogeneous distribution of PARP inhibitors., Nat Commun, PMID 41844641

PXD057250 no publication (from MassIVE)
Dataset title: Sticky organisms create underwater biological adhesives driven by interactions between EGF- and GlcNAc- containing polysaccharides.
Possible reference: Choi, J. et al. (2025) Sticky organisms create underwater biological adhesives driven by interactions between EGF- and GlcNAc- containing polysaccharides., Nat Commun, PMID 39747843

PXD057239 Dataset with its publication pending (from iProX)
Dataset title: Dynamic Single Cell Proteomics Reveals the Functional Shifts of Dermal Sheath Cells during Wound Healing
Possible reference: Zhu, B. et al. (2026) Single-Cell Proteomics Uncovers Dual Traits of Dermal Sheath Cells in Wound Repair., Adv Wound Care (New Rochelle), PMID 39878130

PXD057231 Dataset with its publication pending (from jPOST)
Dataset title: Proteomics-based Receptor-ligand Matching Enhances Differentiation Maturity of Human Stem Cell-derived Neurons
Possible reference: Dimitrov, D. et al. (2025) Proteomics-based receptor-ligand matching enhances differentiation maturity of human-stem-cell-derived neurons., Stem Cell Reports, PMID 40845849

PXD057192 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Profiling Reveals Age-Related Changes in Transporter Proteins in the Human Blood-Brain Barrier
Possible reference: Zhou, X. et al. (2024) Proteomic Profiling Reveals Age-Related Changes in Transporter Proteins in the Human Blood-Brain Barrier., bioRxiv, PMID 39091855

PXD057190 Dataset with its publication pending (from PRIDE)
Dataset title: A Leishmania virulence factor harnesses an allosteric kinase switch to regulate its ubiquitin ligase activity
Possible reference: Fokkens, TJ. et al. (2025) A Leishmania virulence factor harnesses an allosteric kinase switch to regulate its ubiquitin ligase activity., Mol Cell, PMID 40997810

PXD057173 Dataset with its publication pending (from iProX)
Dataset title: NEDD4L mediates intestinal epithelial cell ferroptosis to restrict inflammatory bowel diseases and colorectal tumorigenesis
Possible reference: Liang, J. et al. (2024) NEDD4L mediates intestinal epithelial cell ferroptosis to restrict inflammatory bowel diseases and colorectal tumorigenesis., J Clin Invest, PMID 39688910

PXD057168 Dataset with its publication pending (from iProX)
Dataset title: Identification of Serum Metabolites to improve diagnostic efficacy in pulmonary embolism
Possible reference: Chen, S. et al. (2025) Identification of Serum Metabolites to Improve Diagnostic Efficacy in Pulmonary Embolism., J Proteome Res, PMID 40128110

PXD057159 Dataset with its publication pending (from PRIDE)
Dataset title: P4PP: an universal shotgun proteomics data analysis pipeline for virus identification  
Possible reference: Paauw, A. et al. (2025) P4PP: A Universal Shotgun Proteomics Data Analysis Pipeline for Virus Identification., Mol Cell Proteomics, PMID 40449796

PXD057150 Dataset with its publication pending (from PRIDE)
Dataset title: Histone PTM profiling in breast cancer clinical samples
Possible reference: Vai, A. et al. (2024) Improved Mass Spectrometry-Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles., Mol Cell Proteomics, PMID 38866077

PXD057141 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics revealed novel functions and drought tolerance of Arabidopsis thaliana protein kinase ATG1
Possible reference: Cheng, S. et al. (2025) Proteomics revealed novel functions and drought tolerance of Arabidopsis thaliana protein kinase ATG1., BMC Biol, PMID 39984923

PXD057136 no publication (from MassIVE)
Dataset title: Rescue of sexually dimorphic autistic-like abnormalities in mice carrying biallelic MDGA1 mutation by bazedoxifene
Possible reference: Kim, S. et al. (2026) Bazedoxifene reverses sexually dimorphic autistic-like abnormalities in biallelic MDGA1-mutant mice., EMBO Mol Med, PMID 41862769

PXD057134 no publication (from MassIVE)
Dataset title: Rescue of sexually dimorphic autistic-like abnormalities in mice carrying biallelic MDGA1 mutation by bazedoxifene
Possible reference: Kim, S. et al. (2026) Bazedoxifene reverses sexually dimorphic autistic-like abnormalities in biallelic MDGA1-mutant mice., EMBO Mol Med, PMID 41862769

PXD057132 no publication (from MassIVE)
Dataset title: A Cross-species Proteomic assessment of cost-effective platforms for depleting high-abundant proteins from blood serum
Possible reference: Peng, Z. et al. (2025) A cross-species proteomic assessment of cost-effective platforms for depleting high-abundant proteins from blood serum., BMC Methods, PMID 40989151

PXD057131 Dataset with its publication pending (from iProX)
Dataset title: Vitrification of 3D Mesenchymal Stem Cells Encapsulated in GelMA Hydrogel by Microfluidics: Improved Cryosurvival, Reduced Cryoprotectant Concentration, and Enhanced Wound Healing
Possible reference: Pu, Z. et al. (2025) Vitrification of 3D-MSCs encapsulated in GelMA hydrogel: Improved cryosurvival, reduced cryoprotectant concentration, and enhanced wound healing., Int J Biol Macromol, PMID 39809395

PXD057118 Dataset with its publication pending (from PRIDE)
Dataset title: Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics
Possible reference: Zheng, X. et al. (2025) Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics., Mol Cell, PMID 39814024

PXD057114 Dataset with its publication pending (from PRIDE)
Dataset title: PCBP1 regulates aberrant alternative splicing of AARS2 in congenital cardiomyopathy
Possible reference: Lu, YW. et al. (2023) PCBP1 regulates alternative splicing of AARS2 in congenital cardiomyopathy., bioRxiv, PMID 37293078

PXD057089 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of TAOK1 knockout in C2C12 myotubes
Possible reference: Zhang, R. et al. (2025) The potential of TAOK1 as a new therapeutic target for the treatment of cancer cachexia-associated muscle atrophy., Pharmacol Res, PMID 40339965

PXD057083 Dataset with its publication pending (from iProX)
Dataset title: A stepwise mode of TGFÎ²-SMAD signaling and DNA methylation regulates naÃ¯ve-to-primed pluripotency and differentiation
Possible reference: Zhao, B. et al. (2024) A stepwise mode of TGFβ-SMAD signaling and DNA methylation regulates naïve-to-primed pluripotency and differentiation., Nat Commun, PMID 39578449

PXD057050 Dataset with its publication pending (from PRIDE)
Dataset title: SA-AKI mice and Sepsis mice kidney MS data
Possible reference: Li, J. et al. (2025) Spatial proteomics reveals multiple mechanisms of mitochondrial damage in renal tubules during sepsis-induced acute kidney injury., Arch Biochem Biophys, PMID 40714030

PXD057046 Dataset with its publication pending (from iProX)
Dataset title: GART maintains UCK2 protein stability
Possible reference: Sha, N. et al. (2025) The protection of UCK2 protein stability by GART maintains pyrimidine salvage synthesis for HCC growth under glucose limitation., Oncogene, PMID 39865175

PXD057044 Dataset with its publication pending (from iProX)
Dataset title: Quantitative proteomic analysis based on TMT reveals different responses of Haloxylon ammodendron and Haloxylon persicum to long-term drought
Possible reference: Yang, F. et al. (2025) Quantitative proteomic analysis based on TMT reveals different responses of Haloxylon ammodendron and Haloxylon persicum to long-term drought., BMC Plant Biol, PMID 40234745

PXD057039 Dataset with its publication pending (from iProX)
Dataset title: The High-Intensity Focused Ultrasound combined with IL-2 to activate the JAK-STAT signaling pathway for treating breast cancer
Possible reference: Fu, Q. et al. (2025) High-Intensity Focused Ultrasound Elevates Il-2rb on CD8+ T Cells: Enhancing JAK-STAT and IL-2 Efficacy in Triple-Negative Breast Cancer., J Proteome Res, PMID 40960236

PXD057028 Dataset with its publication pending (from PRIDE)
Dataset title: BXPC3 and PANC1 secretome analysis (SEC61-biotin transferase system)
Possible reference: Amrutkar, M. et al. (2019) Secretion of fibronectin by human pancreatic stellate cells promotes chemoresistance to gemcitabine in pancreatic cancer cells., BMC Cancer, PMID 31208372

PXD057027 no publication (from MassIVE)
Dataset title: Investigating the differential structural organization and gene expression regulatory networks of lamin A Ig fold domain mutants of muscular dystrophy
Possible reference: Dutta, S. et al. (2024) Investigating the differential structural organization and gene expression regulatory networks of lamin A Ig fold domain mutants of muscular dystrophy., Biochem J, PMID 39509247

PXD057026 Dataset with its publication pending (from PRIDE)
Dataset title: Absence of MCJ/DnaJC15 promotes brown adipose tissue thermogenesis
Possible reference: Cicu�ndez, B. et al. (2025) Absence of MCJ/DnaJC15 promotes brown adipose tissue thermogenesis., Nat Commun, PMID 39805849

PXD057024 Dataset with its publication pending (from PRIDE)
Dataset title: Macrocycle-based PROTACs selectively degrade cyclophilin A and inhibit HIV-1 and HCV
Possible reference: Newton, LS. et al. (2025) Macrocycle-based PROTACs selectively degrade cyclophilin A and inhibit HIV-1 and HCV., Nat Commun, PMID 39929804

PXD057017 Dataset with its publication pending (from PRIDE)
Dataset title: Pantothenate kinase 4 controls skeletal muscle substrate metabolism
Possible reference: Miranda-Cervantes, A. et al. (2025) Pantothenate kinase 4 controls skeletal muscle substrate metabolism., Nat Commun, PMID 39746949

PXD057013 no publication (from MassIVE)
Dataset title: Cryo-EM structure of a lysozyme-derived amyloid fibril from hereditary amyloidosis
Possible reference: Karimi-Farsijani, S. et al. (2024) Cryo-EM structure of a lysozyme-derived amyloid fibril from hereditary amyloidosis., Nat Commun, PMID 39511224

PXD057001 Dataset with its publication pending (from iProX)
Dataset title: Direct Data-independent acquisition proteome of the intestinal regenerative tissue of sea cucumbers
Possible reference: Xiao, K. et al. (2025) Apoptosis regulates intestinal regeneration via iPLA2 and EGFL7 signaling in Apostichopus japonicus., Zool Res, PMID 40923302

PXD056979 Dataset with its publication pending (from PRIDE)
Dataset title: Diesel particulate matter-induced proteomic changes in three-dimensional spheroids derived from human primary cells of various tissue origins
Possible reference: Cho, YJ. et al. (2025) Diesel particulate matter-induced proteomic changes in three-dimensional spheroids derived from human primary cells of various tissue origins., Sci Rep, PMID 40993169

PXD056969 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic Analysis Reveals Cadherin, Actin, and Focal Adhesion Molecule-Mediated Formation of Cervical Cancer Spheroid
Possible reference: Molika, P. et al. (2024) Proteomic Analysis Reveals Cadherin, Actin, and Focal Adhesion Molecule-Mediated Formation of Cervical Cancer Spheroids., Cells, PMID 39682752

PXD056964 no publication (from MassIVE)
Dataset title: RNA Structure Coordinates Translation Across the Meiotic Program
Possible reference: Wu, H. et al. (2026) RNA Structure Coordinates Translation Across the Meiotic Program., bioRxiv, PMID 41648600

PXD056959 no publication (from MassIVE)
Dataset title: Jade1 and the HBO1 complex are spatial-selective cofactors of Oct4
Possible reference: Wu, Y. et al. (2025) Jade1 and the HBO1 histone acetyltransferase complex are spatial-selective cofactors of the pluripotency transcription factor Oct4., bioRxiv, PMID 39574712

PXD056947 Dataset with its publication pending (from PRIDE)
Dataset title: Interaction of genetic variants activates latent metabolic pathways in yeast
Possible reference: Sasikumar, S. et al. (2025) Interaction of genetic variants activates latent metabolic pathways in yeast., Nat Commun, PMID 40866353

PXD056946 Dataset with its publication pending (from PRIDE)
Dataset title: The dual life of disordered lysine-rich domains of snoRNPs in rRNA modification and nucleolar compaction
Possible reference: Dominique, C. et al. (2024) The dual life of disordered lysine-rich domains of snoRNPs in rRNA modification and nucleolar compaction., Nat Commun, PMID 39482307

PXD056941 Dataset with its publication pending (from PRIDE)
Dataset title: MYC deregulation sensitizes cancer cells to N-myristoyltransferase inhibition - Mitochondrial fractionation
Possible reference: Lueg, GA. et al. (2025) MYC deregulation sensitizes cancer cells to N-myristoyltransferase inhibition., Cell Rep, PMID 40849903

PXD056925 Dataset with its publication pending (from iProX)
Dataset title: Spatial isotope deep tracing deciphers inter-tissue metabolic crosstalk
Possible reference: Li, X. et al. (2025) Spatial isotope deep tracing deciphers inter-tissue metabolic crosstalk., Nat Commun, PMID 40858577

PXD056916 no publication (from MassIVE)
Dataset title: A single amino acid in the Salmonella effector SarA/SteE triggers supraphysiological activation of STAT3 for anti-inflammatory target gene expression
Possible reference: Gaggioli, MR. et al. (2024) A single amino acid in the Salmonella effector SarA/SteE triggers supraphysiological activation of STAT3 for anti-inflammatory target gene expression., bioRxiv, PMID 38405869

PXD056902 Dataset with its publication pending (from PRIDE)
Dataset title: Multiplexed phosphoproteomics of low cell numbers using SPARCE
Possible reference: Gaizley, EJ. et al. (2025) Multiplexed phosphoproteomics of low cell numbers using SPARCE., Commun Biol, PMID 40287540

PXD056888 Dataset with its publication pending (from PRIDE)
Dataset title: Systematic Metaproteomic Mapping of Ex vivo Gut Microbiota Functional Responses to Therapeutic Drugs (1)
Possible reference: Li, L. et al. (2025) Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs., Nat Commun, PMID 41130938

PXD056884 Dataset with its publication pending (from PRIDE)
Dataset title: Carbonic anhydrase 2 facilitates sorafenib resistance by counteracting MCT4-mediated intracellular pH dysregulation in hepatocellular carcinoma
Possible reference: Lu, H. et al. (2024) Carbonic anhydrase 2 facilitates sorafenib resistance by counteracting MCT4-mediated intracellular pH dysregulation in HCC., Cell Rep, PMID 39607826

PXD056878 Dataset with its publication pending (from iProX)
Dataset title: Mitochondrial proteomics of Th17 and Treg cells
Possible reference: Duscha, A. et al. (2020) Propionic Acid Shapes the Multiple Sclerosis Disease Course by an Immunomodulatory Mechanism., Cell, PMID 32160527

PXD056874 no publication (from MassIVE)
Dataset title: Spindle integrity is regulated by a phospho-dependent interaction between the Ndc80 and Dam1 kinetochore complexes
Possible reference: Nelson, CR. et al. (2025) Spindle integrity is regulated by a phospho-dependent interaction between the Ndc80 and Dam1 kinetochore complexes., PLoS Genet, PMID 40184422

PXD056842 Dataset with its publication pending (from iProX)
Dataset title: IDH2 lactylation promotes angiogenesis in diabetic myocardial infarction
Possible reference: Zang, G. et al. (2025) IDH2 lactylation promotes angiogenesis in murine diabetic myocardial infarction via blocking Cav1-eNOS interaction., Nat Commun, PMID 41419771

PXD056835 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of B cells in peripheral lymphatic system reveals the dynamics during the systemic lupus erythematosus progression
Possible reference: Sun, L. et al. (2025) Proteomic analysis of B cells in peripheral lymphatic system reveals the dynamics during the systemic lupus erythematosus progression., Biophys Rep, PMID 40308935

PXD056834 Dataset with its publication pending (from iProX)
Dataset title: IGFBP2 and IGFBP4 Interact to Activate Complement Pathway in Diabetic Nephropathy
Possible reference: Liang, J. et al. (2025) IGFBP2 and IGFBP4 interact to activate complement pathway in diabetic kidney disease., Ren Fail, PMID 39806768

PXD056827 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of Leucine-Rich Repeat Kinase 2 by inflammation and IL-4
Possible reference: Dikovskaya, D. et al. (2025) Inflammation and IL-4 regulate Parkinson's and Crohn's disease associated kinase LRRK2., EMBO Rep, PMID 40394349

PXD056823 no publication (from MassIVE)
Dataset title: Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity
Possible reference: Lamb, TM. et al. (2025) Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity., Cell Rep, PMID 41160737

PXD056820 no publication (from MassIVE)
Dataset title: Ro5-4864, a Ligand of the Mitochondrial Translocator Protein, Protects Against Heart Failure in Mice
Possible reference: Diloretto, DA. et al. (2026) Ro5-4864, a ligand of the mitochondrial translocator protein, protects against heart failure in mice via regulation of the p62-Keap1-Nrf2 axis., J Physiol, PMID 41935019

PXD056811 Dataset with its publication pending (from PRIDE)
Dataset title: Anionic phospholipids connect barley ROP signaling with resistance and susceptibility to fungal cell entry
Possible reference: Wei�, LS. et al. (2025) Barley resistance and susceptibility to fungal cell entry involve the interplay of ROP signaling with phosphatidylinositol-monophosphates., Plant J, PMID 40680717

PXD056810 Dataset with its publication pending (from PRIDE)
Dataset title: Federated deep learning enables cancer subtyping by proteomics
Possible reference: Cai, Z. et al. (2025) Federated Deep Learning Enables Cancer Subtyping by Proteomics., Cancer Discov, PMID 40488620

PXD056792 no publication (from MassIVE)
Dataset title: Barley grain proteome assessment using multi-environment trial data and machine learning
Possible reference: Ramanan, M. et al. (2024) Barley Grain Proteome Assessment Using Multi-Environment Trial Data and Machine Learning., J Agric Food Chem, PMID 39536264

PXD056791 Dataset with its publication pending (from PRIDE)
Dataset title: Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation
Possible reference: Liu, R. et al. (2025) Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and gliomagenesis., Cell Metab, PMID 39642882

PXD056790 Dataset with its publication pending (from PRIDE)
Dataset title: Remodeling of the neutrophil proteome upon exposure to Pseudomonas aeruginosa biofilms
Possible reference: Rizakos, T. et al. (2025) Remodeling of the neutrophil proteome upon exposure to Pseudomonas aeruginosa biofilms., Microbiol Resour Announc, PMID 40079579

PXD056759 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of hydrogen peroxide-treated human chondrocytes shows endoplasmic reticulum stress, cytoskeleton remodeling, and altered secretome composition
Possible reference: Toledo, TM. et al. (2025) Proteomic analysis of hydrogen peroxide-treated human chondrocytes shows endoplasmic reticulum stress, cytoskeleton remodeling, and altered secretome composition., Cell Commun Signal, PMID 40514670

PXD056756 Dataset with its publication pending (from PRIDE)
Dataset title: Structure and dynamics of GAD65 and its interaction with the autoimmune polyendocrine syndrome type 2-associated autoantibody b96.11.
Possible reference: St�nder, SHD. et al. (2025) Structure and dynamics of GAD65 in complex with an autoimmune polyendocrine syndrome type 2-associated autoantibody., Nat Commun, PMID 40055307

PXD056755 Dataset with its publication pending (from PRIDE)
Dataset title: Temporal and thermal optimization of trypsin digestion for the cryptococcal proteome
Possible reference: Sun, J. et al. (2025) Temporal and thermal optimization of trypsin digestion for the cryptococcal proteome., Microbiol Resour Announc, PMID 40497678

PXD056749 Dataset with its publication pending (from iProX)
Dataset title: 4D Label Free Quantitative Proteome of Mouse Exosomes
Possible reference: Zhao, C. et al. (2025) Blockade of mitochondrial components release by exosome pathway promotes the pathogenesis of Fuchs endothelial corneal dystrophy., Cell Death Discov, PMID 41331241

PXD056746 Dataset with its publication pending (from iProX)
Dataset title: SCASP-PTM multiple PTM enrichment method
Possible reference: Lin, ZP. et al. (2025) Comprehensive PTM profiling with SCASP-PTM uncovers mechanisms of p62 degradation and ALDOA-mediated tumor progression., Cell Rep, PMID 40186868

PXD056729 no publication (from MassIVE)
Dataset title: Lysosomal protein atlas of brain cell types identifies SLC45A1-associated disease as a lysosomal disorder
Possible reference: Ghoochani, A. et al. (2024) Cell-Type Resolved Protein Atlas of Brain Lysosomes Identifies SLC45A1-Associated Disease as a Lysosomal Disorder., bioRxiv, PMID 39464040

PXD056710 Dataset with its publication pending (from PRIDE)
Dataset title: Human plasma proteomics analysis of PAD patients and Healthy control
Possible reference: Ferreira, HB. et al. (2025) Lipidomic Signature of Abdominal Aortic Aneurysm and Peripheral Artery Disease., J Proteome Res, PMID 40910695

PXD056700 Dataset with its publication pending (from PRIDE)
Dataset title: CoREST Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity
Possible reference: Fisher, RJ. et al. (2024) CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity., bioRxiv, PMID 39713349

PXD056674 Dataset with its publication pending (from PRIDE)
Dataset title: JOSD2 inhibits angiotensin II-induced vascular remodeling by deubiquitinating and stabilizing SMAD7
Possible reference: Shen, SR. et al. (2025) JOSD2 inhibits angiotensin II-induced vascular remodeling by deubiquitinating and stabilizing SMAD7., Acta Pharmacol Sin, PMID 39833306

PXD056668 no publication (from MassIVE)
Dataset title: Harmonized peptide libraries enable practical biofluid selection for developing biomarker assays
Possible reference: Brusach, KB. et al. (2025) Harmonized Peptide Libraries Enable Practical Biofluid Selection for Developing Biomarker Assays., Mol Cell Proteomics, PMID 41086942

PXD056657 no publication (from MassIVE)
Dataset title: Lysosomal protein atlas of brain cell types identifies SLC45A1-associated disease as a lysosomal disorder
Possible reference: Ghoochani, A. et al. (2024) Cell-Type Resolved Protein Atlas of Brain Lysosomes Identifies SLC45A1-Associated Disease as a Lysosomal Disorder., bioRxiv, PMID 39464040

PXD056653 Dataset with its publication pending (from PRIDE)
Dataset title: The secreted proteases Aur, ScpA, SspA and SspB suppress virulence of Staphylococcus aureus USA300 by shaping the extracellular proteome
Possible reference: Li, X. et al. (2025) The secreted proteases aur, scpA, sspA and sspB suppress the virulence of Staphylococcus aureus USA300 by shaping the extracellular proteome., Virulence, PMID 40495541

PXD056650 Dataset with its publication pending (from PRIDE)
Dataset title: A m6A methyltransferase fine-tune m6A modification and ubiquitination to balance antiviral immunity and yield
Possible reference: Guo, J. et al. (2025) An m6A methyltransferase confers host resistance by degrading viral proteins through ubiquitination., Nat Commun, PMID 40410199

PXD056613 Dataset with its publication pending (from PRIDE)
Dataset title: The proteome of circulating extracellular vesicles and their functional effect on platelets vary with the isolation method
Possible reference: Fern�ndez-S�ez, EM. et al. (2025) The proteome of circulating extracellular vesicles and their functional effect on platelets vary with the isolation method., Sci Rep, PMID 40594329

PXD056566 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative analysis of the Progesterone Receptor interactome in the human ovarian granulosa cell line KGN and other female reproductive cells
Possible reference: Foot, NJ. et al. (2025) Comparative Analysis of the Progesterone Receptor Interactome in the Human Ovarian Granulosa Cell Line KGN and Other Female Reproductive Cells., Proteomics, PMID 40357704

PXD056549 Dataset with its publication pending (from jPOST)
Dataset title: Structural Analysis of the 20S Proteasome using Native Mass Spectrometry and Ultraviolet Photodissociation
Possible reference: Walker, JN. et al. (2024) Structural Analysis of the 20S Proteasome Using Native Mass Spectrometry and Ultraviolet Photodissociation., J Proteome Res, PMID 39475212

PXD056545 Dataset with its publication pending (from PRIDE)
Dataset title: An ancient lysozyme in placozoans
Possible reference: Berndt, H. et al. (2026) An ancient lysozyme in placozoans participates in acidic extracellular digestion., Commun Biol, PMID 41495279

PXD056543 Dataset with its publication pending (from PRIDE)
Dataset title: PSKH1 kinase activity is differentially modulated via allosteric binding of Ca2+ sensor proteins
Possible reference: Horne, CR. et al. (2025) PSKH1 kinase activity is differentially modulated via allosteric binding of Ca2+ sensor proteins., Proc Natl Acad Sci U S A, PMID 39964718

PXD056513 no publication (from MassIVE)
Dataset title: Distinct Perception Mechanisms of BACH1 Quaternary Structure Degrons by Two F-box Proteins under Oxidative Stress
Possible reference: Cao, S. et al. (2024) Distinct Perception Mechanisms of BACH1 Quaternary Structure Degrons by Two F-box Proteins under Oxidative Stress., bioRxiv, PMID 38895309

PXD056507 Dataset with its publication pending (from PRIDE)
Dataset title: Shatavari Supplementation During Eight Weeks of Resistance Training Increases Training Load, Enhances Skeletal Muscle Contractility and Alters the Skeletal Muscle Proteome in Older Women.
Possible reference: Greed, E. et al. (2024) Shatavari supplementation during eight weeks of resistance training increases training load, enhances skeletal muscle contractility and alters the skeletal muscle proteome in older women., Front Nutr, PMID 39834460

PXD056506 no publication (from MassIVE)
Dataset title: Sirtuin-5 is recruited to hepatic peroxisomes in mice fed dodecanedioic acid but has little impact on the peroxisomal succinylome
Possible reference: Zhang, Y. et al. (2024) Sirtuin-5 Is Recruited to Hepatic Peroxisomes in Mice Fed Dodecanedioic Acid but Has Little Impact on the Peroxisomal Succinylome., Biomolecules, PMID 39766215

PXD056500 Dataset with its publication pending (from PRIDE)
Dataset title: Chromatin loops are an ancestral hallmark of the animal regulatory genome
Possible reference: Kim, IV. et al. (2025) Chromatin loops are an ancestral hallmark of the animal regulatory genome., Nature, PMID 40335694

PXD056493 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling linkage-specific ubiquitin chain functions reveals a key role of K29-linked ubiquitylation in epigenome maintenance
Possible reference: Arroyo-Gomez, J. et al. (2025) Functional landscape of ubiquitin linkages couples K29-linked ubiquitylation to epigenome integrity., EMBO J, PMID 41125851

PXD056483 no publication (from MassIVE)
Dataset title: PU.1 Eviction at Lymphocyte-Specific Chromatin Domains Mediates Glucocorticoid Response in Acute Lymphoblastic Leukemia
Possible reference: Beck, D. et al. (2024) PU.1 eviction at lymphocyte-specific chromatin domains mediates glucocorticoid response in acute lymphoblastic leukemia., Nat Commun, PMID 39516193

PXD056481 no publication (from MassIVE)
Dataset title: Lysosomal protein atlas of brain cell types identifies SLC45A1-associated disease as a lysosomal disorder
Possible reference: Ghoochani, A. et al. (2024) Cell-Type Resolved Protein Atlas of Brain Lysosomes Identifies SLC45A1-Associated Disease as a Lysosomal Disorder., bioRxiv, PMID 39464040

PXD056472 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic variation in the oral secretion of Spodoptera exigua and Spodoptera littoralis larvae in response to different food sources
Possible reference: Garc�a-Mar�n, E. et al. (2025) Proteomic Variation in the Oral Secretion of Spodoptera exigua and Spodoptera littoralis Larvae in Response to Different food Sources., J Chem Ecol, PMID 39853486

PXD056457 Dataset with its publication pending (from PRIDE)
Dataset title: C-COMPASS: A user-friendly neural network tool profiles cell compartments at protein and lipid levels
Possible reference: Haas, DT. et al. (2026) C-COMPASS: a user-friendly neural network tool profiles cell compartments at protein and lipid levels., Nat Methods, PMID 41345772

PXD056453 Dataset with its publication pending (from PRIDE)
Dataset title: Glucose-dependent glycosphingolipid biosynthesis fuels CD8+ T cell function and tumor control
Possible reference: Longo, J. et al. (2024) Glucose-dependent glycosphingolipid biosynthesis fuels CD8+ T cell function and tumor control., bioRxiv, PMID 39464161

PXD056448 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative ASCL1 interactome analysis reveals CDK2-Cyclin A2 as suppressors of differentiation in MYCN-amplified neuroblastoma
Possible reference: Mykhaylechko, L. et al. (2026) Comparative ASCL1 interactome analysis reveals CDK2-Cyclin A2 as suppressors of differentiation in MYCN-amplified neuroblastoma., Mol Cancer Res, PMID 41979602

PXD056447 Dataset with its publication pending (from jPOST)
Dataset title: Heart Failure with Preserved Ejection Fraction - Mouse Heart and Lung Tissue & Comorbidities
Possible reference: Costantino, S. et al. (2025) Chromatin Rewiring by SETD2 Drives Lipotoxic Injury in Cardiometabolic HFpEF., Circ Res, PMID 40211947

PXD056412 Dataset with its publication pending (from PRIDE)
Dataset title: Adipose tissue protein kinase D (PKD): regulation of signalling networks and its effect on metabolism
Possible reference: Renton, MC. et al. (2025) Adipose tissue protein kinase D: regulation of signaling networks and its sex-dependent effects on metabolism., Am J Physiol Endocrinol Metab, PMID 40454664

PXD056410 Dataset with its publication pending (from jPOST)
Dataset title: Longitudinal analysis of B- and T-cell responses to SARS-CoV-2 recombinant S-protein vaccine S-268019-b in phase 1/2 priming and booster study
Possible reference: Fujitani, M. et al. (2025) Longitudinal analysis of immune responses to SARS-CoV-2 recombinant vaccine S-268019-b in phase 1/2 prime-boost study., Front Immunol, PMID 40109335

PXD056408 Dataset with its publication pending (from jPOST)
Dataset title: FMRP immunoprecipitation using human HEK293T cells
Possible reference: Ma, Y. et al. (2016) CMP‑N‑acetylneuraminic acid synthetase interacts with fragile X related protein 1., Mol Med Rep, PMID 27357083

PXD056407 no publication (from MassIVE)
Dataset title: Establishing a Top-Down Proteomics Platform on a Time-of-Flight Instrument with Electron-Activated Dissociation
Possible reference: Searfoss, RM. et al. (2025) Establishing a Top-Down Proteomics Platform on a Time-of-Flight Instrument with Electron-Activated Dissociation., J Proteome Res, PMID 39957600

PXD056404 Dataset with its publication pending (from PRIDE)
Dataset title: Human RCC Binding Protein in Prostate Cancer Cell Line DU145
Possible reference: Cho, MC. et al. (2015) EphA2 Is a Potential Player of Malignant Cellular Behavior in Non-Metastatic Renal Cell Carcinoma Cells but Not in Metastatic Renal Cell Carcinoma Cells., PLoS One, PMID 26177500

PXD056402 no publication (from MassIVE)
Dataset title: Post-transcriptional regulation of Dufours gland reproductive signals in bumble bees
Possible reference: Derstine, N. et al. (2024) Post-transcriptional regulation of Dufour's gland reproductive signals in bumble bees., BMC Genomics, PMID 39420273

PXD056400 Dataset with its publication pending (from PRIDE)
Dataset title: Structural proteomics defines a sequential priming mechanism for the progesterone receptor (HDX-MS)
Possible reference: Mann, MD. et al. (2025) Structural proteomics defines a sequential priming mechanism for the progesterone receptor., Nat Commun, PMID 40355435

PXD056399 Dataset with its publication pending (from PRIDE)
Dataset title: Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference
Possible reference: Čepaitė, R. et al. (2024) Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference., Nat Commun, PMID 39468082

PXD056392 Dataset with its publication pending (from PRIDE)
Dataset title: VARS1 overexpression in hepatocellular carcinoma cell lines
Possible reference: Herm�n-S�nchez, N. et al. (2025) Quantitative proteomic analysis unveils a critical role of VARS1 in hepatocellular carcinoma aggressiveness through the modulation of MAGI1 expression., Mol Cancer, PMID 39810176

PXD056390 Dataset with its publication pending (from PRIDE)
Dataset title: A chemical-genetic system to rapidly inhibit the PP2A-B56 phosphatase
Possible reference: Allan, LA. et al. (2025) A chemical-genetic system to rapidly inhibit the PP2A-B56 phosphatase reveals a role at metaphase kinetochores., Nat Commun, PMID 40157924

PXD056378 Dataset with its publication pending (from PRIDE)
Dataset title: MNX1-mediated Histone Modifications and PBX Family Role in MNX1-AML Leukemogenesis
Possible reference: Malmh�ll-Bah, E. et al. (2026) Role of MNX1-mediated histone modifications and PBX gene family in MNX1-induced leukemogenesis., Sci Rep, PMID 41554854

PXD056376 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial VHL rewires cell metabolism in hypoxia
Possible reference: Meléndez-Rodríguez, F. et al. (2019) HIF1α Suppresses Tumor Cell Proliferation through Inhibition of Aspartate Biosynthesis., Cell Rep, PMID 30811976

PXD056364 Dataset with its publication pending (from PRIDE)
Dataset title: Dysregulation of mTOR signaling is a converging mechanism in lissencephaly
Possible reference: Zhang, C. et al. (2025) Dysregulation of mTOR signalling is a converging mechanism in lissencephaly., Nature, PMID 39743596

PXD056358 no publication (from MassIVE)
Dataset title: Decoding Microbial Plastic Colonisation: Multi-Omic Insights into the Fast-Evolving Dynamics of Early-Stage Biofilms
Possible reference: Lee, CE. et al. (2025) Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms., Proteomics, PMID 39760247

PXD056353 no publication (from MassIVE)
Dataset title: Temporal Dynamics of the Milk Proteome in Women with Gestational Diabetes Mellitus
Possible reference: Mu, Q. et al. (2026) Temporal Dynamics of the Milk Proteome in Women with Gestational Diabetes Mellitus., J Proteome Res, PMID 41362056

PXD056351 Dataset with its publication pending (from iProX)
Dataset title: AMPK-regulated glycerol excretion maintains metabolic crosstalk between reductive and energetic stress
Possible reference: Zhai, X. et al. (2025) AMPK-regulated glycerol excretion maintains metabolic crosstalk between reductive and energetic stress., Nat Cell Biol, PMID 39747579

PXD056348 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of tendon overuse injury and repair mechanism
Possible reference: Zhang, G. et al. (2026) Comparative proteomic analysis reveals the pathological mechanisms of overuse achilles tendinopathy and the therapeutic mechanisms of ESWT and PRP., Tissue Cell, PMID 42250534

PXD056339 Dataset with its publication pending (from jPOST)
Dataset title: Serum Proteomic Profiling During the Periovulatory Period Identifies Candidate Biomarkers of Oocyte Maturation in Deslorelin-Induced Ovulation in Dogs
Possible reference: Udomthanaisit, L. et al. (2025) Serum proteomic profiling during the periovulatory period identifies preliminary candidate biomarkers of oocyte maturation in deslorelin-induced ovulation in dogs., PeerJ, PMID 41112769

PXD056331 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of colorectal tumors identifies the role of CAVIN1 in tumor relapse
Possible reference: Martinez-Val, A. et al. (2025) Proteomics of colorectal tumors identifies the role of CAVIN1 in tumor relapse., Mol Syst Biol, PMID 40269326

PXD056328 Dataset with its publication pending (from PRIDE)
Dataset title: Structural recognition and stabilization of tyrosine hydroxylase by the J-domain protein DNAJC12
Possible reference: Tai, MDS. et al. (2025) Structural recognition and stabilization of tyrosine hydroxylase by the J-domain protein DNAJC12., Nat Commun, PMID 40113792

PXD056313 Dataset with its publication pending (from jPOST)
Dataset title: Reprogramming of flagellin receptor responses with surrogate ligands
Possible reference: Lee, DH. et al. (2024) Reprogramming of flagellin receptor responses with surrogate ligands., Nat Commun, PMID 39532858

PXD056295 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling linkage-specific ubiquitin chain functions reveals a key role of K29-linked ubiquitylation in epigenome maintenance
Possible reference: Arroyo-Gomez, J. et al. (2025) Functional landscape of ubiquitin linkages couples K29-linked ubiquitylation to epigenome integrity., EMBO J, PMID 41125851

PXD056294 Dataset with its publication pending (from jPOST)
Dataset title: Quantitative Proteomic Analysis of Residual Host Cell Protein Retention Across Adeno- Associated Virus (AAV) Affinity Chromatography
Possible reference: Leibiger, TM. et al. (2024) Quantitative proteomic analysis of residual host cell protein retention across adeno-associated virus affinity chromatography., Mol Ther Methods Clin Dev, PMID 39691383

PXD056276 Dataset with its publication pending (from PRIDE)
Dataset title: SORLA upregulation suppresses global pathological effects in aged tauopathy mouse brain
Possible reference: Huang, H. et al. (2025) SORLA upregulation suppresses global pathological effects in aged tauopathy mouse brain., bioRxiv, PMID 40667014

PXD056270 Dataset with its publication pending (from iProX)
Dataset title: Migrions, a Migrasome-mediated unit for Intercellular Viral Transmission
Possible reference: Huang, Y. et al. (2026) Migrion: a Migrasome-mediated unit for intercellular viral transmission., Sci Bull (Beijing), PMID 40914694

PXD056264 Dataset with its publication pending (from iProX)
Dataset title: Inhibition of osteosarcoma progression by sporoderm-removed ganoderma lucidum spores
Possible reference: Pan, H. et al. (2025) Multi-omics analysis reveals inhibition of osteosarcoma progression by sporoderm-removed Ganoderma lucidum spores via targeting glycerophospholipid and fatty acid metabolism., Sci Rep, PMID 40596188

PXD056261 Dataset with its publication pending (from jPOST)
Dataset title: Mechanisms of amphibian arrestin 1 self-association and dynamic distribution in retinal photoreceptors
Possible reference: Barnes, CL. et al. (2024) Mechanisms of amphibian arrestin 1 self-association and dynamic distribution in retinal photoreceptors., J Biol Chem, PMID 39510183

PXD056244 no publication (from MassIVE)
Dataset title: The Role of the Co-Chaperone DNAJB11 in Polycystic Kidney Disease: Molecular Mechanisms and Cellular Origin of Cyst Formation
Possible reference: Busch, T. et al. (2024) The role of the co-chaperone DNAJB11 in polycystic kidney disease: Molecular mechanisms and cellular origin of cyst formation., FASEB J, PMID 39530576

PXD056240 no publication (from MassIVE)
Dataset title: The Role of the Co-Chaperone DNAJB11 in Polycystic Kidney Disease: Molecular Mechanisms and Cellular Origin of Cyst Formation
Possible reference: Busch, T. et al. (2024) The role of the co-chaperone DNAJB11 in polycystic kidney disease: Molecular mechanisms and cellular origin of cyst formation., FASEB J, PMID 39530576

PXD056187 Dataset with its publication pending (from PRIDE)
Dataset title: BAF60/SWP73 Subunits Define Subclasses of SWI/SNF Chromatin Remodelling Complexes in Arabidopsis
Possible reference: Sacharowski, SP. et al. (2025) BAF60/SWP73 subunits define subclasses of SWI/SNF chromatin remodelling complexes in Arabidopsis., New Phytol, PMID 40404167

PXD056186 Dataset with its publication pending (from PRIDE)
Dataset title: An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs
Possible reference: Wang, L. et al. (2025) An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs., Nat Genet, PMID 40186057

PXD056184 Dataset with its publication pending (from PRIDE)
Dataset title: Validation of potential growth-related proteins in chick vitreous during emmetropization using targeted-based proteomics (MRMHR)
Possible reference: Cheung, JK. et al. (2024) Identification of Potential Growth-Related Proteins in Chick Vitreous during Emmetropization Using SWATH-MS and Targeted-Based Proteomics (MRMHR)., Int J Mol Sci, PMID 39408973

PXD056178 no publication (from MassIVE)
Dataset title: Unveiling signaling pathways inducing MHC class II expression in neutrophils
Possible reference: Forrer, P. et al. (2024) Unveiling signaling pathways inducing MHC class II expression in neutrophils., Front Immunol, PMID 39403371

PXD056177 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of fecal microbes as potential biomarkers for early diagnosis of fatty liver disease in cattle
Possible reference: Sun, H. et al. (2025) Identification of fecal microbes as potential biomarkers for early diagnosis of fatty liver disease in cattle., Virulence, PMID 40635268

PXD056173 Dataset with its publication pending (from PRIDE)
Dataset title: Proximity-based activation of AURORA A by MPS1 potentiates error correction
Possible reference: Le�a, N. et al. (2024) Proximity-based activation of AURORA A by MPS1 potentiates error correction., bioRxiv, PMID 38948877

PXD056172 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting KPNB1 suppresses DNA damage repair in AML cells by inhibiting HMGB2 nuclear translocation
Possible reference: Xie, Y. et al. (2025) Targeting KPNB1 suppresses AML cells by inhibiting HMGB2 nuclear import., Oncogene, PMID 40082556

PXD056167 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular Vesicles From Xylella fastidiosa Carry sRNAs and Genomic Islands, Suggesting Roles in Recipient Cells
Possible reference: Ruf, A. et al. (2025) Extracellular Vesicles From Xylella fastidiosa Carry sRNAs and Genomic Islands, Suggesting Roles in Recipient Cells., J Extracell Vesicles, PMID 40560800

PXD056124 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of a large scale of ccRCC and normal kidney tissues
Possible reference: White, NM. et al. (2014) Quantitative proteomic analysis reveals potential diagnostic markers and pathways involved in pathogenesis of renal cell carcinoma., Oncotarget, PMID 24504108

PXD056121 Dataset with its publication pending (from iProX)
Dataset title: Global Analysis of Protein Acetylation in the Kidneys of C57BL/6 Mice with Cisplatin-Induced Renal Fibrosis (label-free quantitative proteomic data)
Possible reference: Yang, H. et al. (2026) Global Analysis of the Acetylome in Cisplatin-Induced Renal Fibrosis in C57BL/6 Mice., J Proteome Res, PMID 41459981

PXD056120 Dataset with its publication pending (from iProX)
Dataset title: A New Approach for Isolating Chromatin-Associated Proteins and Optimizing Chromatin Immunoprecipitation
Possible reference: Bournaud, C. et al. (2026) Profiling DNA-protein interactions in Meloidogyne incognita using dCas9-based affinity purification., Plant Methods, PMID 41486156

PXD056100 no publication (from MassIVE)
Dataset title: A comprehensive multi-omics signature of doxorubicin-induced cellular senescence in the postmenopausal human ovary
Possible reference: Devrukhkar, PR. et al. (2025) A Comprehensive Multiomics Signature of Doxorubicin-Induced Cellular Senescence in the Postmenopausal Human Ovary., Aging Cell, PMID 40452152

PXD056097 Dataset with its publication pending (from PRIDE)
Dataset title: Validation of potential growth-related proteins in chick vitreous during emmetropization using targeted-based proteomics (MRMHR)
Possible reference: Cheung, JK. et al. (2024) Identification of Potential Growth-Related Proteins in Chick Vitreous during Emmetropization Using SWATH-MS and Targeted-Based Proteomics (MRMHR)., Int J Mol Sci, PMID 39408973

PXD056096 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression
Possible reference: Tuechler, N. et al. (2025) Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression., Mol Syst Biol, PMID 40473842

PXD056075 Dataset with its publication pending (from PRIDE)
Dataset title: Meltome of P. falciparum across intraerythrocytic developmental cycle
Possible reference: Pazicky, S. et al. (2025) MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages., Nat Microbiol, PMID 41315737

PXD056068 no publication (from MassIVE)
Dataset title: An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions
Possible reference: Rajagopal, V. et al. (2024) An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions., bioRxiv, PMID 39386702

PXD056009 Dataset with its publication pending (from PRIDE)
Dataset title: Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase
Possible reference: Schmidt, N. et al. (2024) Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase., Nat Commun, PMID 39715735

PXD056006 Dataset with its publication pending (from PRIDE)
Dataset title: Brucella suis S2 strain inhibits IRE1/Caspase-12/Caspase-3 pathway-mediated apoptosis of microglia HMC3 by affecting the ubiquitination of CALR
Possible reference: Wang, Z. et al. (2025) Brucella suis S2 strain inhibits IRE1/caspase-12/caspase-3 pathway-mediated apoptosis of microglia HMC3 by affecting the ubiquitination of CALR., mSphere, PMID 40019270

PXD056004 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring the vault interactome in the divergent eukaryote Trypanosoma brucei
Possible reference: Zavrelova, A. et al. (2025) The trypanosome vault particle is composed of multiple major vault protein paralogs and harbors vault RNA., J Biol Chem, PMID 40945728

PXD055982 Dataset with its publication pending (from PRIDE)
Dataset title: Selective targeting of TBXT with DARPins identifies regulatory networks and therapeutic vulnerabilities in chordoma
Possible reference: Umbaugh, CS. et al. (2025) Selective targeting of TBXT with DARPins identifies regulatory networks and therapeutic vulnerabilities in chordoma., Sci Adv, PMID 40901948

PXD055971 Dataset with its publication pending (from jPOST)
Dataset title: Angiogenic performance of human skeletal muscle microvascular endothelial cells compared to human umbilical vein endothelial cells
Possible reference: Min, Y. et al. (2018) Human adipose mesenchymal stem cells overexpressing dual chemotactic gene showed enhanced angiogenic capacity in ischaemic hindlimb model., Cardiovasc Res, PMID 29659744

PXD055965 Dataset with its publication pending (from PRIDE)
Dataset title: Multi tissue proteomic analysis of cold exposure
Possible reference: Gillette, MA. et al. (2020) Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma., Cell, PMID 32649874

PXD055963 Dataset with its publication pending (from jPOST)
Dataset title: Comparative Proteomic Analysis of Astrocytoma Tissues from Patients with and without Seizures
Possible reference: Khaosuwan, T. et al. (2025) Comparative proteomic analysis of astrocytoma tissues from patients with and without seizures., Sci Rep, PMID 39849075

PXD055956 Dataset with its publication pending (from PRIDE)
Dataset title: lncRNA-protein interactions in hematopoietic progenitor cells by hybridization capture and mass spectrometry
Possible reference: Dai, Y. et al. (2025) Identifying lncRNA-Protein Interactions in Hematopoietic Progenitor Cells by Hybridization Capture and Mass Spectrometry., J Proteome Res, PMID 40747827

PXD055951 Dataset with its publication pending (from jPOST)
Dataset title: In vivo transformations of positively charged nanoparticles alter the formation and function of RuBisCO photosynthetic protein corona
Possible reference: Castillo, C. et al. (2025) In vivo transformations of positively charged nanoparticles alter the formation and function of RuBisCO photosynthetic protein corona., Nat Nanotechnol, PMID 40461790

PXD055947 no publication (from MassIVE)
Dataset title: CRL4-DCAF12 regulation of MCMBP ensures optimal licensing of DNA replication
Possible reference: Yadav, AK. et al. (2025) CRL4DCAF12 regulation of MCMBP ensures optimal licensing of DNA replication., Nat Commun, PMID 41145411

PXD055945 no publication (from MassIVE)
Dataset title: Investigation of natural dyes and taxonomic identification of fibers used in Chancay textiles by vibrational spectroscopy and mass spectrometry
Possible reference: Diaz-Granados, KS. et al. (2025) Investigation of Natural Dyes and Taxonomic Identification of Fibers Used in Chancay Textiles by Vibrational Spectroscopy and Mass Spectrometry., J Proteome Res, PMID 39752566

PXD055943 Dataset with its publication pending (from PRIDE)
Dataset title: Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines
Possible reference: Bakhtina, AA. et al. (2024) Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines., bioRxiv, PMID 38915502

PXD055937 Dataset with its publication pending (from PRIDE)
Dataset title: USP7 protects TFEB from proteasome-mediated degradation
Possible reference: Keshri, S. et al. (2024) USP7 protects TFEB from proteasome-mediated degradation., Cell Rep, PMID 39412987

PXD055924 Dataset with its publication pending (from PRIDE)
Dataset title: LC-MS/MS: Identification of a new type of histone modification
Possible reference: Lee, KC. et al. (2023) Use of iTRAQ-based quantitative proteomic identification of CHGA and UCHL1 correlated with lymph node metastasis in colorectal carcinoma., J Cell Mol Med, PMID 37246623

PXD055919 Dataset with its publication pending (from PRIDE)
Dataset title: Optimization of ultra fast nDIA proteomics approach
Possible reference: Xiong, Y. et al. (2024) Ultra-Fast Multi-Organ Proteomics Unveils Tissue-Specific Mechanisms of Drug Efficacy and Toxicity., bioRxiv, PMID 39386681

PXD055917 Dataset with its publication pending (from PRIDE)
Dataset title: Selective Labeling of Tyrosine Residues in Proteins: Insights from PTAD Labeling and Tandem Mass Spectrometry Analysis
Possible reference: Zacharias, AO. et al. (2025) Selective labeling of tyrosine residues in proteins: insights from PTAD labeling and tandem mass spectrometry analysis., Mol Omics, PMID 39717905

PXD055911 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting supramammillary circuits restores cognitive and noncognitive function in Alzheimer’s disease
Possible reference: Luo, YJ. et al. (2025) Segregated supramammillary-dentate gyrus circuits modulate cognitive and affective function in healthy and Alzheimer's disease model mice., Neuron, PMID 41045929

PXD055898 Dataset with its publication pending (from PRIDE)
Dataset title: Structure of a Gcn2 dimer in complex with the large 60S ribosomal subunit
Possible reference: Paternoga, H. et al. (2025) Structure of a Gcn2 dimer in complex with the large 60S ribosomal subunit., Proc Natl Acad Sci U S A, PMID 40198700

PXD055885 Dataset with its publication pending (from PRIDE)
Dataset title: The transaminase-Ï-amidase pathway is a redox switch in glutamine metabolism that generates Î±-ketoglutarate
Possible reference: Herrle, N. et al. (2026) The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cells., EMBO J, PMID 41408486

PXD055876 Dataset with its publication pending (from PRIDE)
Dataset title: Identification and functional characterization of a fructose-inducible phosphotransferase system in Azospirillum brasilense Sp7
Possible reference: Rai, S. et al. (2025) Identification and functional characterization of a fructose-inducible phosphotransferase system in Azospirillum brasilense Sp7., Appl Environ Microbiol, PMID 39817736

PXD055865 Dataset with its publication pending (from PRIDE)
Dataset title: Glycosite Mapping and in situ Mass Spectrometry Imaging of MUC2 Glycopeptides via On-slide Mucinase Digestion
Possible reference: Lowery, SC. et al. (2026) Glycosite mapping and in situ mass spectrometry imaging of MUC2 glycopeptides via on-slide mucinase digestion., Nat Commun, PMID 42098121

PXD055858 Dataset with its publication pending (from PRIDE)
Dataset title: ERH regulates type II interferon immune signaling through post-transcriptional regulation of JAK2 mRNA
Possible reference: Soderholm, A. et al. (2025) ERH regulates type II interferon immune signaling through post-transcriptional regulation of JAK2 mRNA., Nucleic Acids Res, PMID 40586312

PXD055854 Dataset with its publication pending (from PRIDE)
Dataset title: Deep learning to decode sites of RNA translation in normal and cancerous tissues
Possible reference: Clauwaert, J. et al. (2024) Deep learning to decode sites of RNA translation in normal and cancerous tissues., bioRxiv, PMID 38585907

PXD055844 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of Cortical Neurogenesis by MED13L via Transcriptional Priming and its Implications for MED13L Syndrome
Possible reference: Li, J. et al. (2025) Regulation of cortical neurogenesis by MED13L via transcriptional priming and its implications for MED13L syndrome., Commun Biol, PMID 40775066

PXD055827 no publication (from MassIVE)
Dataset title: The phase I GlutaPanc trial L glutamine in combination with first line gemcitabine and nab paclitaxel in metastatic pancreatic ductal adenocarcinoma
Possible reference: Gong, J. et al. (2023) Combination L-Glutamine with Gemcitabine and Nab-Paclitaxel in Treatment-Na�ve Advanced Pancreatic Cancer: The Phase I GlutaPanc Study Protocol., Biomedicines, PMID 37239063

PXD055822 no publication (from MassIVE)
Dataset title: Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain
Possible reference: Di Fraia, D. et al. (2024) Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain., bioRxiv, PMID 38260253

PXD055814 Dataset with its publication pending (from PRIDE)
Dataset title: C-terminal amides mark proteins for degradation via SCF/FBXO31 – CTAP discovery
Possible reference: Muhar, MF. et al. (2025) C-terminal amides mark proteins for degradation via SCF-FBXO31., Nature, PMID 39880951

PXD055790 Dataset with its publication pending (from jPOST)
Dataset title: Comparative characterization of the seven H3K4 methyltransferase in Arabidopsis thaliana
Possible reference: Oya, S. et al. (2026) Comparative characterization of chromatin-targeting mechanisms across seven H3K4 methyltransferases in Arabidopsis., Plant Commun, PMID 41496450

PXD055780 no publication (from MassIVE)
Dataset title: MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation
Possible reference: Fields, L. et al. (2025) MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation., J Proteome Res, PMID 40197022

PXD055775 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphorylation of a nuclear condensate regulates cohesion and mRNA retention
Possible reference: McIntyre, ABR. et al. (2025) Phosphorylation of a nuclear condensate regulates cohesion and mRNA retention., Nat Commun, PMID 39755675

PXD055750 Dataset with its publication pending (from PRIDE)
Dataset title: A proteome-wide dependency map of protein interaction motifs
Possible reference: Castello, A. et al. (2016) Comprehensive Identification of RNA-Binding Domains in Human Cells., Mol Cell, PMID 27453046

PXD055743 Dataset with its publication pending (from PRIDE)
Dataset title: Reliability of Serum-Derived Connectome Indicators in Identifying Cirrhosis
Possible reference: Guo, J. et al. (2024) Reliability of Serum-Derived Connectome Indicators in Identifying Cirrhosis., J Proteome Res, PMID 39305261

PXD055738 Dataset with its publication pending (from PRIDE)
Dataset title: Ckmt2 for Evaluating Reperfusion Injury in Acute Myocardial Infarction
Possible reference: Lang, A. et al. (2024) Mitochondrial Creatine Kinase 2 (Ckmt2) as a Plasma-Based Biomarker for Evaluating Reperfusion Injury in Acute Myocardial Infarction., Biomedicines, PMID 39457679

PXD055733 Dataset with its publication pending (from iProX)
Dataset title: Integrative multi-omics analyses reveal the global regulation network of the microalga Nannochloropsis oceanica under nitrogen stress adaptation
Possible reference: You, W. et al. (2025) Integrative Multi-Omics Analyses Reveal the Global Regulation Network of the Microalga Nannochloropsis oceanica Under Nitrogen Stress Adaptation., Biology (Basel), PMID 41300389

PXD055725 Dataset with its publication pending (from iProX)
Dataset title: Human-derived proteome characterization of tongue coating in colorectal cancer
Possible reference: Chen, Q. et al. (2025) Human-Derived Proteome Characterization of Tongue Coating in Colorectal Cancer., J Proteome Res, PMID 40378345

PXD055648 no publication (from MassIVE)
Dataset title: Nitrogen Limitation Causes a Seismic Shift in the Redox States and Phosphorylation of Proteins Implicated in Carbon Flux and Lipidome Remodeling for Rhodotorula toruloides
Possible reference: Gluth, A. et al. (2025) Nitrogen limitation causes a seismic shift in redox state and phosphorylation of proteins implicated in carbon flux and lipidome remodeling in Rhodotorula toruloides., Biotechnol Biofuels Bioprod, PMID 40691609

PXD055646 Dataset with its publication pending (from PRIDE)
Dataset title: The Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links
Possible reference: Altshuller, M. et al. (2024) The Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links., bioRxiv, PMID 38352618

PXD055631 Dataset with its publication pending (from PRIDE)
Dataset title: A network of interacting ciliary tip proteins with opposing activities imparts slow and processive microtubule growth
Possible reference: Saunders, HAJ. et al. (2025) A network of interacting ciliary tip proteins with opposing activities imparts slow and processive microtubule growth., Nat Struct Mol Biol, PMID 39856351

PXD055609 Dataset with its publication pending (from PRIDE)
Dataset title: Immunogenic noncoding cryptic peptides dominate the antigenic landscape of ovarian cancer
Possible reference: Raja, R. et al. (2025) Immunogenic cryptic peptides dominate the antigenic landscape of ovarian cancer., Sci Adv, PMID 39970218

PXD055592 Dataset with its publication pending (from PRIDE)
Dataset title: Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness
Possible reference: Rosen, BP. et al. (2024) Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness., bioRxiv, PMID 37205540

PXD055547 Dataset with its publication pending (from PRIDE)
Dataset title: Maximizing immunopeptidomics-based bacterial epitope discovery by rescoring and integrating the results of multiple search engines
Possible reference: Willems, P. et al. (2025) Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring., J Proteome Res, PMID 40080147

PXD055536 Dataset with its publication pending (from PRIDE)
Dataset title: The impact of exercise on skeletal muscle proteome of prediabetic subjects analyzed with data independent mass spectrometry.
Possible reference: Czajkowska, A. et al. (2025) The impact of exercise on skeletal muscle proteome of prediabetic subjects analyzed with data independent mass spectrometry., Sci Rep, PMID 40775511

PXD055530 Dataset with its publication pending (from iProX)
Dataset title: CysMP reveals metal ion-specific metalloproteomes and copper-regulated PGK1 activity in glycolysis
Possible reference: Yuan, Y. et al. (2025) CysMP reveals metal ion-specific metalloproteomes and copper-regulated PGK1 activity in glycolysis., Sci Adv, PMID 41105763

PXD055526 Dataset with its publication pending (from iProX)
Dataset title: iTRAQ quantitative proteomics of Natranaerobius thermophilus adaptation to combined hypersaline, alkaline pH, and elevated temperature environments
Possible reference: Xing, Q. et al. (2025) Cross and unique stress adaptation strategies of the polyextremophile Natranaerobius thermophilus to individual high salt, alkaline pH, and elevated temperature., J Proteomics, PMID 40482852

PXD055518 Dataset with its publication pending (from PRIDE)
Dataset title: C-terminal amides mark proteins for degradation via SCF/FBXO31
Possible reference: Muhar, MF. et al. (2025) C-terminal amides mark proteins for degradation via SCF-FBXO31., Nature, PMID 39880951

PXD055503 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting TNK2 reverses the immunosuppressive tumor microenvironment and synergizes with immunochemotherapy in pancreatic cancer
Possible reference: Wu, C. et al. (2025) Targeting TNK2/ACK1 reverses the immunosuppressive tumor microenvironment and synergizes with immunochemotherapy in pancreatic cancer., Nat Commun, PMID 41350522

PXD055475 Dataset with its publication pending (from PRIDE)
Dataset title: A dual-mechanism antimicrobial peptide with antimutagenic activity targets the replisome and induces cell envelope stress
Possible reference: Singleton, AH. et al. (2025) A dual-mechanism antimicrobial peptide with antimutagenic activity targets the replisome and induces cell envelope stress., mSphere, PMID 40879398

PXD055474 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of Cortical Neurogenesis by MED13L via Transcriptional Priming and its Implications for MED13L Syndrome
Possible reference: Li, J. et al. (2025) Regulation of cortical neurogenesis by MED13L via transcriptional priming and its implications for MED13L syndrome., Commun Biol, PMID 40775066

PXD055473 Dataset with its publication pending (from PRIDE)
Dataset title: Untargeted proteomics enables ultra-rapid variant prioritization in mitochondrial and other rare diseases
Possible reference: Hock, DH. et al. (2025) Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases., Genome Med, PMID 40400026

PXD055453 Dataset with its publication pending (from iProX)
Dataset title: Clinical response characteristics of salivary proteins in the management strategy of diabetes-associated periodontitis
Possible reference: Jia, S. et al. (2025) Clinical Response Characteristics of Salivary Proteins in the Management Strategy of Diabetes-Associated Periodontitis., J Proteome Res, PMID 40008981

PXD055441 Dataset with its publication pending (from iProX)
Dataset title: Ubiquitin independent degradation pathway regulates browning of white adipose tissue
Possible reference: Chen, H. et al. (2025) NRF2-REGγ-ACADM/KLF15 Signaling Pathway Regulates the Browning of White Adipose Tissue to Modulate Obesity., Adv Sci (Weinh), PMID 40971725

PXD055438 Dataset with its publication pending (from iProX)
Dataset title: phosphorylation site of ATG101
Possible reference: Nagy, P. et al. (2014) Atg17/FIP200 localizes to perilysosomal Ref(2)P aggregates and promotes autophagy by activation of Atg1 in Drosophila., Autophagy, PMID 24419107

PXD055437 Dataset with its publication pending (from iProX)
Dataset title: EtEC81 reprograms alternative splicing
Possible reference: Yu, H. et al. (2025) The Exserohilum turcicum effector EtEC81 reprograms alternative splicing in maize and activates immunity., Cell Rep, PMID 40173045

PXD055433 Dataset with its publication pending (from iProX)
Dataset title: Zika virus disrupts steroidogenesis and impairs spermatogenesis by stalling the translation of CYP17A1 mRNA
Possible reference: Yang, W. et al. (2025) Zika virus disrupts steroidogenesis and impairs spermatogenesis by stalling the translation of CYP17A1 mRNA., Nat Commun, PMID 40695837

PXD055403 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of the developmental programs in Toxoplasma by a novel SNF2L-containing chromatin remodeling complex
Possible reference: Zhu, Y. et al. (2025) Regulation of the developmental programs in Toxoplasma by a novel SNF2L-containing chromatin remodeling complex., Nat Commun, PMID 40593611

PXD055400 Dataset with its publication pending (from PRIDE)
Dataset title: A Kinetic Scout Approach Accelerates Targeted Protein Degrader Discovery
Possible reference: Fan, AT. et al. (2024) A Kinetic Scout Approach Accelerates Targeted Protein Degrader Development., bioRxiv, PMID 39345570

PXD055376 Dataset with its publication pending (from PRIDE)
Dataset title: Nucleus-Translocated GCLM Promotes Chemoresistance in Colorectal Cancer through a Moonlighting Function
Possible reference: Lin, JF. et al. (2025) Nucleus-translocated GCLM promotes chemoresistance in colorectal cancer through a moonlighting function., Nat Commun, PMID 39747101

PXD055366 Dataset with its publication pending (from PRIDE)
Dataset title: HBV remodels PP2A complexes to rewire kinase signaling in hepatocellular carcinoma
Possible reference: Turnham, RE. et al. (2025) HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma., Cancer Res, PMID 39652575

PXD055331 Dataset with its publication pending (from jPOST)
Dataset title: Retention of DLK1 in the endoplasmic reticulum identifies roles for EGF domain-specific O-glycans in the secretory pathway
Possible reference: Tashima, Y. et al. (2025) Retention of DLK1 in the endoplasmic reticulum identifies roles for EGF-like-domain-specific O-glycans in the secretory pathway., FEBS J, PMID 40637009

PXD055311 Dataset with its publication pending (from jPOST)
Dataset title: Age-related TFEB Downregulation in Proximal Tubules Causes Systemic Metabolic Disorders and Occasional Apolipoprotein A4-related Amyloidosis
Possible reference: Nakamura, J. et al. (2024) Age-related TFEB downregulation in proximal tubules causes systemic metabolic disorders and occasional apolipoprotein A4-related amyloidosis., JCI Insight, PMID 39699959

PXD055304 no publication (from MassIVE)
Dataset title: Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes
Possible reference: Cueny, RR. et al. (2024) Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes., bioRxiv, PMID 39185182

PXD055289 Dataset with its publication pending (from PRIDE)
Dataset title: Decoding pancreatic islet cell diversity through cell type-resolved proteomics and phosphoproteomics
Possible reference: Thielert, M. et al. (2025) Decoding adult murine pancreatic islet cell diversity through cell type-resolved proteomics and phosphoproteomics., Commun Biol, PMID 41107455

PXD055275 Dataset with its publication pending (from PRIDE)
Dataset title: Data for Cross-platform Construction of Comprehensive Proteomic Database for Human Corneal Epithelial Cell
Possible reference: Chan, KK. et al. (2025) A Comprehensive Proteome of Human Corneal Epithelial Cells Constructed by Cross-platform DIA-Mass Spectrometry., Sci Data, PMID 40410165

PXD055227 Dataset with its publication pending (from PRIDE)
Dataset title: Temporal control of acute protein aggregate turnover by UBE3C and NRF1-dependent proteasomal pathways
Possible reference: Hickey, KL. et al. (2024) Temporal control of acute protein aggregate turnover by UBE3C and NRF1-dependent proteasomal pathways., bioRxiv, PMID 39282280

PXD055203 Dataset with its publication pending (from PRIDE)
Dataset title: A Proteogenomic Analysis of Cervical Cancer Reveals Therapeutic and Biological Insights
Possible reference: Yu, J. et al. (2024) A proteogenomic analysis of cervical cancer reveals therapeutic and biological insights., Nat Commun, PMID 39578447

PXD055174 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring the Biological Mechanisms of Severe COVID-19 in the Elderly: Insights from an Aged Mouse
Possible reference: Ma, L. et al. (2025) Exploring the biological mechanisms of severe COVID-19 in the elderly: Insights from an aged mouse model., Virulence, PMID 40228062

PXD055169 Dataset with its publication pending (from PRIDE)
Dataset title: Cysteine-enabled Cleavability to Advance Cross-linking Mass Spectrometry for Global Analysis of Endogenous Protein-Protein Interactions
Possible reference: Jiao, F. et al. (2025) Cysteine-enabled cleavability to advance cross-linking mass spectrometry for global analysis of endogenous protein-protein interactions., Nat Commun, PMID 41387687

PXD055150 no publication (from MassIVE)
Dataset title: Multiomics Profiling of Extracellular Vesicles Supports Their Involvement in Endothelial Senescence-Associated Vascular Dysfunction
Possible reference: Hogans, RE. et al. (2025) Multiomics Profiling of Extracellular Vesicles Supports Their Involvement in Endothelial Senescence-Associated Vascular Dysfunction., J Extracell Biol, PMID 40755907

PXD055131 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of the eutopic endometrium of patients with internal or external ademomyosis
Possible reference: Lu, Q. et al. (2020) T-cadherin inhibits invasion and migration of endometrial stromal cells in endometriosis., Hum Reprod, PMID 31886853

PXD055112 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting G1–S Checkpoint–Compromised Cancers with Cyclin A/B RxL Inhibitors
Possible reference: Singh, S. et al. (2025) Targeting G1-S-checkpoint-compromised cancers with cyclin A/B RxL inhibitors., Nature, PMID 40836083

PXD055100 Dataset with its publication pending (from iProX)
Dataset title: Proteomics analysis of nitrogen stress on the influence of carbon and nitrogen metabolism of flue-cured tobacco
Possible reference: Zhang, X. et al. (2025) Proteomics analysis of nitrogen stress on the influence of carbon and nitrogen metabolism of flue-cured tobacco., BMC Genomics, PMID 41146059

PXD055082 no publication (from MassIVE)
Dataset title: mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation
Possible reference: McCormick, CA. et al. (2024) mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation., bioRxiv, PMID 38766185

PXD055061 Dataset with its publication pending (from PRIDE)
Dataset title: the interactome of H3K4me3 in RAW264.7 cells
Possible reference: Wang, Y. et al. (2025) Development of nucleus-targeted histone-tail-based photoaffinity probes to profile the epigenetic interactome in native cells., Nat Commun, PMID 39762271

PXD055058 Dataset with its publication pending (from PRIDE)
Dataset title: the interactome of H3K4me3 in HeLa cells
Possible reference: Wang, Y. et al. (2025) Development of nucleus-targeted histone-tail-based photoaffinity probes to profile the epigenetic interactome in native cells., Nat Commun, PMID 39762271

PXD055035 Dataset with its publication pending (from iProX)
Dataset title: Integrating multi-omics to reveal the molecular mechanism of lipid metabolism regulated by a splice variant of Lysyl-oxidase like-2, LOXL2Î13
Possible reference: Chen, Y. et al. (2025) Integrating multi-omics to reveal the molecular mechanism of lipid metabolism regulated by a splice variant of Lysyl-oxidase like-2, LOXL2Δ13., Commun Biol, PMID 41272297

PXD055029 no publication (from MassIVE)
Dataset title: An intrinsically disordered region of histone demethylase KDM5A regulates catalysis through interactions with the nucleosomal acidic patch and DNA
Possible reference: Palla, AM. et al. (2025) An Intrinsically Disordered Region of Histone Demethylase KDM5A Activates Catalysis Through Interactions With the Nucleosomal Acidic Patch and DNA., J Mol Biol, PMID 40545232

PXD055026 Dataset with its publication pending (from iProX)
Dataset title: Phosphoproteomics Delineates Hepatocellular Carcinoma Subtypes and Pinpoints Therapeutic Targets
Possible reference: Zhang, Z. et al. (2025) Phosphoproteomics delineates hepatocellular carcinoma subtypes and pinpoints therapeutic targets., Hepatology, PMID 39887258

PXD055018 Dataset with its publication pending (from jPOST)
Dataset title: PRMT1-mediated methylation regulates MLL2 stability and gene expression
Possible reference: An, D. et al. (2025) PRMT1-mediated methylation regulates MLL2 stability and gene expression., Nucleic Acids Res, PMID 39698834

PXD055006 Dataset with its publication pending (from PRIDE)
Dataset title: A druggable redox switch on SHP1 controls macrophage inflammation
Possible reference: Ng, MY. et al. (2026) A druggable redox switch on SHP1 controls macrophage inflammation., bioRxiv, PMID 41757102

PXD055003 Dataset with its publication pending (from PRIDE)
Dataset title: Human Papillomavirus-encoded Circular RNA circE7 Promotes Immune Evasion in Head and Neck Squamous Cell Carcinoma
Possible reference: Ge, J. et al. (2024) Human papillomavirus-encoded circular RNA circE7 promotes immune evasion in head and neck squamous cell carcinoma., Nat Commun, PMID 39366979

PXD054976 no publication (from MassIVE)
Dataset title: Biofunctionalized dissolvable hydrogel microbeads enable efficient characterization of native protein complexes
Possible reference: Shao, X. et al. (2024) Biofunctionalized dissolvable hydrogel microbeads enable efficient characterization of native protein complexes., Nat Commun, PMID 39366952

PXD054966 no publication (from MassIVE)
Dataset title: A human gut bacterium antagonizes neighboring bacteria by altering their protein folding ability
Possible reference: Lim, B. et al. (2025) A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability., Cell Host Microbe, PMID 39909037

PXD054941 Dataset with its publication pending (from iProX)
Dataset title: Multi-omics reveals changes in astrocyte fatty acid metabolism during early stages of Alzheimer's disease
Possible reference: Zhong, J. et al. (2025) Multi-omics reveals changes in astrocyte fatty acid metabolism during early stages of Alzheimer's disease., Neurochem Int, PMID 40889558

PXD054928 Dataset with its publication pending (from PRIDE)
Dataset title: Control of cell identity and early neural fate commitment by the enhancer module of Integrator
Possible reference: Zhang, Y. et al. (2025) The enhancer module of Integrator controls cell identity and early neural fate commitment., Nat Cell Biol, PMID 39592860

PXD054884 Dataset with its publication pending (from jPOST)
Dataset title: Characteristics and Bioinformatics identification of Peptides from Natural and cultured sandfish (Holothuria scabra) Using Double Hydrolysis
Possible reference: Daopa, P. et al. (2025) Characteristics and bioinformatics of peptides from natural and cultured sandfish (Holothuria scabra)., Food Chem (Oxf), PMID 39995497

PXD054881 Dataset with its publication pending (from PRIDE)
Dataset title: MTCH2 modulates CPT1 activity to regulate lipid metabolism of adipocytes
Possible reference: Wu, C. et al. (2025) MTCH2 modulates CPT1 activity to regulate lipid metabolism of adipocytes., Nat Commun, PMID 41044057

PXD054869 Dataset with its publication pending (from PRIDE)
Dataset title: Myeloid lineage C3 induces reactive gliosis and neuronal stress during CNS inflammation
Possible reference: Garton, T. et al. (2025) Myeloid lineage C3 induces reactive gliosis and neuronal stress during CNS inflammation., Nat Commun, PMID 40216817

PXD054844 Dataset with its publication pending (from jPOST)
Dataset title: LETMD1 regulates mitochondrial protein synthesis and import to guard brown fat mitochondrial integrity and function
Possible reference: Snyder, M. et al. (2024) LETMD1 regulates mitochondrial protein synthesis and import to guard brown fat mitochondrial integrity and function., iScience, PMID 39398236

PXD054843 no publication (from MassIVE)
Dataset title: EZH2 loss during metabolic stress drives restoration of MHC Class I machinery in melanoma
Possible reference: Edmondson, JL. et al. (2025) EZH2 loss during metabolic stress drives restoration of MHC class I machinery in melanoma., iScience, PMID 40546964

PXD054836 Dataset with its publication pending (from iProX)
Dataset title: CKAP4 in Hepatocellular Carcinoma: Competitive RETREG1/FAM134B Binding, ER-phagy Regulation, and Cancer Progression
Possible reference: Mo, J. et al. (2025) CKAP4 in hepatocellular carcinoma: competitive RETREG1/FAM134B binding, reticulophagy regulation, and cancer progression., Autophagy, PMID 39689859

PXD054830 Dataset with its publication pending (from jPOST)
Dataset title: Tissue Proteomics of Feline Mammary Carcinoma: Different in protein profiles among Histological Grades using Liquid chromatography‑Tandem Mass Spectrometry
Possible reference: Aruvornlop, P. et al. (2026) Tissue Proteomics of Feline Mammary Carcinoma: Differences in Protein Profiles Among Histological Grades Using Liquid Chromatography-Tandem Mass Spectrometry., Vet Comp Oncol, PMID 41420294

PXD054821 no publication (from MassIVE)
Dataset title: Acetate enhances long-term memory in female mice by sex-, context-, and brain region–specific epigenetic and transcriptional remodeling
Possible reference: Periandri, EM. et al. (2026) Acetate enhances long-term memory in female mice by sex-, context-, and brain region-specific epigenetic and transcriptional remodeling., Sci Signal, PMID 41734254

PXD054820 no publication (from MassIVE)
Dataset title: Inhibition of Cbl-b restores effector functions of human intratumoral NK cells
Possible reference: Tundo, S. et al. (2024) Inhibition of Cbl-b restores effector functions of human intratumoral NK cells., J Immunother Cancer, PMID 39551607

PXD054805 Dataset with its publication pending (from PRIDE)
Dataset title: The p-MYH9/USP22/HIF-1Î± axis promotes lenvatinib resistance and cancer stemness in hepatocellular carcinoma
Possible reference: Shan, Q. et al. (2024) The p-MYH9/USP22/HIF-1α axis promotes lenvatinib resistance and cancer stemness in hepatocellular carcinoma., Signal Transduct Target Ther, PMID 39300073

PXD054783 Dataset with its publication pending (from PRIDE)
Dataset title: CXCL12 restricts tumor growth by suppressing the Ras, ERK1/2, c-Myc and the immune checkpoint PDL1 pathways
Possible reference: Kravtsova-Ivantsiv, Y. et al. (2024) CXCL12 restricts tumor growth by suppressing the Ras, ERK1/2, c-Myc, and the immune checkpoint PD-L1 pathways., Proc Natl Acad Sci U S A, PMID 39689179

PXD054769 no publication (from MassIVE)
Dataset title: Scnn1b transgenic mice: BALF exosome proteomics
Possible reference: Mao, Y. et al. (2024) Airspaces-derived exosomes contain disease-relevant protein signatures in a mouse model of cystic fibrosis (CF)-like mucoinflammatory lung disease., Front Pharmacol, PMID 39386033

PXD054760 Dataset with its publication pending (from PRIDE)
Dataset title: The USP12/46 deubiquitinases protect integrins from ESCRT-mediated lysosomal degradation
Possible reference: Yu, K. et al. (2024) The USP12/46 deubiquitinases protect integrins from ESCRT-mediated lysosomal degradation., EMBO Rep, PMID 39506038

PXD054751 Dataset with its publication pending (from PRIDE)
Dataset title: Structuring lipid nanoparticles, DNA, and protein corona into stealth bionanoarchitectures for in vivo gene delivery
Possible reference: Renzi, S. et al. (2024) Structuring lipid nanoparticles, DNA, and protein corona into stealth bionanoarchitectures for in vivo gene delivery., Nat Commun, PMID 39438484

PXD054748 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53
Possible reference: Wendrich, K. et al. (2025) Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53., Nat Chem Biol, PMID 39587316

PXD054724 no publication (from MassIVE)
Dataset title: In vivo and in vitro analysis of the role of the Prc protease in inducing mucoidy in Pseudomonas aeruginosa
Possible reference: Sommerfield, AG. et al. (2024) In vivo and in vitro analysis of the role of the Prc protease in inducing mucoidy in Pseudomonas aeruginosa., bioRxiv, PMID 38854061

PXD054722 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of phosphorylation sites of BAG3
Possible reference: Xue, L. et al. (2014) Identification of extracellular signal-regulated kinase 1 (ERK1) direct substrates using stable isotope labeled kinase assay-linked phosphoproteomics., Mol Cell Proteomics, PMID 25022875

PXD054719 Dataset with its publication pending (from PRIDE)
Dataset title: FUCCI Based Study of Toxoplasma Endodyogeny
Possible reference: Batra, M. et al. (2025) Deciphering cell cycle organization of Toxoplasma endodyogeny., mBio, PMID 40590555

PXD054689 Dataset with its publication pending (from jPOST)
Dataset title: Korean Tissue Phosphoproteome Analysis
Possible reference: Zhao, D. et al. (2024) Multi-omics characterization of esophageal squamous cell carcinoma identifies molecular subtypes and therapeutic targets., JCI Insight, PMID 38652547

PXD054678 Dataset with its publication pending (from PRIDE)
Dataset title: A platform for mapping reactive cysteines within the immunopeptidome
Possible reference: Zhang, C. et al. (2024) A platform for mapping reactive cysteines within the immunopeptidome., Nat Commun, PMID 39516457

PXD054663 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics dataset of knockdown of AKT3 on protein expression and function in female germline stem cells
Possible reference: Shen, Y. et al. (2024) Proteomic dataset of knockdown of AKT3 on protein expression and function in female germline stem cells., Data Brief, PMID 39687386

PXD054654 Dataset with its publication pending (from jPOST)
Dataset title: Therapeutic Targeting of Dihydroorotate Dehydrogenase (DHODH) in Neuroblastoma: Modulating Lipid Metabolism and Ferroptosis
Possible reference: Shir, JC. et al. (2025) DHODH Blockade Induces Ferroptosis in Neuroblastoma by Modulating the Mevalonate Pathway., Mol Cell Proteomics, PMID 40513779

PXD054635 Dataset with its publication pending (from PRIDE)
Dataset title: Photoactivated adenylyl cyclase in cortical astrocytes promotes synaptic potentiation and reveals alterations in Huntington’s Disease
Possible reference: Sitj�-Roqueta, L. et al. (2025) Photoactivated adenylyl cyclase in cortical astrocytes promotes synaptic potentiation and reveals alterations in Huntington's disease., iScience, PMID 41146711

PXD054633 Dataset with its publication pending (from PRIDE)
Dataset title: Photoactivated adenylyl cyclase in cortical astrocytes promotes synaptic potentiation and reveals alterations in Huntington’s Disease
Possible reference: Sitj�-Roqueta, L. et al. (2025) Photoactivated adenylyl cyclase in cortical astrocytes promotes synaptic potentiation and reveals alterations in Huntington's disease., iScience, PMID 41146711

PXD054625 Dataset with its publication pending (from jPOST)
Dataset title: Quantitative Proteomics Unveils Synergistic Effects of Combination drugs on Cytoskeleton Composition and Autophagy-Mediated Cell Death in Neuroblastoma
Possible reference: Yu, PC. et al. (2025) Quantitative Proteomics Unveils the Synergistic Effects of Combination Drugs on Cytoskeleton Composition and Autophagy-Mediated Cell Death in Neuroblastoma., J Proteome Res, PMID 40526398

PXD054623 Dataset with its publication pending (from PRIDE)
Dataset title: LRRTM2 controls presynapse nano-organization and AMPA receptor sub-positioning through Neurexin-binding interface
Possible reference: Liouta, K. et al. (2024) LRRTM2 controls presynapse nano-organization and AMPA receptor sub-positioning through Neurexin-binding interface., Nat Commun, PMID 39394199

PXD054579 Dataset with its publication pending (from PRIDE)
Dataset title: Rational engineering of minimally immunogenic nucleases for gene therapy
Possible reference: Raghavan, R. et al. (2025) Rational engineering of minimally immunogenic nucleases for gene therapy., Nat Commun, PMID 39747875

PXD054577 Dataset with its publication pending (from PRIDE)
Dataset title: Intragenic DNA inversions expand bacterial coding capacity
Possible reference: Chanin, RB. et al. (2023) Intragenic DNA inversions expand bacterial coding capacity., bioRxiv, PMID 36945655

PXD054559 Dataset with its publication pending (from PRIDE)
Dataset title: Achieving a 35plex Tandem Mass Tag Reagent Set Through Deuterium Incorporation
Possible reference: Zuniga, NR. et al. (2024) Achieving a 35-Plex Tandem Mass Tag Reagent Set through Deuterium Incorporation., J Proteome Res, PMID 39380184

PXD054557 Dataset with its publication pending (from jPOST)
Dataset title: Multi-omics analysis using antibody-based in situ biotinylation technique reveals the mechanism of Cajal body formation
Possible reference: Noguchi, K. et al. (2024) Multi-omics analysis using antibody-based in situ biotinylation technique suggests the mechanism of Cajal body formation., Cell Rep, PMID 39283744

PXD054551 Dataset with its publication pending (from PRIDE)
Dataset title: Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks
Possible reference: Yu, C. et al. (2024) Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks., bioRxiv, PMID 39211111

PXD054547 Dataset with its publication pending (from PRIDE)
Dataset title: Isoflurane Aggravates Pre-Existing Proteotoxicity in Adult Nematodes by Suppressing Mitochondrial Fitness
Possible reference: Elami, T. et al. (2026) Isoflurane aggravates pre-existing proteotoxicity in adult nematodes by suppressing mitochondrial fitness., Sci Rep, PMID 41667565

PXD054534 Dataset with its publication pending (from PRIDE)
Dataset title: In vitro investigations on the impact of constituents on fermented dairy on fecal microbiota composition
Possible reference: Li, Q. et al. (2025) In vitro investigations on the impact of fermented dairy constituents on fecal microbiota composition and fermentation activity., Microbiol Spectr, PMID 39902955

PXD054525 Dataset with its publication pending (from PRIDE)
Dataset title: Josephin Domain Containing 2 (JOSD2) Inhibition as Pan-KRAS-Mutation-Targeting Strategy for Colorectal Cancer
Possible reference: Yuan, T. et al. (2025) Josephin Domain Containing 2 (JOSD2) inhibition as Pan-KRAS-mutation-targeting strategy for colorectal cancer., Nat Commun, PMID 40240366

PXD054504 Dataset with its publication pending (from PRIDE)
Dataset title: Aberrant troponin post-translational modifications with TNNT1 mutations
Possible reference: Laitila, J. et al. (2025) Pathogenic TNNT1 variants are associated with aberrant thin filament compliance and myofibre hyper-contractility., J Physiol, PMID 40320982

PXD054457 no publication (from MassIVE)
Dataset title: Exploring Protein Post-Translational Modifications of Breast Cancer Cells Using a Novel Combinatorial Search Algorithm
Possible reference: Vasileva-Slaveva, M. et al. (2024) Exploring Protein Post-Translational Modifications of Breast Cancer Cells Using a Novel Combinatorial Search Algorithm., Int J Mol Sci, PMID 39337390

PXD054445 Dataset with its publication pending (from PRIDE)
Dataset title: Formaldehyde fixation helps preserving proteome state during single-cell proteomics sample processing and analysis
Possible reference: Piga, I. et al. (2025) Formaldehyde Fixation Helps Preserve the Proteome State during Single-Cell Proteomics Sample Processing and Analysis., J Proteome Res, PMID 39901769

PXD054430 no publication (from MassIVE)
Dataset title: Size Exclusion Chromatography Based Proteomic and Degradomic Profiling of Inflammasome-Activated, Murine Bone Marrow-Derived Dendritic Cells
Possible reference: Vogele, D. et al. (2024) Size exclusion chromatography based proteomic and degradomic profiling of inflammasome-activated, murine bone marrow-derived dendritic cells highlights complex retention and release of cleavage products., Mol Omics, PMID 39378052

PXD054426 Dataset with its publication pending (from iProX)
Dataset title: pH-Controlled chemoselective rapid azo-coupling reaction (CRACR) enables global profiling of serotonylation proteome in cancer cells
Possible reference: Zhang, N. et al. (2024) pH-Controlled chemoselective rapid azo-coupling reaction (CRACR) enables global profiling of serotonylation proteome in cancer cells., bioRxiv, PMID 38766043

PXD054416 Dataset with its publication pending (from PRIDE)
Dataset title: The role of the cotyledons after germination/during seedling development in Lupinus albus
Possible reference: Angermann, C. et al. (2025) Balancing nutrient remobilization and photosynthesis: proteomic insights into the dual role of lupin cotyledons after germination., Plant J, PMID 40690914

PXD054393 Dataset with its publication pending (from PRIDE)
Dataset title: B7-H4 post-translational modifications
Possible reference: Song, X. et al. (2020) Pharmacologic Suppression of B7-H4 Glycosylation Restores Antitumor Immunity in Immune-Cold Breast Cancers., Cancer Discov, PMID 32938586

PXD054386 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial translation regulates terminal erythroid differentiation by maintaining iron homeostasis
Possible reference: Zhang, S. et al. (2019) HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis., Elife, PMID 31033440

PXD054356 Dataset with its publication pending (from PRIDE)
Dataset title: PLpro inhibition protects in post-acute sequelae mouse model of COVID-19
Possible reference: M Bader, S. et al. (2025) A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID., Nat Commun, PMID 40180914

PXD054349 no publication (from MassIVE)
Dataset title: The promiscuous biotin ligase TurboID reveals the proxisome of the T3SS chaperone IpgC in the cytoplasm of Shigella flexneri
Possible reference: Haidar-Ahmad, N. et al. (2024) The promiscuous biotin ligase TurboID reveals the proxisome of the T3SS chaperone IpgC in Shigella flexneri., mSphere, PMID 39480076

PXD054344 no publication (from MassIVE)
Dataset title: A MULTI-MINERAL INTERVENTION TO IMPROVE DISEASE-RELATED AND MECHANISTIC BIOMARKERS IN ULCERATIVE COLITIS PATIENTS
Possible reference: Aslam, MN. et al. (2025) A multi-mineral intervention to improve disease-related and mechanistic biomarkers in ulcerative colitis patients: Results from a randomized trial., PLoS One, PMID 41359652

PXD054341 Dataset with its publication pending (from PRIDE)
Dataset title: Gtf2i-encoded transcription factor Tfii-i regulates myelination
Possible reference: Levy, G. et al. (2025) Gtf2i-encoded transcription factor Tfii-i regulates myelination via Sox10 and Mbp regulatory elements., Nat Commun, PMID 41006289

PXD054321 Dataset with its publication pending (from iProX)
Dataset title: Proteome of synthetic ribosomal 40S subunit
Possible reference: Xing, W. et al. (2018) Salidroside influences the cellular cross-talk of human fetal lung diploid fibroblasts: A proteomic approach., Environ Toxicol Pharmacol, PMID 29329019

PXD054314 Dataset with its publication pending (from PRIDE)
Dataset title: The proto-oncogene tyrosine kinase c-SRC facilitates glioblastoma progression by remodeling fatty acid synthesis
Possible reference: Zhao, W. et al. (2024) The proto-oncogene tyrosine kinase c-SRC facilitates glioblastoma progression by remodeling fatty acid synthesis., Nat Commun, PMID 39198451

PXD054289 no publication (from MassIVE)
Dataset title: Advanced multimodal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution
Possible reference: Veličković, M. et al. (2025) Advanced multi-modal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution., Nat Commun, PMID 40021619

PXD054256 Dataset with its publication pending (from iProX)
Dataset title: CSF proteomics of leptomeningeal metastasis mouse models
Possible reference: Remsik, J. et al. (2023) Leptomeningeal anti-tumor immunity follows unique signaling principles., bioRxiv, PMID 36993586

PXD054211 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Profile of Circulating Extracellular Vesicles in the Brain after Î 9-Tetrahydrocannabinol Inhalation
Possible reference: Lallai, V. et al. (2024) Proteomic Profile of Circulating Extracellular Vesicles in the Brain after Δ9-Tetrahydrocannabinol Inhalation., Biomolecules, PMID 39334909

PXD054205 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteomics and proteomics of insulin signaling in aged mouse bone
Possible reference: Dutt, M. et al. (2025) Phosphoproteomics of aged insulin-resistant bone identifies P70S6K phosphorylation of AFF4 as a gene-specific transcriptional regulator., Nat Commun, PMID 41476161

PXD054180 Dataset with its publication pending (from PRIDE)
Dataset title: Lapatinib-Induced Enhancement Of Mitochondrial Respiration In HER2-Positive SK-BR-3 Cells: Mechanism Revealed By Analysis Of Proteomic But Not Transcriptomic Data
Possible reference: Kamashev, D. et al. (2024) Lapatinib-induced enhancement of mitochondrial respiration in HER2-positive SK-BR-3 cells: mechanism revealed by analysis of proteomic but not transcriptomic data., Front Mol Biosci, PMID 39403185

PXD054151 no publication (from MassIVE)
Dataset title: Identification of Disease-relevant, Sex-based Proteomic Differences in iPSC-derived Vascular Smooth Muscle
Possible reference: Ariyasinghe, NR. et al. (2024) Identification of Disease-relevant, Sex-based Proteomic Differences in iPSC-derived Vascular Smooth Muscle., bioRxiv, PMID 39211096

PXD054138 no publication (from MassIVE)
Dataset title: Autophosphorylation of conserved yeast and human casein kinase 1 isozymes regulates Elongator dependent tRNA modifications
Possible reference: Landrock, MF. et al. (2025) Autophosphorylation of conserved yeast and human casein kinase 1 isozymes regulates Elongator-dependent tRNA modifications., Nucleic Acids Res, PMID 40930532

PXD054112 Dataset with its publication pending (from jPOST)
Dataset title: Single-Cell Secretome Profiling by NanoLC-MS/MS Analysis
Possible reference: He, Y. et al. (2025) Single-Cell Secretome Profiling Enabled by Selective Enrichment and NanoLC-MS/MS Analysis., Angew Chem Int Ed Engl, PMID 39609103

PXD054102 Dataset with its publication pending (from PRIDE)
Dataset title: Disruption of basal cell identity by Rank signaling drives mammary tumorigenesis
Possible reference: Redondo-Pedraza, J. et al. (2026) Rank signaling drives basal cell-lineage infidelity leading to mammary tumorigenesis., Nat Commun, PMID 41760656

PXD054084 no publication (from MassIVE)
Dataset title: Haloacetonitriles Induce Structure-related Cellular Toxicity through Distinct Proteome Thiol Reaction Mechanisms
Possible reference: Yeung, K. et al. (2025) Haloacetonitriles Induce Structure-Related Cellular Toxicity Through Distinct Proteome Thiol Reaction Mechanisms., ACS Environ Au, PMID 39830722

PXD054080 no publication (from MassIVE)
Dataset title: DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci
Possible reference: Liu, Y. et al. (2025) DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci., bioRxiv, PMID 39091817

PXD054054 Dataset with its publication pending (from iProX)
Dataset title: Proteome analysis of 11 organs of RJBs and ITBs nursing bee
Possible reference: Wang, R. et al. (2025) Multi-organ proteome reveals different nursing ability between two honeybee srocks., J Proteomics, PMID 40037490

PXD054036 no publication (from MassIVE)
Dataset title: Proteomic profiling of acoustically isolated extracellular vesicles from blood plasma during murine bacterial sepsis
Possible reference: Broman, A. et al. (2025) Proteomic Profiling of Acoustically Isolated Extracellular Vesicles from Blood Plasma during Murine Bacterial Sepsis., J Proteome Res, PMID 40641435

PXD054033 Dataset with its publication pending (from PRIDE)
Dataset title: OmpA controls order in the outer membrane and shares the mechanical load
Possible reference: Benn, G. et al. (2024) OmpA controls order in the outer membrane and shares the mechanical load., Proc Natl Acad Sci U S A, PMID 39630873

PXD054020 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial L-2-hydroxyglutarate is a physiologic signaling metabolite
Possible reference: Ryan, DG. et al. (2019) Coupling Krebs cycle metabolites to signalling in immunity and cancer., Nat Metab, PMID 31032474

PXD054015 no publication (from MassIVE)
Dataset title: An inflection point in high-throughput proteomics with Orbitrap Astral: analysis of biofluids, cells, and tissues
Possible reference: Hendricks, NG. et al. (2024) An inflection point in high-throughput proteomics with Orbitrap Astral: analysis of biofluids, cells, and tissues., bioRxiv, PMID 38712179

PXD054014 Dataset with its publication pending (from PRIDE)
Dataset title: Hbo1 and Msl complexes preserve differential compaction and H3K27me3 marking of active and inactive X chromosomes during mitosis
Possible reference: Djeghloul, D. et al. (2025) Hbo1 and Msl complexes preserve differential compaction and H3K27me3 marking of active and inactive X chromosomes during mitosis., Nat Cell Biol, PMID 40921734

PXD054003 Dataset with its publication pending (from PRIDE)
Dataset title: The hGID GID4 E3 ubiquitin ligase complex targets ARHGAP11A to regulate cell migration
Possible reference: Bagci, H. et al. (2024) The hGIDGID4 E3 ubiquitin ligase complex targets ARHGAP11A to regulate cell migration., Life Sci Alliance, PMID 39389782

PXD053999 Dataset with its publication pending (from PRIDE)
Dataset title: The sodium leak channel NALCN is regulated by the neuronal SNARE complex
Possible reference: Usher, S. et al. (2025) The sodium leak channel NALCN is regulated by neuronal SNARE complex proteins., Sci Adv, PMID 40085699

PXD053987 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of two leukemia cell lines K562 and Lucena-1.
Possible reference: Beraldo-Neto, E. et al. (2024) Proteomic Dynamics of Multidrug Resistance Mechanisms in Lucena 1 Cell Line., Cells, PMID 39272999

PXD053978 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibition of MBTPS1 enhances antitumor immunity and potentiates anti-PD-1 immunotherapy
Possible reference: Wang, YY. et al. (2025) Inhibition of MBTPS1 enhances antitumor immunity and potentiates anti-PD-1 immunotherapy., Nat Commun, PMID 40307212

PXD053948 Dataset with its publication pending (from PRIDE)
Dataset title: A WYL transcription factor regulates Lactiplantibacillus plantarum intestinal colonization via perceiving c-di-GMP
Possible reference: Guo, Q. et al. (2025) A WYL domain transcription factor regulates Lactiplantibacillus plantarum intestinal colonization via perceiving c-di-GMP., Nat Commun, PMID 40038299

PXD053947 Dataset with its publication pending (from PRIDE)
Dataset title: Sulfoglycolysis sustains Eubacterium rectale in low-fiber diets
Possible reference: Sharma, M. et al. (2025) Sulfoglycolysis sustains Eubacterium rectale in low-fiber diets., J Biol Chem, PMID 39956340

PXD053942 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial KMT9 methylates DLAT to control pyruvate dehydrogenase activity, de novo lipogenesis, and prostate cancer growth
Possible reference: Jia, Y. et al. (2025) Mitochondrial KMT9 methylates DLAT to control pyruvate dehydrogenase activity and prostate cancer growth., Nat Commun, PMID 39885202

PXD053940 Dataset with its publication pending (from PRIDE)
Dataset title: Uncover proteins binding HBV rcDNA
Possible reference: Li, Z. et al. (2025) Highly stable Cas9 promotes HBV genome destruction by antagonizing HSC70-mediated degradation., Emerg Microbes Infect, PMID 40904316

PXD053922 no publication (from MassIVE)
Dataset title: Therapeutic reduction of rad23a extends lifespan and mitigates pathology in TDP-43 mice.
Possible reference: Guo, X. et al. (2024) Reduction of RAD23A extends lifespan and mitigates pathology in TDP-43 mice., bioRxiv, PMID 39314471

PXD053908 Dataset with its publication pending (from PRIDE)
Dataset title: p38 mediated ACSL4 phosphorylation drives stress-induced esophageal squamous cell carcinoma growth through Src myristoylation
Possible reference: Yuan, Q. et al. (2025) p38 mediated ACSL4 phosphorylation drives stress-induced esophageal squamous cell carcinoma growth through Src myristoylation., Nat Commun, PMID 40195298

PXD053906 Dataset with its publication pending (from PRIDE)
Dataset title: Increased viral tolerance mediates by antiviral RNA interference in bat cells
Possible reference: Dai, Y. et al. (2024) Increased viral tolerance mediates by antiviral RNA interference in bat cells., Cell Rep, PMID 39102336

PXD053900 Dataset with its publication pending (from jPOST)
Dataset title: Cysteine redoxome landscape in the liver of male mice fed a high-fat high sucrose diet
Possible reference: Galicia-Medina, CM. et al. (2025) Cysteine redoxome landscape in the liver of male mice fed a high-fat high-sucrose diet., J Biol Chem, PMID 40967437

PXD053894 Dataset with its publication pending (from PRIDE)
Dataset title: �Macropinocytosis mediates metabolic resistance to loss of glutamine transport in triple-negative breast cancer
Possible reference: Wahi, K. et al. (2024) Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer., EMBO J, PMID 39420093

PXD053893 Dataset with its publication pending (from PRIDE)
Dataset title: Distinct mechanistic, conformational and substrate selectivity profiles emerging in the evolution of high catalytic activity enzymes via parallel trajectories
Possible reference: Karamitros, CS. et al. (2024) Mechanistic conformational and substrate selectivity profiles emerging in the evolution of enzymes via parallel trajectories., Nat Commun, PMID 39152129

PXD053881 Dataset with its publication pending (from PRIDE)
Dataset title: Bacterial RNA sensing by TLR8 requires RNase 6 processing and is inhibited by RNA 2’O-methylation
Possible reference: Nunes, IV. et al. (2024) Bacterial RNA sensing by TLR8 requires RNase 6 processing and is inhibited by RNA 2'O-methylation., EMBO Rep, PMID 39363059

PXD053872 Dataset with its publication pending (from PRIDE)
Dataset title: Co-culture CRISPR screens reveal ATG9A as a regulator to macrophage-mediated cytotoxicity in cancer
Possible reference: Liu, T. et al. (2025) Exploitable mechanisms of antibody and CAR mediated macrophage cytotoxicity., Nat Commun, PMID 40595560

PXD053859 no publication (from MassIVE)
Dataset title: High-throughput cell-based proteomics perturbation: HTP Perturbation
Possible reference: Seyedmohammad, S. et al. (2025) High-Throughput Workflow for Detergent-free Cell-Based Proteomic Characterization., J Proteome Res, PMID 40255039

PXD053855 no publication (from MassIVE)
Dataset title: High-throughput cell-based proteomics perturbation: Buffer Optimization
Possible reference: Seyedmohammad, S. et al. (2025) High-Throughput Workflow for Detergent-free Cell-Based Proteomic Characterization., J Proteome Res, PMID 40255039

PXD053832 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics analysis of lipid droplets proteins in ccRCC cells
Possible reference: Liu, S. et al. (2019) HADHA overexpression disrupts lipid metabolism and inhibits tumor growth in clear cell renal cell carcinoma., Exp Cell Res, PMID 31472118

PXD053819 Dataset with its publication pending (from PRIDE)
Dataset title: ACKR3 Degradation by the Novel Scutellarein Derivative TBS6b Potently Suppresses Hepatocellular Carcinoma
Possible reference: Jiang, X. et al. (2025) Binding and ubiquitination-mediated degradation of ACKR3 by the novel Scutellarein derivative TBS6b potently suppresses hepatocellular carcinoma., Bioorg Chem, PMID 41075613

PXD053800 Dataset with its publication pending (from PRIDE)
Dataset title: Mutant CEBPA promotes tolerance to inflammatory stress through deficient AP-1 activation
Possible reference: Cadefau-Fabregat, M. et al. (2025) Mutant CEBPA promotes tolerance to inflammatory stress through deficient AP-1 activation., Nat Commun, PMID 40221437

PXD053794 no publication (from MassIVE)
Dataset title: EvoSep-timsTOF proximity dependent biotinylation optimization
Possible reference: Kitaygorodsky, J. et al. (2025) Optimizing Proximity Proteomics on the EvoSep-timsTOF LC-MS System., Proteomics, PMID 40641299

PXD053750 Dataset with its publication pending (from PRIDE)
Dataset title: An INS-1 ð½-cell proteome highlights the role of fatty acid biosynthesis in glucose-stimulated insulin secretion
Possible reference: Stremmel, N. et al. (2025) An INS-1 832/13 𝛽-Cell Proteome Highlights the Rapid Regulation of Fatty Acid Biosynthesis in Glucose-Stimulated Insulin Secretion., Proteomics, PMID 40685699

PXD053736 Dataset with its publication pending (from iProX)
Dataset title: Targeted and non-targeted proteomics to identify the urinary protein biomarkers for Wilson disease
Possible reference: Dong, S. et al. (2025) Targeted and non-targeted proteomics to identify the urinary protein biomarkers for Wilson disease., Clin Chim Acta, PMID 39672253

PXD053730 Dataset with its publication pending (from iProX)
Dataset title: Comprehensive Transcriptomic and Proteomic Analysis Reveals Biological Changes and Potential Regulatory Mechanisms of Endothelial Cells under Heat Stress Conditions
Possible reference: Jia, K. et al. (2025) Comprehensive transcriptomic and proteomic analysis reveals biological changes and potential regulatory mechanisms of endothelial cells under heat stress conditions., J Therm Biol, PMID 40408820

PXD053693 Dataset with its publication pending (from PRIDE)
Dataset title: Auto-inhibition of PRC2 by the broadly expressed long isoform of AEBP2.
Possible reference: Mucha, M. et al. (2025) Auto-inhibition of PRC2 by the broadly expressed long isoform of AEBP2., EMBO J, PMID 41168462

PXD053687 Dataset with its publication pending (from iProX)
Dataset title: Deciphering the phosphorylation-based regulatory strategies of Haemaphysalis longicornis in Heat Stress
Possible reference: Zhang, XL. et al. (2025) Deciphering the phosphorylation-based regulatory strategies of Haemaphysalis longicornis in heat stress., Parasit Vectors, PMID 40993790

PXD053667 Dataset with its publication pending (from iProX)
Dataset title: Protein Profile of Bovine Oviductal Extracellular Vesicles
Possible reference: Mazzarella, R. et al. (2025) Embryo-Induced Changes in the Protein Profile of Bovine Oviductal Extracellular Vesicles., Mol Cell Proteomics, PMID 40024377

PXD053648 no publication (from MassIVE)
Dataset title: Proteomic Investigation of Neurotrophic trans-Banglene Reveals Potential Link to Iron Homeostasis
Possible reference: Gunawardana, PBW. et al. (2025) Proteomic Investigation of Neurotrophic trans-Banglene Reveals Potential Link to Iron Homeostasis., Mol Neurobiol, PMID 40085355

PXD053637 Dataset with its publication pending (from jPOST)
Dataset title: Cysteine redoxome landscape in mouse brown adipose tissue under acute cold exposure
Possible reference: Oo, HK. et al. (2025) Cysteine redoxome landscape in mouse brown adipose tissue under acute cold exposure., iScience, PMID 40104075

PXD053620 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes
Possible reference: Thorpe, P. et al. (2024) Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes., BMC Genomics, PMID 39528973

PXD053614 no publication (from MassIVE)
Dataset title: Sirt5 regulates chondrocyte metabolism and osteoarthritis development through protein lysine malonylation
Possible reference: Zhu, S. et al. (2021) Sirt5 Deficiency Causes Posttranslational Protein Malonylation and Dysregulated Cellular Metabolism in Chondrocytes Under Obesity Conditions., Cartilage, PMID 33567897

PXD053612 no publication (from MassIVE)
Dataset title: Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms
Possible reference: Frankenfield, AM. et al. (2025) Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms., Mol Cell Proteomics, PMID 40315959

PXD053605 no publication (from MassIVE)
Dataset title: Arf1-dependent LRBA recruitment to Rab4 endosomes is required for endolysosome homeostasis
Possible reference: Szentgy�rgyi, V. et al. (2024) Arf1-dependent LRBA recruitment to Rab4 endosomes is required for endolysosome homeostasis., J Cell Biol, PMID 39325073

PXD053604 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic and phosphoproteomic profiling revealed distinct cellular responses during Tilapia Lake Virus infection
Possible reference: Lertwanakarn, T. et al. (2025) Proteomic and phosphoproteomic profilings reveal distinct cellular responses during Tilapinevirus tilapiae entry and replication., PeerJ, PMID 39995988

PXD053600 Dataset with its publication pending (from PRIDE)
Dataset title: Conserved role of the SERK‒BIR module in development and immunity across land plants
Possible reference: Yan, Y. et al. (2025) Conserved role of the SERK-BIR module in development and immunity across land plants., Curr Biol, PMID 40250435

PXD053595 Dataset with its publication pending (from PRIDE)
Dataset title: SART3 promotes homologous recombination repair by stimulating DNA–RNA hybrids removal and DNA end resection
Possible reference: Fu, H. et al. (2025) SART3 promotes homologous recombination repair by stimulating DNA-RNA hybrids removal and DNA end resection., Nat Commun, PMID 40050279

PXD053562 Dataset with its publication pending (from PRIDE)
Dataset title: Polysulfur-based bulking of dynamin-related protein 1 prevents ischemic sulfide catabolism and heart failure
Possible reference: Nishimura, A. et al. (2025) Polysulfur-based bulking of dynamin-related protein 1 prevents ischemic sulfide catabolism and heart failure in mice., Nat Commun, PMID 39747092

PXD053528 no publication (from MassIVE)
Dataset title: MbtK contributes to mycobacterial pathogenesis by promoting PDIM biosynthesis
Possible reference: Jones, BS. et al. (2025) N-acetyltransferases required for iron uptake and aminoglycoside resistance promote virulence lipid production in Mycobacterium marinum., Proc Natl Acad Sci U S A, PMID 40680026

PXD053523 no publication (from MassIVE)
Dataset title: A new genetic code with all TAG codons as pyrrolysine in diverse archaea
Possible reference: Borrel, G. et al. (2014) Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine., BMC Genomics, PMID 25124552

PXD053520 Dataset with its publication pending (from PRIDE)
Dataset title: A Leishmania virulence factor harnesses an allosteric kinase switch to regulate its ubiquitin ligase activity
Possible reference: Fokkens, TJ. et al. (2025) A Leishmania virulence factor harnesses an allosteric kinase switch to regulate its ubiquitin ligase activity., Mol Cell, PMID 40997810

PXD053519 no publication (from MassIVE)
Dataset title: altered proteomic events induced by a beta in SHSY5Y
Possible reference: Ai, X. et al. (2024) Proteomic Analysis Reveals Physiological Activities of Aβ Peptide for Alzheimer's Disease., Int J Mol Sci, PMID 39125907

PXD053516 Dataset with its publication pending (from jPOST)
Dataset title: TAS1440, an LSD1 inhibitor, activates TGF-β and NOTCH signaling in neuroendocrine small-cell lung cancer
Possible reference: Machida, T. et al. (2026) LSD1 inhibitor, TAS1440, disrupts INSM1-LSD1 complex activating tumor-suppressive pathways via transcriptional reprogramming in neuroendocrine SCLC., Nat Commun, PMID 41881985

PXD053511 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of the exponential and stationary of phases of CHO cell culture.
Possible reference: Sebasti�o, MJ. et al. (2023) Identification of Mispairing Omic Signatures in Chinese Hamster Ovary (CHO) Cells Producing a Tri-Specific Antibody., Biomedicines, PMID 38001891

PXD053508 Dataset with its publication pending (from PRIDE)
Dataset title: Aspergillus fumigatus spore proteases alter the respiratory mucosa architecture and facilitate equine herpesvirus 1 infection
Possible reference: Portaels, J. et al. (2024) Aspergillus Fumigatus Spore Proteases Alter the Respiratory Mucosa Architecture and Facilitate Equine Herpesvirus 1 Infection., Viruses, PMID 39205182

PXD053504 Dataset with its publication pending (from jPOST)
Dataset title: Plasma proteomic profiles of patients with HIV infection and coinfection with hepatitis B/C virus undergoing anti-retroviral therapy
Possible reference: Tarnathummanan, C. et al. (2024) Plasma proteomic profiles of patients with HIV infection and coinfection with hepatitis B/C virus undergoing anti‑retroviral therapy., Biomed Rep, PMID 39268407

PXD053500 Dataset with its publication pending (from PRIDE)
Dataset title: Kinetic principles of chemical cross-link formation for protein-protein interactions
Possible reference: Kammer, KM. et al. (2024) Kinetic principles of chemical cross-link formation for protein-protein interactions., Proc Natl Acad Sci U S A, PMID 39652756

PXD053493 no publication (from MassIVE)
Dataset title: The PNUTS phosphatase complex controls transcription pause release
Possible reference: Kelley, JR. et al. (2024) The PNUTS phosphatase complex controls transcription pause release., Mol Cell, PMID 39603239

PXD053487 no publication (from MassIVE)
Dataset title: Accessing the proteome of extracellular vesicles via rapid acoustic isolation of a minute human blood plasma sample
Possible reference: Havers, M. et al. (2025) Accessing the proteome of extracellular vesicles via rapid acoustic isolation of a minute human blood plasma sample., Anal Chim Acta, PMID 41167904

PXD053481 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping the interaction surface between CaVÎ² and actin and its role in calcium channel clearance
Possible reference: Castilla, F. et al. (2025) Mapping the interaction surface between CaVβ and actin and its role in calcium channel clearance., Nat Commun, PMID 40348749

PXD053476 Dataset with its publication pending (from iProX)
Dataset title: HERC5 interaction protein profile
Possible reference: Xiu, MX. et al. (2022) Identification of hub genes, miRNAs and regulatory factors relevant for Duchenne muscular dystrophy by bioinformatics analysis., Int J Neurosci, PMID 32791870

PXD053456 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping the interaction surface between CaVÎ² and actin and its role in calcium channel clearance
Possible reference: Castilla, F. et al. (2025) Mapping the interaction surface between CaVβ and actin and its role in calcium channel clearance., Nat Commun, PMID 40348749

PXD053428 Dataset with its publication pending (from PRIDE)
Dataset title: Conserved role of the SERK‒BIR module in development and immunity across land plants
Possible reference: Yan, Y. et al. (2025) Conserved role of the SERK-BIR module in development and immunity across land plants., Curr Biol, PMID 40250435

PXD053412 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of Serine/Threonine Protein Phosphatase 6 Severely Impairs Sexual Stage Development in Malaria Parasite Plasmodium berghei
Possible reference: Feng, Y. et al. (2025) Loss of serine/threonine protein phosphatase 6 severely impairs sexual stage development in malaria parasite Plasmodium berghei., PLoS Pathog, PMID 40623036

PXD053407 Dataset with its publication pending (from iProX)
Dataset title: Downregulation of STAT1 improved learning and memory impairments in aging mice
Possible reference: Li, X. et al. (2025) Downregulation of STAT1 improved learning and memory impairments in aging mice., Neurosci Lett, PMID 39933634

PXD053405 Dataset with its publication pending (from PRIDE)
Dataset title: GUK1 activation is a metabolic liability in oncogene-driven lung cancer
Possible reference: Schneider, JL. et al. (2025) GUK1 activation is a metabolic liability in lung cancer., Cell, PMID 39919745

PXD053395 Dataset with its publication pending (from PRIDE)
Dataset title: REPURPOSING OF GLATIRAMER ACETATE TO TREAT CARDIAC ISCHEMIA IN ANIMAL MODELS
Possible reference: Aviel, G. et al. (2024) Repurposing of glatiramer acetate to treat cardiac ischemia in rodent models., Nat Cardiovasc Res, PMID 39215106

PXD053383 Dataset with its publication pending (from PRIDE)
Dataset title: MORC2 phosphorylation fine tunes its DNA compaction activity
Possible reference: Tan, W. et al. (2024) MORC2 phosphorylation fine tunes its DNA compaction activity., bioRxiv, PMID 38979330

PXD053380 Dataset with its publication pending (from jPOST)
Dataset title: MORC2 phosphorylation fine tunes its DNA compaction activity
Possible reference: Tan, W. et al. (2024) MORC2 phosphorylation fine tunes its DNA compaction activity., bioRxiv, PMID 38979330

PXD053374 no publication (from MassIVE)
Dataset title: diaPASEF for HLA-I peptide analysis enables quantification of common cancer neoantigens
Possible reference: Oliinyk, D. et al. (2025) diaPASEF Analysis for HLA-I Peptides Enables Quantification of Common Cancer Neoantigens., Mol Cell Proteomics, PMID 40044040

PXD053373 Dataset with its publication pending (from jPOST)
Dataset title: Proteomics and Bioinformatics Identify Drug-Resistant-Related Genes with Prognostic Potential in Cholangiocarcinoma
Possible reference: Kerdkumthong, K. et al. (2024) Proteomics and Bioinformatics Identify Drug-Resistant-Related Genes with Prognostic Potential in Cholangiocarcinoma., Biomolecules, PMID 39199357

PXD053371 no publication (from MassIVE)
Dataset title: Histone H3.3 lysine 9 and 27 control repressive chromatin states at cryptic cis-regulatory elements and bivalent promoters in mouse embryonic stem cells
Possible reference: Trovato, M. et al. (2024) Histone H3.3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters., Nat Commun, PMID 39214979

PXD053359 Dataset with its publication pending (from PRIDE)
Dataset title: Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules
Possible reference: Ashkarran, AA. et al. (2024) Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules., bioRxiv, PMID 38496642

PXD053355 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes
Possible reference: Thorpe, P. et al. (2024) Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes., BMC Genomics, PMID 39528973

PXD053354 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial VHL rewires cell metabolism in hypoxia
Possible reference: Meléndez-Rodríguez, F. et al. (2019) HIF1α Suppresses Tumor Cell Proliferation through Inhibition of Aspartate Biosynthesis., Cell Rep, PMID 30811976

PXD053340 Dataset with its publication pending (from iProX)
Dataset title: Brain protein lactylation after exercise training
Possible reference: Qian, P. et al. (2024) Transcriptional Expression of Histone Acetyltransferases and Deacetylases During the Recovery of Acute Exercise in Mouse Hippocampus., J Mol Neurosci, PMID 38565829

PXD053333 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted immunotherapy rescues pulmonary fibrosis by reducing activated fibroblasts and regulating alveolar cell profile
Possible reference: Yan, J. et al. (2025) Targeted immunotherapy rescues pulmonary fibrosis by reducing activated fibroblasts and regulating alveolar cell profile., Nat Commun, PMID 40258811

PXD053322 Dataset with its publication pending (from iProX)
Dataset title: Proteomic Analysis of SiHa cells and Ect1/E6E7
Possible reference: Wang, Y. et al. (2025) Elevated VAMP8 expression promotes cervical cancer progression by enhancing autophagy via HIF-1 pathway., BMC Med, PMID 41063209

PXD053300 Dataset with its publication pending (from PRIDE)
Dataset title: Histone dynamics at replication forks in embryonic stem cells
Possible reference: Almeida, R. et al. (2018) Chromatin conformation regulates the coordination between DNA replication and transcription., Nat Commun, PMID 29686321

PXD053285 no publication (from MassIVE)
Dataset title: Multi-Omics after O-GlcNAc Alteration Identifies Cellular Processes Working Synergistically to Promote Aneuploidy
Possible reference: Boyd, SS. et al. (2024) Multi-Omics after O-GlcNAc Alteration Identifies Cellular Processes Working Synergistically to Promote Aneuploidy., bioRxiv, PMID 38659829

PXD053277 no publication (from MassIVE)
Dataset title: IER3IP1-mutations cause microcephaly by selective inhibition of ER-Golgi transport
Possible reference: Anitei, M. et al. (2024) IER3IP1-mutations cause microcephaly by selective inhibition of ER-Golgi transport., Cell Mol Life Sci, PMID 39115595

PXD053261 Dataset with its publication pending (from PRIDE)
Dataset title: Conserved Role of FOXC1 in TNBC is parallel to FOXA1 in ER+ Breast Cancer
Possible reference: Ramachandran, R. et al. (2024) Conserved role of FOXC1 in TNBC is parallel to FOXA1 in ER+ breast cancer., iScience, PMID 39171293

PXD053239 no publication (from MassIVE)
Dataset title: Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain
Possible reference: Di Fraia, D. et al. (2024) Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain., bioRxiv, PMID 38260253

PXD053235 no publication (from MassIVE)
Dataset title: Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain
Possible reference: Di Fraia, D. et al. (2024) Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain., bioRxiv, PMID 38260253

PXD053232 no publication (from MassIVE)
Dataset title: Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain
Possible reference: Di Fraia, D. et al. (2024) Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain., bioRxiv, PMID 38260253

PXD053231 no publication (from MassIVE)
Dataset title: Serum Proteomics Reveals Survival-Associated Biomarkers in Pancreatic Cancer Patients Treated with Chemoimmunotherapy
Possible reference: Tognetti, M. et al. (2025) Serum proteomics reveals survival-associated biomarkers in pancreatic cancer patients treated with chemoimmunotherapy., iScience, PMID 40235590

PXD053229 no publication (from MassIVE)
Dataset title: Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain
Possible reference: Di Fraia, D. et al. (2024) Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain., bioRxiv, PMID 38260253

PXD053204 no publication (from MassIVE)
Dataset title: Outer membrane vesicles from Bacteroides fragilis contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells.
Possible reference: Sheikh, A. et al. (2025) Outer membrane vesicles from Bacteroides fragilis contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells., bioRxiv, PMID 40666935

PXD053202 no publication (from MassIVE)
Dataset title: Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain
Possible reference: Di Fraia, D. et al. (2024) Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain., bioRxiv, PMID 38260253

PXD053201 no publication (from MassIVE)
Dataset title: Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain
Possible reference: Di Fraia, D. et al. (2024) Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain., bioRxiv, PMID 38260253

PXD053188 Dataset with its publication pending (from iProX)
Dataset title: Lysine acetylomic analysis during seedling deetiolation in Arabidopsis thaliana
Possible reference: Zheng, F. et al. (2025) HDT2-mediated lysine deacetylation promotes phytochrome A degradation during photomorphogenesis in Arabidopsis., Mol Plant, PMID 40776444

PXD053181 Dataset with its publication pending (from PRIDE)
Dataset title: Smoking carcinogen induced inflammation promotes lung carcinogenesis via IRAK4 activation
Possible reference: Aggarwal, RK. et al. (2025) Smoking-Associated Carcinogen-Induced Inflammation Promotes Lung Carcinogenesis via IRAK4 Activation., Clin Cancer Res, PMID 39704655

PXD053179 no publication (from MassIVE)
Dataset title: Effects Beta-hydroxybutyrate on human islet proteome
Possible reference: Banerjee, R. et al. (2024) Beta-Hydroxybutyrate Promotes Basal Insulin Secretion While Decreasing Glucagon Secretion in Mouse and Human Islets., Endocrinology, PMID 38970533

PXD053162 Dataset with its publication pending (from iProX)
Dataset title: Proteome sequencing of tobacco yellow leaf mutants
Possible reference: Chen, S. et al. (2019) Cucurbit Chlorotic Yellows Virus p22 Protein Interacts with Cucumber SKP1LB1 and Its F-Box-Like Motif Is Crucial for Silencing Suppressor Activity., Viruses, PMID 31487883

PXD053141 Dataset with its publication pending (from PRIDE)
Dataset title: PLK1-Mediated Phosphorylation Cascade Activates the Mis18 Complex to Ensure Centromere Inheritance
Possible reference: Parashara, P. et al. (2024) PLK1-mediated phosphorylation cascade activates Mis18 complex to ensure centromere inheritance., Science, PMID 39236175

PXD053125 no publication (from MassIVE)
Dataset title: Design and application of synthetic 17B-HSD13 substrates to drug discovery, and to reveal preserved catalytic activity of protective human variants
Possible reference: Garnsey, MR. et al. (2025) Design and application of synthetic 17B-HSD13 substrates reveals preserved catalytic activity of protective human variants., Nat Commun, PMID 39746932

PXD053082 Dataset with its publication pending (from PRIDE)
Dataset title: METABOLIC DISRUPTION IMPAIRS RIBOSOMAL PROTEIN LEVELS, RESULTING IN ENHANCED AMINOGLYCOSIDE TOLERANCE
Possible reference: Shiraliyev, R. et al. (2024) METABOLIC DISRUPTION IMPAIRS RIBOSOMAL PROTEIN LEVELS, RESULTING IN ENHANCED AMINOGLYCOSIDE TOLERANCE., bioRxiv, PMID 38187583

PXD053073 Dataset with its publication pending (from jPOST)
Dataset title: Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure
Possible reference: Yamaura, K. et al. (2025) Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure., Nat Commun, PMID 39971902

PXD053061 Dataset with its publication pending (from PRIDE)
Dataset title: LGR signaling mediates muscle-adipose tissue crosstalk and protects against diet-induced insulin resistance
Possible reference: Kubrak, O. et al. (2024) LGR signaling mediates muscle-adipose tissue crosstalk and protects against diet-induced insulin resistance., Nat Commun, PMID 39033139

PXD053049 Dataset with its publication pending (from PRIDE)
Dataset title: Recurrent innovation of protein-protein interactions in the Drosophila piRNA pathway
Possible reference: Riedelbauch, S. et al. (2026) Recurrent innovation of protein-protein interactions in the Drosophila piRNA pathway., EMBO J, PMID 40275032

PXD053043 Dataset with its publication pending (from PRIDE)
Dataset title: Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis
Possible reference: Lim, B. et al. (2025) Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis., Nat Genet, PMID 39948437

PXD053033 Dataset with its publication pending (from PRIDE)
Dataset title: Biogenesis of DNA-carrying extracellular vesicles by the dominant human gut methanogenic archaeon
Possible reference: Baquero, DP. et al. (2025) Biogenesis of DNA-carrying extracellular vesicles by the dominant human gut methanogenic archaeon., Nat Commun, PMID 40461479

PXD053003 Dataset with its publication pending (from PRIDE)
Dataset title: Matrisome Proteomics Reveals Novel Mediators of Muscle Remodeling with Aerobic Exercise Training
Possible reference: Pattamaprapanont, P. et al. (2024) Matrisome proteomics reveals novel mediators of muscle remodeling with aerobic exercise training., Matrix Biol Plus, PMID 39220302

PXD052986 Dataset with its publication pending (from iProX)
Dataset title: The proteomics analysis of Chimeric exosomes
Possible reference: Gualdr�n-L�pez, M. et al. (2018) Characterization of Plasmodium vivax Proteins in Plasma-Derived Exosomes From Malaria-Infected Liver-Chimeric Humanized Mice., Front Microbiol, PMID 29988527

PXD052976 Dataset with its publication pending (from PRIDE)
Dataset title: Haplotype variability in mitochondrial rRNA predisposes to metabolic syndrome
Possible reference: Pecina, P. et al. (2024) Haplotype variability in mitochondrial rRNA predisposes to metabolic syndrome., Commun Biol, PMID 39261587

PXD052975 no publication (from MassIVE)
Dataset title: Discovery of Monovalent Direct Degraders of BRD4 That Act Via the Recruitment of DCAF11
Possible reference: Parker, GS. et al. (2024) Discovery of Monovalent Direct Degraders of BRD4 that Act via the Recruitment of DCAF11., Mol Cancer Ther, PMID 38907538

PXD052963 Dataset with its publication pending (from jPOST)
Dataset title: Stress-induced condensation of TDP-43 in the nucleus
Possible reference: Huang, WP. et al. (2024) Stress-induced TDP-43 nuclear condensation causes splicing loss of function and STMN2 depletion., Cell Rep, PMID 38941189

PXD052961 no publication (from MassIVE)
Dataset title: Esophagitis-related precision medicine
Possible reference: Mattern, S. et al. (2025) An AI-assisted morphoproteomic approach is a supportive tool in esophagitis-related precision medicine., EMBO Mol Med, PMID 39901020

PXD052954 Dataset with its publication pending (from PRIDE)
Dataset title: Coxiella burnetii manipulates the lysosomal protease cathepsin B to facilitate intracellular success:CvpB_WCLandsup
Possible reference: Bird, LE. et al. (2025) Coxiella burnetii manipulates the lysosomal protease cathepsin B to facilitate intracellular success., Nat Commun, PMID 40274809

PXD052937 no publication (from MassIVE)
Dataset title: Liver tissue proteins improve the accuracy of plasma proteins as biomarkers in diagnosing metabolic dysfunction-associated steatohepatitis
Possible reference: Larsen, FT. et al. (2023) Stellate cell expression of SPARC-related modular calcium-binding protein 2 is associated with human non-alcoholic fatty liver disease severity., JHEP Rep, PMID 36687468

PXD052932 Dataset with its publication pending (from PRIDE)
Dataset title: A Labrador PeptideAtlas - resource for proteomics research in dogs
Possible reference: Kusebauch, U. et al. (2026) A Labrador PeptideAtlas and DIA spectral assay library - resources for proteomics research in dogs., Sci Data, PMID 41927601

PXD052931 Dataset with its publication pending (from jPOST)
Dataset title: Plasmodium falciparum SET10 is a histone H3 lysine K18 methyltransferase regulating nucleic acid metabolic processes during intraerythrocytic development
Possible reference: Musabyimana, J-P. et al. (2024) The Plasmodium falciparum histone methyltransferase SET10 participates in a chromatin modulation network crucial for intraerythrocytic development., mSphere, PMID 39445823

PXD052903 Dataset with its publication pending (from jPOST)
Dataset title: Exploring the Functional Diversity and Metabolic Activities of the Human Gut Microbiome in Thai Adults in Response to a Prebiotic Diet
Possible reference: Kingkaw, A. et al. (2025) Exploring the functional diversity and metabolic activities of the human gut microbiome in Thai adults in response to a prebiotic diet., Microbiol Spectr, PMID 39670767

PXD052902 Dataset with its publication pending (from PRIDE)
Dataset title: A Labrador DIA spectral assay library - resource for proteomics research in dogs
Possible reference: Kusebauch, U. et al. (2026) A Labrador PeptideAtlas and DIA spectral assay library - resources for proteomics research in dogs., Sci Data, PMID 41927601

PXD052890 Dataset with its publication pending (from PRIDE)
Dataset title: Coxiella burnetii manipulates lysosomal proteases to facilitate intracellular success
Possible reference: Bird, LE. et al. (2025) Coxiella burnetii manipulates the lysosomal protease cathepsin B to facilitate intracellular success., Nat Commun, PMID 40274809

PXD052885 Dataset with its publication pending (from iProX)
Dataset title: Osmanthus fragrans leaf color proteomics
Possible reference: Zhang, C. et al. (2024) SWATH-MS based proteomics reveals the role of photosynthesis related proteins and secondary metabolic pathways in the colored leaves of sweet olive (Osmanthus fragrans)., BMC Genomics, PMID 39487388

PXD052884 Dataset with its publication pending (from jPOST)
Dataset title: A comparative study of velvet worm slime major proteins
Possible reference: Graham, LD. et al. (2013) The adhesive skin exudate of Notaden bennetti frogs (Anura: Limnodynastidae) has similarities to the prey capture glue of Euperipatoides sp. velvet worms (Onychophora: Peripatopsidae)., Comp Biochem Physiol B Biochem Mol Biol, PMID 23665109

PXD052871 Dataset with its publication pending (from PRIDE)
Dataset title: iDIA-QC: AI-empowered Data-Independent Acquisition Mass Spectrometry-based Quality Control
Possible reference: Gao, H. et al. (2025) iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control., Nat Commun, PMID 39837863

PXD052868 Dataset with its publication pending (from PRIDE)
Dataset title: Mice lacking Astn2 have ASD-like behaviors and altered cerebellar circuit properties
Possible reference: Hanzel, M. et al. (2024) Mice lacking Astn2 have ASD-like behaviors and altered cerebellar circuit properties., bioRxiv, PMID 38405978

PXD052840 Dataset with its publication pending (from jPOST)
Dataset title: Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA Polymerase II productive elongation
Possible reference: Cornejo, KG. et al. (2023) Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA Polymerase II productive elongation., bioRxiv, PMID 38234780

PXD052825 Dataset with its publication pending (from PRIDE)
Dataset title: the Interaction Proteome of Ribosomal 40S Components PNO1 and NOB1 Using TurboID Proximity Labeling Technology
Possible reference: Xu, X. et al. (2025) The proximity proteome of pre-40S pre-ribosomal particle components PNO1 and NOB1 using turboID proximity labeling technology., Gene, PMID 40157618

PXD052805 Dataset with its publication pending (from PRIDE)
Dataset title: RNF157 targets RIG-I/DDX58 promotes proliferation in hepatocellular carcinoma
Possible reference: Ma, C. et al. (2025) RNF157 targets RIG-I/DDX58 to promote proliferation in liver cancer., BMC Cancer, PMID 40312343

PXD052803 Dataset with its publication pending (from PRIDE)
Dataset title: Subfamily C7 Raf-like kinases MRK1, RAF26, and RAF39 regulate immune homeostasis and stomatal opening in Arabidopsis thaliana
Possible reference: Gon�alves Dias, M. et al. (2024) Subfamily C7 Raf-like kinases MRK1, RAF26, and RAF39 regulate immune homeostasis and stomatal opening in Arabidopsis thaliana., New Phytol, PMID 39449177

PXD052800 Dataset with its publication pending (from PRIDE)
Dataset title: And-1 is required for NER repair and promotes skin carcinogenesis
Possible reference: Zhou, S. et al. (2025) And-1 coordinates with polymerase δ to regulate nucleotide excision repair and UVB-induced skin tumorigenesis., Nat Commun, PMID 41120356

PXD052782 Dataset with its publication pending (from iProX)
Dataset title: Lysine crotonylation in cyanobacteria
Possible reference: Lin, J. et al. (2025) The role of CddA and cGNAT2 in crotonylation of proteins in cyanobacteria., New Phytol, PMID 40619854

PXD052781 Dataset with its publication pending (from iProX)
Dataset title: USP5 stabilizes YTHDF1 to control cancer immune surveillance through mTORC1-mediated phosphorylation
Possible reference: Shao, N. et al. (2025) USP5 stabilizes YTHDF1 to control cancer immune surveillance through mTORC1-mediated phosphorylation., Nat Commun, PMID 39900921

PXD052775 Dataset with its publication pending (from jPOST)
Dataset title: Identification of Peptidome-Based Biomarkers of Cassava Mosaic Disease Resistance in Cassava Varieties Using PMF and LC-MS/MS
Possible reference: Siriwan, W. et al. (2025) Identification of peptidome-based biomarkers of cassava mosaic disease resistance in different cassava varieties., Sci Rep, PMID 40221509

PXD052769 no publication (from MassIVE)
Dataset title: mRNA lipid nanoparticles expressing cell-surface cleavage independent HIV Env trimers elicit autologous tier-2 neutralizing antibodies
Possible reference: Guenaga, J. et al. (2024) mRNA lipid nanoparticles expressing cell-surface cleavage independent HIV Env trimers elicit autologous tier-2 neutralizing antibodies., Front Immunol, PMID 39119336

PXD052763 Dataset with its publication pending (from PRIDE)
Dataset title: Zbtb48 is a regulator of Mtfp1 expression in zebrafish
Possible reference: Goh, SYC. et al. (2025) Zbtb48 is a regulator of Mtfp1 expression in zebrafish., Commun Biol, PMID 39987415

PXD052751 Dataset with its publication pending (from jPOST)
Dataset title: SWATH-Proteomics of Mathurameha in High Glucose-Induced Endothelial Dysfunction
Possible reference: Aluksanasuwan, S. et al. (2024) SWATH-proteomics reveals Mathurameha, a traditional anti-diabetic herbal formula, attenuates high glucose-induced endothelial dysfunction through the EGF/NO/IL-1β regulatory axis., J Proteomics, PMID 39047940

PXD052745 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive Dataset of Interactors for the Entire PARP Family Using TurboID Proximity Labeling
Possible reference: Zheng, J. et al. (2025) Comprehensive dataset of interactors for the entire PARP family using TurboID proximity labeling., Sci Data, PMID 40057523

PXD052736 Dataset with its publication pending (from iProX)
Dataset title: HSP70 and APX1 play important roles in cotton male fertility
Possible reference: Ma, L. et al. (2024) HSP70 and APX1 play important roles in cotton male fertility by mediating ROS homeostasis., Int J Biol Macromol, PMID 39168224

PXD052718 Dataset with its publication pending (from PRIDE)
Dataset title: Glycosphingolipid synthesis mediates immune evasion in Kras-driven cancer
Possible reference: Soula, M. et al. (2024) Glycosphingolipid synthesis mediates immune evasion in KRAS-driven cancer., Nature, PMID 39112706

PXD052703 Dataset with its publication pending (from PRIDE)
Dataset title: The flavonoid-sensing regulator AefR is involved in modulating quorum sensing through repressing the MexEF-OprN efflux pump in Pseudomonas fluorescens
Possible reference: Xiao-Quan, Y. et al. (2025) The flavonoid-sensing regulator AefR is involved in modulating quorum sensing through repressing the MexEF-OprN efflux pump in Pseudomonas fluorescens., mSystems, PMID 40013790

PXD052702 Dataset with its publication pending (from PRIDE)
Dataset title: The flavonoid-sensing regulator AefR is involved in modulating quorum sensing through repressing the MexEF-OprN efflux pump in Pseudomonas fluorescens
Possible reference: Xiao-Quan, Y. et al. (2025) The flavonoid-sensing regulator AefR is involved in modulating quorum sensing through repressing the MexEF-OprN efflux pump in Pseudomonas fluorescens., mSystems, PMID 40013790

PXD052698 Montaser AB, Gao F, Peters D, Vainionp�� K, Zhibin N, Skowronska-Krawczyk D, Figeys D, Palczewski K, Leinonen H. Retinal proteome profiling of inherited retinal degeneration across three different mouse models suggests common drug targets in retinitis pig (from PanoramaPublic)
Dataset title: Retinal proteome profiling of inherited retinal degeneration across three different mouse models suggests common drug targets in retinitis pigmentosa
Possible reference: Montaser, AB. et al. (2024) Retinal Proteome Profiling of Inherited Retinal Degeneration Across Three Different Mouse Models Suggests Common Drug Targets in Retinitis Pigmentosa., Mol Cell Proteomics, PMID 39389360

PXD052689 Dataset with its publication pending (from PRIDE)
Dataset title: UBAC2 phosphorylation is essential for its role in ER-phagy
Possible reference: He, X. et al. (2024) ER-phagy restrains inflammatory responses through its receptor UBAC2., EMBO J, PMID 39284914

PXD052682 Dataset with its publication pending (from jPOST)
Dataset title: Proteome-wide quantification of inositol pyrophosphate-protein interactions
Possible reference: Richter, A. et al. (2026) Proteome-wide quantification of inositol pyrophosphate-protein interactions., Nat Commun, PMID 42243085

PXD052671 Dataset with its publication pending (from PRIDE)
Dataset title: The structural and functional significance of Aedes aegypti AgBR1 flavivirus immunomodulator
Possible reference: Martinez-Castillo, A. et al. (2025) Structural and functional significance of Aedes aegypti AgBR1 flavivirus immunomodulator., J Virol, PMID 40272158

PXD052661 Dataset with its publication pending (from PRIDE)
Dataset title: Krill oil supplementation in vivo promotes increased fuel metabolism and protein synthesis in cultured human skeletal muscle cells
Possible reference: Katare, PB. et al. (2024) Krill oil supplementation in vivo promotes increased fuel metabolism and protein synthesis in cultured human skeletal muscle cells., Front Nutr, PMID 39555189

PXD052645 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of human eosinophils stimulated with aspergillus fumigatus extract and IL-5
Possible reference: Sasaki, H. et al. (2025) Aspergillus fumigatus extract modulates human eosinophils via NOD2 and oxidative stress., Allergol Int, PMID 39307590

PXD052631 Dataset with its publication pending (from PRIDE)
Dataset title: G-CSF/NAMPT signaling drives neutrophil dysfunction and enhances bacterial infection susceptibility in cancer patients
Possible reference: Pylaeva, E. et al. (2025) G-CSF/NAMPT signaling drives neutrophil dysfunction and enhances bacterial infection susceptibility in cancer patients., Nat Commun, PMID 41387444

PXD052619 no publication (from MassIVE)
Dataset title: The extracellular serine protease from Staphylococcus epidermidis elicits a type 2-biased immune response in atopic dermatitis patients
Possible reference: Abdurrahman, G. et al. (2024) The extracellular serine protease from Staphylococcus epidermidis elicits a type 2-biased immune response in atopic dermatitis patients., Front Immunol, PMID 38895118

PXD052618 Dataset with its publication pending (from PRIDE)
Dataset title: Chlamydomonas reinhardtii photosystem II repair factors identification
Possible reference: Wang, X. et al. (2025) The HIGH CHLOROPHYLL FLUORESCENCE 244 homolog CrHCF244 is required for psbA (D1) translation in Chlamydomonas reinhardtii., J Exp Bot, PMID 40810357

PXD052615 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of human eosinophils stimulated with IFN-gamma and IL-5
Possible reference: Pazdrak, K. et al. (2016) Cytokine-Induced Glucocorticoid Resistance from Eosinophil Activation: Protein Phosphatase 5 Modulation of Glucocorticoid Receptor Phosphorylation and Signaling., J Immunol, PMID 27742828

PXD052614 no publication (from MassIVE)
Dataset title: Chemical crosslinking extends and complements UV crosslinking in analysis of RNA and DNA nucleic acid protein interactions by mass spectrometry
Possible reference: Welp, LM. et al. (2025) Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry., bioRxiv, PMID 39257782

PXD052611 Dataset with its publication pending (from PRIDE)
Dataset title: Elusive elapid: Biogeographic venom variation in Indian kraits and its repercussion on snakebite therapy
Possible reference: Rashmi, U. et al. (2024) Elusive elapids: biogeographic venom variation in Indian kraits and its repercussion on snakebite therapy., Front Pharmacol, PMID 39575383

PXD052606 Dataset with its publication pending (from iProX)
Dataset title: Identification of WDR11 and its cargo-interaction-defect-mutant interacting proteins
Possible reference: Neocleous, V. et al. (2020) GnRH Deficient Patients With Congenital Hypogonadotropic Hypogonadism: Novel Genetic Findings in ANOS1, RNF216, WDR11, FGFR1, CHD7, and POLR3A Genes in a Case Series and Review of the Literature., Front Endocrinol (Lausanne), PMID 32982993

PXD052598 Montaser AB, Gao F, Peters D, Vainionp�� K, Zhibin N, Skowronska-Krawczyk D, Figeys D, Palczewski K, Leinonen H. Retinal proteome profiling of inherited retinal degeneration across three different mouse models suggests common drug targets in retinitis pig (from PanoramaPublic)
Dataset title: Retinal proteome profiling of inherited retinal degeneration across three different mouse models suggests common drug targets in retinitis pigmentosa
Possible reference: Montaser, AB. et al. (2024) Retinal Proteome Profiling of Inherited Retinal Degeneration Across Three Different Mouse Models Suggests Common Drug Targets in Retinitis Pigmentosa., Mol Cell Proteomics, PMID 39389360

PXD052591 Dataset with its publication pending (from PRIDE)
Dataset title: Direct ionic stress sensing and mitigation by the transcription factor NFAT5
Possible reference: Khandwala, CB. et al. (2023) Direct ionic stress sensing and mitigation by the transcription factor NFAT5., bioRxiv, PMID 37886503

PXD052551 Dataset with its publication pending (from PRIDE)
Dataset title: Differential alkylation of PHLPP2
Possible reference: Liu, J. et al. (2018) m6A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer., Nat Cell Biol, PMID 30154548

PXD052550 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of human eosinophils in patients with asthma-COPD overlap and eosinophilic COPD
Possible reference: Sunata, K. et al. (2024) Inflammatory profile of eosinophils in asthma-COPD overlap and eosinophilic COPD: a multi-omics study., Front Immunol, PMID 39439801

PXD052527 Dataset with its publication pending (from PRIDE)
Dataset title: E3 ligase substrate adaptor SPOP fine tunes the UPR of pancreatic beta cells
Possible reference: Oguh, AU. et al. (2025) E3 ligase substrate adaptor SPOP fine-tunes the UPR of pancreatic β cells., Genes Dev, PMID 39797759

PXD052506 Dataset with its publication pending (from jPOST)
Dataset title: Therapeutic Targeting of Dihydroorotate Dehydrogenase (DHODH) in Neuroblastoma: Modulating Lipid Metabolism and Ferroptosis
Possible reference: Shir, JC. et al. (2025) DHODH Blockade Induces Ferroptosis in Neuroblastoma by Modulating the Mevalonate Pathway., Mol Cell Proteomics, PMID 40513779

PXD052504 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Insight into Early Establishment of Seed Dormancy in Xanthium Strumarium
Possible reference: Nemati, I. et al. (2024) Proteomic analysis during seed development provides insight into the early establishment of seed dormancy in Xanthium strumarium., Physiol Plant, PMID 39415749

PXD052475 Dataset with its publication pending (from PRIDE)
Dataset title: C. albicans cells exhibit specific proteomic profiles depending on the medium used to induce the filamentation process
Possible reference: V�ronique, L. et al. (2024) Candida albicans cells exhibit media specific proteomic profiles during induction of filamentation., BMC Microbiol, PMID 39592958

PXD052472 Dataset with its publication pending (from PRIDE)
Dataset title: Sterol 14-alpha demethylase (CYP51) activity in Leishmania donovani is likely dependent upon cytochrome P450 reductase 1
Possible reference: Tulloch, LB. et al. (2024) Sterol 14-alpha demethylase (CYP51) activity in Leishmania donovani is likely dependent upon cytochrome P450 reductase 1., PLoS Pathog, PMID 38991025

PXD052471 Dataset with its publication pending (from jPOST)
Dataset title: SLFN11 Induces Apoptosis Through Ribosome Biogenesis Impairment
Possible reference: Ogawa, A. et al. (2025) SLFN11-mediated ribosome biogenesis impairment induces TP53-independent apoptosis., Mol Cell, PMID 39909041

PXD052426 Dataset with its publication pending (from iProX)
Dataset title: Chemical proteomic profiling of protein dopaminylation in colorectal cancer cells
Possible reference: Zhang, N. et al. (2024) Chemical proteomic profiling of protein dopaminylation in colorectal cancer cells., bioRxiv, PMID 38712070

PXD052425 Dataset with its publication pending (from iProX)
Dataset title: Quantitative phosphoproteomics of Mycolicibacterium smegmatis
Possible reference: Abo-Kadoum, MA. et al. (2021) Mycobacterium tuberculosis Raf kinase inhibitor protein (RKIP) Rv2140c is involved in cell wall arabinogalactan biosynthesis via phosphorylation., Microbiol Res, PMID 33189070

PXD052412 Dataset with its publication pending (from PRIDE)
Dataset title: An essential role for EROS in redox-dependent endothelial signal transduction
Possible reference: Waldeck-Weiermair, M. et al. (2024) An essential role for EROS in redox-dependent endothelial signal transduction., Redox Biol, PMID 38805973

PXD052401 Dataset with its publication pending (from PRIDE)
Dataset title: The red alga Porphyridium as a host for molecular farming: Efficient production of immunologically active hepatitis C virus glycoprotein
Possible reference: Hammel, A. et al. (2024) The red alga Porphyridium as a host for molecular farming: Efficient production of immunologically active hepatitis C virus glycoprotein., Proc Natl Acad Sci U S A, PMID 38833465

PXD052383 no publication (from MassIVE)
Dataset title: diaTracer enables spectrum-centric analysis of diaPASEF proteomics data
Possible reference: Li, K. et al. (2024) diaTracer enables spectrum-centric analysis of diaPASEF proteomics data., bioRxiv, PMID 38854051

PXD052378 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of Drosophila brain development and organ growth by the Minibrain/Rala signaling network
Possible reference: Brown, M. et al. (2024) Regulation of brain development by the Minibrain/Rala signaling network., bioRxiv, PMID 38766038

PXD052370 no publication (from MassIVE)
Dataset title: Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity
Possible reference: Cutler, R. et al. (2024) Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity., bioRxiv, PMID 39211145

PXD052367 Dataset with its publication pending (from jPOST)
Dataset title: Cysteine S-acetylation is a post-translational modification involved in metabolic regulation
Possible reference: Keenan, EK. et al. (2024) Cysteine S-acetylation is a post-translational modification involved in metabolic regulation., bioRxiv, PMID 38826225

PXD052360 Dataset with its publication pending (from PRIDE)
Dataset title: ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC
Possible reference: Tran, NL. et al. (2024) ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC., bioRxiv, PMID 38826238

PXD052357 no publication (from MassIVE)
Dataset title: Benchmarking and automating the biotinylation proteomics workflow
Possible reference: Li, H. et al. (2024) Benchmarking and Automating the Biotinylation Proteomics Workflow., Res Sq, PMID 39011118

PXD052354 no publication (from MassIVE)
Dataset title: Online Mixed-Bed Ion Exchange Chromatography for Native Top-Down Proteomics of Complex Mixtures
Possible reference: Fischer, MS. et al. (2024) Online Mixed-Bed Ion Exchange Chromatography for Native Top-Down Proteomics of Complex Mixtures., J Proteome Res, PMID 38913967

PXD052347 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of the Clostridioides difficile 630Îerm putative Pro-Pro endopeptidase CD1597
Possible reference: Claushuis, B. et al. (2024) Characterization of the Clostridioides difficile 630Δerm putative Pro-Pro endopeptidase CD1597., Access Microbiol, PMID 39381498

PXD052340 Dataset with its publication pending (from PRIDE)
Dataset title: Increased antioxidative defense and reduced advanced glycation end-product formation by metabolic adaptation in Non-Small-Cell-Lung-Cancer patients
Possible reference: Tomin, T. et al. (2025) Increased antioxidative defense and reduced advanced glycation end-product formation by metabolic adaptation in non-small-cell-lung-cancer patients., Nat Commun, PMID 40461450

PXD052337 Dataset with its publication pending (from PRIDE)
Dataset title: Inherited mitochondrial dysfunction impacts corneal innervation fibre identity, fonctionnality and regenerative potential
Possible reference: Meneux, L. et al. (2024) Inherited mitochondrial dysfunction triggered by OPA1 mutation impacts the sensory innervation fibre identity, functionality and regenerative potential in the cornea., Sci Rep, PMID 39138286

PXD052325 no publication (from MassIVE)
Dataset title: Single-cell signaling analysis reveals that Major Vault Protein facilitates RasG12C inhibitor resistance
Possible reference: Zhang, JZ. et al. (2023) Single-cell signaling analysis reveals that Major Vault Protein facilitates RasG12C inhibitor resistance., bioRxiv, PMID 37873412

PXD052315 no publication (from MassIVE)
Dataset title: A highly potent bi-thiazole inhibitor of LOX rewires collagen architecture and enhances chemoresponse in triple-negative breast cancer
Possible reference: Cetin, M. et al. (2024) A highly potent bi-thiazole inhibitor of LOX rewires collagen architecture and enhances chemoresponse in triple-negative breast cancer., Cell Chem Biol, PMID 39043186

PXD052288 Dataset with its publication pending (from PRIDE)
Dataset title: Pangolin scales as adaptations for innate immunity against pathogens
Possible reference: Tian, X. et al. (2024) Pangolin scales as adaptations for innate immunity against pathogens., BMC Biol, PMID 39397000

PXD052281 Dataset with its publication pending (from jPOST)
Dataset title: OGE sensitizes HCC to cisplatin
Possible reference: Chen, JH. et al. (2024) Aqueous Extracts of Ocimum gratissimum Sensitize Hepatocellular Carcinoma Cells to Cisplatin through BRCA1 Inhibition., Int J Mol Sci, PMID 39125994

PXD052273 no publication (from MassIVE)
Dataset title: FOXA2 rewires AP-1 for transcriptional reprogramming and lineage plasticity in prostate cancer
Possible reference: Wang, Z. et al. (2024) FOXA2 rewires AP-1 for transcriptional reprogramming and lineage plasticity in prostate cancer., Nat Commun, PMID 38851846

PXD052263 no publication (from MassIVE)
Dataset title: The influence of APOE4 on the pTau interactome in sporadic Alzheimers disease
Possible reference: Thierry, M. et al. (2024) The influence of APOEε4 on the pTau interactome in sporadic Alzheimer's disease., Acta Neuropathol, PMID 38772917

PXD052255 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic dataset of two contrasting sorghum genotypes to drought, heat and combined drought and heat stress
Possible reference: Ali, AEE. et al. (2025) Proteomic dataset of sorghum leaf and root responses to single and combined drought and heat stress., Sci Data, PMID 39824864

PXD052250 Dataset with its publication pending (from PRIDE)
Dataset title: Persistent epithelial barrier dysfunction and Periostin accumulation in histologic remission Eosinophilic Esophagitis
Possible reference: Hoelz, H. et al. (2025) Persistent desmoglein-1 downregulation and periostin accumulation in histologic remission of eosinophilic esophagitis., J Allergy Clin Immunol, PMID 39343172

PXD052230 no publication (from MassIVE)
Dataset title: Human Secretome Dependence on the Signal Recognition Particle
Possible reference: Miller, SC. et al. (2026) Signal recognition particle-dependent secretome in humans., Sci Rep, PMID 41680224

PXD052229 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omics analysis reveals the impact of influenza A virus host adaptation on immune signatures in pig tracheal tissue
Possible reference: Laybourn, HA. et al. (2024) Multi-omics analysis reveals the impact of influenza a virus host adaptation on immune signatures in pig tracheal tissue., Front Immunol, PMID 39247193

PXD052200 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of human eosinophils stimulated with IL-4 and IL-5
Possible reference: Pazdrak, K. et al. (2016) Cytokine-Induced Glucocorticoid Resistance from Eosinophil Activation: Protein Phosphatase 5 Modulation of Glucocorticoid Receptor Phosphorylation and Signaling., J Immunol, PMID 27742828

PXD052188 Dataset with its publication pending (from PRIDE)
Dataset title: Getting over it? A proteomic analysis of mechanisms driving multigenerational acclimation to organic ultraviolet filters in Daphnia magna
Possible reference: Boyd, A. et al. (2025) Getting over it? A proteomic analysis of mechanisms driving multigenerational acclimation to organic ultraviolet filters in Daphnia magna., Environ Pollut, PMID 40754163

PXD052176 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting MGAT4A-mediated N-glycosylation as a therapeutic strategy to inhibit glioblastoma stem cell invasion
Possible reference: Niu, R. et al. (2026) Targeting MGAT4A-Mediated N-Glycosylation as a Therapeutic Strategy to Inhibit Glioblastoma Stem Cell Invasion., Exploration (Beijing), PMID 41810076

PXD052172 Dataset with its publication pending (from PRIDE)
Dataset title: A chemoenzymatic method for simultaneous profiling N- and O-glycans on glycoproteins using one-pot format
Possible reference: Ortega-Rodriguez, U. et al. (2024) A chemoenzymatic method for simultaneous profiling N- and O-glycans on glycoproteins using one-pot format., Cell Rep Methods, PMID 39116882

PXD052157 Dataset with its publication pending (from jPOST)
Dataset title: Phosphorylation of SNW 1 Protein associated with Equine Melanocytic Neoplasm identified in Serum and Feces
Possible reference: Vinijkumthorn, R. et al. (2024) Phosphorylation of SNW1 protein associated with equine melanocytic neoplasm identified in serum and feces., Sci Rep, PMID 39730520

PXD052154 Dataset with its publication pending (from PRIDE)
Dataset title: The temporal dynamics of proteins in aged skin wound healing and comparison to gene expression
Possible reference: Torres, M. et al. (2025) The Temporal Dynamics of Proteins in Aged Skin Wound Healing and Comparison with Gene Expression., J Invest Dermatol, PMID 39675661

PXD052147 Dataset with its publication pending (from jPOST)
Dataset title: SHIP1 modulation and proteome characterization of microglia
Possible reference: Ahat, E. et al. (2024) SHIP1 modulation and proteome characterization of microglia., J Proteomics, PMID 38777089

PXD052115 Dataset with its publication pending (from PRIDE)
Dataset title: hnRNP R promotes O-GlcNAcylation of eIF4G to facilitate axonal protein synthesis
Possible reference: Zare, A. et al. (2024) hnRNP R promotes O-GlcNAcylation of eIF4G and facilitates axonal protein synthesis., Nat Commun, PMID 39198412

PXD052111 Dataset with its publication pending (from jPOST)
Dataset title: Serum Proteomic characterization in Stump-tailed macaque (Macaca arctoides) with neutralizing antibodies against Dengue virus in Thailand
Possible reference: Ruengket, P. et al. (2026) Serum proteomic characterization of stump-tailed macaques (Macaca arctoides) with neutralizing antibodies against Dengue virus in Thailand., PLoS One, PMID 41729959

PXD052107 Dataset with its publication pending (from PRIDE)
Dataset title: Strigolactones positively regulate HY5-dependent autophagy and the degradation of ubiquitinated proteins in response to cold stress in tomato
Possible reference: Chi, C. et al. (2025) Strigolactones positively regulate HY5-dependent autophagy and the degradation of ubiquitinated proteins in response to cold stress in tomato., New Phytol, PMID 39155750

PXD052041 Dataset with its publication pending (from iProX)
Dataset title: ATPase activity of RIOK2 transports FADD–RIPK1–Caspase-8 complex from lysosome to ER and triggers spatial cleavage of GSDMD
Possible reference: Ma, M. et al. (2025) RIOK2 kinase regulates the translocation of the FADD-RIPK1-Caspase-8 complex to the ER and the cleavage of Gasdermin D to drive pyroptosis., Nat Commun, PMID 41249793

PXD052034 Dataset with its publication pending (from PRIDE)
Dataset title: Two H3K23 histone methyltransferases, SET-32 and SET-21, function synergistically to promote nuclear RNAi-mediated transgenerational epigenetic inheritance in Caenorhabditis elegans
Possible reference: Zhebrun, A. et al. (2024) Two H3K23 histone methyltransferases, SET-32 and SET-21, function synergistically to promote nuclear RNAi-mediated transgenerational epigenetic inheritance in Caenorhabditis elegans., bioRxiv, PMID 39574755

PXD052023 no publication (from MassIVE)
Dataset title: Signal transduction pathways controlling Ins2 gene activity and beta cell state transitions
Possible reference: Chu, CM. et al. (2025) Signal transduction pathways controlling Ins2 gene activity and beta cell state transitions., iScience, PMID 40144638

PXD051999 Dataset with its publication pending (from iProX)
Dataset title: Serum proteomics data of patients with brucellosis
Possible reference: Wu, Q. et al. (2024) Preparation and application of a Brucella multiepitope fusion protein based on bioinformatics and Tandem Mass Tag-based proteomics technology., Front Immunol, PMID 39867886

PXD051998 Dataset with its publication pending (from iProX)
Dataset title: Effects of Chlorogenic Acid on Hepatocytes: From Beneficial Effects to Potential Toxicity
Possible reference: Garc�a-Varela, R. et al. (2016) Cancer cell specific cytotoxic effect of Rhoeo discolor extracts and solvent fractions., J Ethnopharmacol, PMID 27235722

PXD051993 no publication (from MassIVE)
Dataset title: MI-AEG-TKK-YL-JSB_8LFQ_ ARL5_ARMH3
Possible reference: Ishida, M. et al. (2024) ARMH3 is an ARL5 effector that promotes PI4KB-catalyzed PI4P synthesis at the trans-Golgi network., Nat Commun, PMID 39580461

PXD051964 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring modes of microbial interactions with implications for methane cycling.
Possible reference: Brenzinger, K. et al. (2024) Exploring modes of microbial interactions with implications for methane cycling., FEMS Microbiol Ecol, PMID 39122657

PXD051948 Dataset with its publication pending (from PRIDE)
Dataset title: Differential antibody capture pneumonia samples Munich cohort
Possible reference: Bertrams, W. et al. (2026) Surface proteome of plasma extracellular vesicles differentiates between SARS-CoV-2 and influenza infection., Virulence, PMID 41263641

PXD051940 no publication (from MassIVE)
Dataset title: TermineR: extracting information on proteolytic processing from shotgun proteomics data
Possible reference: Cosenza-Contreras, M. et al. (2024) TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data., Proteomics, PMID 39126236

PXD051927 Dataset with its publication pending (from PRIDE)
Dataset title: Lysosomal damage triggers a p38 MAPK-dependent phosphorylation cascade to promote lysophagy via the small heat shock protein HSP27
Possible reference: Gallagher, ER. et al. (2024) Lysosomal damage triggers a p38 MAPK-dependent phosphorylation cascade to promote lysophagy via the small heat shock protein HSP27., Curr Biol, PMID 39541976

PXD051912 Dataset with its publication pending (from PRIDE)
Dataset title: DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2
Possible reference: Rezi, CK. et al. (2024) DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2., bioRxiv, PMID 37987012

PXD051888 Dataset with its publication pending (from jPOST)
Dataset title: Multi-omics analysis using antibody-based in situ biotinylation technique reveals the mechanism of Cajal body formation
Possible reference: Noguchi, K. et al. (2024) Multi-omics analysis using antibody-based in situ biotinylation technique suggests the mechanism of Cajal body formation., Cell Rep, PMID 39283744

PXD051884 Dataset with its publication pending (from PRIDE)
Dataset title: TRAF7 determines circadian period through ubiquitination and degradation of DBP
Possible reference: Masuda, S. et al. (2024) TRAF7 determines circadian period through ubiquitination and degradation of DBP., Commun Biol, PMID 39379486

PXD051883 Dataset with its publication pending (from jPOST)
Dataset title: The BAF complex enhances transcription through interaction with H3K56ac in the histone globular domain
Possible reference: Hyun, K. et al. (2024) The BAF complex enhances transcription through interaction with H3K56ac in the histone globular domain., Nat Commun, PMID 39511190

PXD051879 Dataset with its publication pending (from PRIDE)
Dataset title: Tracking the dynamics of the glycolytic metabolite fructose 1,6-bisphosphate in liver cancer cells with a fluorescent biosensor
Possible reference: P�rez-Ch�vez, I. et al. (2024) Tracking fructose 1,6-bisphosphate dynamics in liver cancer cells using a fluorescent biosensor., iScience, PMID 39640569

PXD051863 Dataset with its publication pending (from jPOST)
Dataset title: isoAsp analysis of bovine lens alpha-crystallin
Possible reference: Sakaue, H. et al. (2025) isoAsp-Quest: workflow development for isoAsp identification using database searches., J Biochem, PMID 39441692

PXD051860 Dataset with its publication pending (from jPOST)
Dataset title: Changes in Protein Fluxes and Gene Expression in Non-Injured Muscle Tissue Distant from an Acute Myotoxic Injury in Male Mice
Possible reference: Bizieff, A. et al. (2024) Changes in protein fluxes and gene expression in non-injured muscle tissue distant from an acute myotoxic injury in male mice., J Physiol, PMID 38968395

PXD051847 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of Ganoderma lucidum dikaryon and monokaryons
Possible reference: Yu, H. et al. (2025) Proteome study of dikaryotic and monokaryotic mycelia reveals the transfer between biological processes contributing to dikaryon growth advantage of the medicinal fungus Ganoderma lucidum., BMC Genomics, PMID 40751175

PXD051787 Dataset with its publication pending (from jPOST)
Dataset title: p53-inducible lncRNA LOC644656 causes genotoxic stress-induced stem cell maldifferentiation and cancer chemoresistance
Possible reference: Tamura, A. et al. (2025) p53-inducible lncRNA LOC644656 causes genotoxic stress-induced stem cell maldifferentiation and cancer chemoresistance., Nat Commun, PMID 40410129

PXD051786 Dataset with its publication pending (from PRIDE)
Dataset title: Increased expression of ATase1/NAT8B or ATase2/NAT8 in the mouse results in an autistic-like phenotype with altered dendritic branching and spine formation
Possible reference: Rigby, MJ. et al. (2020) The endoplasmic reticulum acetyltransferases ATase1/NAT8B and ATase2/NAT8 are differentially regulated to adjust engagement of the secretory pathway., J Neurochem, PMID 31945187

PXD051784 Dataset with its publication pending (from jPOST)
Dataset title: Bioinformatics-Guided Identification and Quantification of Biomarkers of Crotalus atrox Envenoming and its Neutralization by Antivenom
Possible reference: Bala, AA. et al. (2025) Bioinformatics-Guided Identification and Quantification of Biomarkers of Crotalus atrox Envenoming and Its Neutralization by Antivenom., Mol Cell Proteomics, PMID 40147718

PXD051782 Dataset with its publication pending (from PRIDE)
Dataset title: The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum
Possible reference: Min, H. et al. (2024) The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum., Nat Commun, PMID 38702310

PXD051778 Dataset with its publication pending (from PRIDE)
Dataset title: A proteomics approach to isolating neuropilin-dependent Î±5 integrin trafficking pathways: neuropilin 1 and 2 co-traffic Î±5 integrin through endosomal p120RasGAP to promote polarised fibronectin fibrillogenesis in endothelial cells
Possible reference: Benwell, CJ. et al. (2024) A proteomics approach to isolating neuropilin-dependent α5 integrin trafficking pathways: neuropilin 1 and 2 co-traffic α5 integrin through endosomal p120RasGAP to promote polarised fibronectin fibrillogenesis in endothelial cells., Commun Biol, PMID 38789481

PXD051762 Dataset with its publication pending (from PRIDE)
Dataset title: Covalent 14-3-3 Molecular Glues and Heterobifunctional Molecules Against Nuclear Transcription Factors and Regulators
Possible reference: Shao, Q. et al. (2023) Covalent 14-3-3 Molecular Glues and Heterobifunctional Molecules Against Nuclear Transcription Factors and Regulators., bioRxiv, PMID 37986959

PXD051720 Dataset with its publication pending (from PRIDE)
Dataset title: STK19 drives transcription-coupled nucleotide excision repair by stimulating Pol II ubiquitylation and TFIIH recruitment
Possible reference: Ramadhin, AR. et al. (2024) STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment., Mol Cell, PMID 39547223

PXD051706 Dataset with its publication pending (from PRIDE)
Dataset title: Novel protocol for spatial proteome analysis of microdissected formalin-fixed paraffin-embedded tissues
Possible reference: Gasparello, T. et al. (2026) Artificial Intelligence-Driven Laser Capture Microdissection., Methods Mol Biol, PMID 41629719

PXD051703 Dataset with its publication pending (from PRIDE)
Dataset title: Aerobic Adaptation and Metabolic Dynamics of Propionibacterium freudenreichii DSM 20271: Insights from Comparative Transcriptomics and Surfaceome Analysis
Possible reference: Loivamaa, I. et al. (2024) Aerobic adaptation and metabolic dynamics of Propionibacterium freudenreichii DSM 20271: insights from comparative transcriptomics and surfaceome analysis., mSystems, PMID 39345151

PXD051702 no publication (from MassIVE)
Dataset title: Proteomic insights into the impact of COVID-19 on peripheral blood mononuclear cells in kidney transplant recipients
Possible reference: Leite, GGF. et al. (2024) Proteomic profiling of peripheral blood mononuclear cells reveals immune dysregulation and metabolic alterations in kidney transplant recipients with COVID-19., Front Immunol, PMID 39737170

PXD051694 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of Parkinson’s Disease Protein 7 upregulates cytoskeletal protein Palladin and is associated with pregnancy loss
Possible reference: Yang, Z. et al. (2025) Loss of Parkinson Disease Protein 7 (PARK7) upregulates ROS and cell migration and is associated with recurrent pregnancy loss., Mol Med, PMID 41350809

PXD051693 Dataset with its publication pending (from PRIDE)
Dataset title: Single electron transfer between sulfonium and tryptophan enables site-selective photo crosslinking of methyllysine reader proteins
Possible reference: Feng, F. et al. (2024) Single-electron transfer between sulfonium and tryptophan enables site-selective photo crosslinking of methyllysine reader proteins., Nat Chem, PMID 39079947

PXD051671 no publication (from MassIVE)
Dataset title: Fish species authentication in commercial fish products using mass spectrometry and spectra library approach
Possible reference: Varunjikar, MS. et al. (2024) Fish species authentication in commercial fish products using mass spectrometry and spectral library matching approach., Food Res Int, PMID 39147490

PXD051667 no publication (from MassIVE)
Dataset title: Redox control of the deubiquitinating enzyme Ubp2 regulates translation during stress
Possible reference: Sim�es, V. et al. (2022) Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes., Cell Rep, PMID 35613580

PXD051662 Dataset with its publication pending (from PRIDE)
Dataset title: Cytoplasmic mRNA decay controlling inflammatory gene expression is determined by pre-mRNA fate decision
Possible reference: Bestehorn, A. et al. (2025) Cytoplasmic mRNA decay controlling inflammatory gene expression is determined by pre-mRNA fate decision., Mol Cell, PMID 39862867

PXD051655 Dataset with its publication pending (from iProX)
Dataset title: SRXN1 Accelerates Erastin-Induced Ferroptosis in HT-22 Hippocampal Neurons by Driving HO-1 Activation
Possible reference: Guo, S. et al. (2024) Sulfiredoxin-1 accelerates erastin-induced ferroptosis in HT-22 hippocampal neurons by driving heme Oxygenase-1 activation., Free Radic Biol Med, PMID 39159887

PXD051654 Dataset with its publication pending (from iProX)
Dataset title: Characterization of dsRNA Binding Proteins through Solubility Analysis Identifies ZNF385A as a dsRNA Homeostasis Regulator
Possible reference: Jiang, N. et al. (2025) Characterization of dsRNA binding proteins through solubility analysis identifies ZNF385A as a dsRNA homeostasis regulator., Nat Commun, PMID 40210660

PXD051638 Dataset with its publication pending (from PRIDE)
Dataset title: DDA1, a novel factor in transcription-coupled repair, modulates CRL4CSA dynamics at DNA damage-stalled RNA polymerase II
Possible reference: Schiffmacher, DL. et al. (2023) DDA1, a novel factor in transcription-coupled repair, modulates CRL4CSA dynamics at DNA damage-stalled RNA polymerase II., Res Sq, PMID 37886519

PXD051593 Dataset with its publication pending (from PRIDE)
Dataset title: Spatial hepatocyte plasticity of gluconeogenesis during the metabolic transitions between fed, fasted and starvation states
Possible reference: Okada, J. et al. (2024) Spatial hepatocyte plasticity of gluconeogenesis during the metabolic transitions between fed, fasted and starvation states., bioRxiv, PMID 38746329

PXD051583 Dataset with its publication pending (from PRIDE)
Dataset title: Signal peptide-independent secretion of keratin-19 by pancreatic cancer cells
Possible reference: Moresco, P. et al. (2025) Signal peptide-independent secretion of keratin-19 by pancreatic cancer cells., bioRxiv, PMID 39896665

PXD051571 Dataset with its publication pending (from jPOST)
Dataset title: Pronounced expression of extracellular matrix proteoglycans regulated by Wnt pathway underlies the parallel evolution of lip hypertrophy in East African cichlids
Possible reference: Machii, N. et al. (2025) Pronounced expression of extracellular matrix proteoglycans regulated by Wnt pathway underlies the parallel evolution of lip hypertrophy in East African cichlids., Elife, PMID 40259743

PXD051567 no publication (from MassIVE)
Dataset title: Cold Storage Disrupts the Proteome Landscape in Rat Kidney Transplants
Possible reference: Sharma, A. et al. (2025) Cold Storage Disrupts the Proteome and Phosphoproteome Landscape in Rat Kidney Transplants., Transplantation, PMID 39716351

PXD051561 no publication (from MassIVE)
Dataset title: High-density CRISPRi screens reveal adaptive transcriptional gradients in cyanobacteria
Possible reference: Hren, A. et al. (2025) High-density CRISPRi screens reveal diverse routes to improved acclimation in cyanobacteria., Proc Natl Acad Sci U S A, PMID 40117303

PXD051544 Dataset with its publication pending (from jPOST)
Dataset title: Cold Atmospheric Plasma Jet Promotes Wound Healing through CK2- coordinated PI3K/AKT and MAPK Signaling Pathways
Possible reference: Wu, PS. et al. (2025) Cold Atmospheric Plasma Jet Promotes Wound Healing Through CK2-Coordinated PI3K/AKT and MAPK Signaling Pathways., Mol Cell Proteomics, PMID 40187493

PXD051532 Dataset with its publication pending (from iProX)
Dataset title: Identification of WNK1 as a therapeutic target to suppress IgH/MYC expression in multiple myeloma
Possible reference: Ye, T. et al. (2024) Identification of WNK1 as a therapeutic target to suppress IgH/MYC expression in multiple myeloma., Cell Rep, PMID 38722741

PXD051523 Dataset with its publication pending (from jPOST)
Dataset title: RNA-binding proteins control glycolysis via regulation of mRNA stability under chronic hypoxia
Possible reference: Ogura, Y. et al. (2025) Fragile X messenger ribonucleoprotein 1 (FMRP) regulates glycolytic gene expression under chronic hypoxia in HCT116 cells., Sci Rep, PMID 40246883

PXD051512 Dataset with its publication pending (from iProX)
Dataset title: Draper interacts with autophagy-related protein 3 to positively regulate autophagy during silk gland degradation in Bombyx mori
Possible reference: Zou, S. et al. (2025) Draper-ATG3 Interaction Positively Regulates Autophagy to Mediate Silk Gland Degradation in Bombyx mori., Adv Sci (Weinh), PMID 40953285

PXD051489 Dataset with its publication pending (from PRIDE)
Dataset title: Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists
Possible reference: Hollingsworth, LR. et al. (2024) Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists., bioRxiv, PMID 38659763

PXD051484 Dataset with its publication pending (from PRIDE)
Dataset title: Global lysine succinylation analysis unveils post-translational regulation effect on phenylpropanoids metabolism remodeling during Lonicera japonica flowering development
Possible reference: Chen, Y. et al. (2024) Global lysine succinylation analysis unveils post-translational regulation effect on phenylpropanoid metabolism remodeling during Lonicera japonica flower development., Plant Physiol Biochem, PMID 39084169

PXD051473 Dataset with its publication pending (from PRIDE)
Dataset title: GABA/Glutamate neuron differentiation imbalance and increased AKT/mTOR signalling in CNTNAP2-/- cerebral organoids
Possible reference: Chalkiadaki, K. et al. (2025) GABA/Glutamate Neuron Differentiation Imbalance and Increased AKT/mTOR Signaling in CNTNAP2-/- Cerebral Organoids., Biol Psychiatry Glob Open Sci, PMID 39758604

PXD051469 no publication (from MassIVE)
Dataset title: Suppression of astrocyte BMP signaling improves fragile X syndrome molecular signatures and functional deficits
Possible reference: Deng, J. et al. (2024) Suppression of astrocyte BMP signaling improves fragile X syndrome molecular signatures and functional deficits., bioRxiv, PMID 38979341

PXD051454 Dataset with its publication pending (from PRIDE)
Dataset title: Acetylomics reveals an extensive acetylation diversity within Pseudomonas aeruginosa
Possible reference: Broeckaert, N. et al. (2024) Acetylomics reveals an extensive acetylation diversity within Pseudomonas aeruginosa., Microlife, PMID 39464744

PXD051441 Dataset with its publication pending (from PRIDE)
Dataset title: Glycoproteomic and single-protein glycomic analyses reveal zwitterionic N-glycans on natural and recombinant proteins derived from insect cells
Possible reference: Yan, S. et al. (2025) Glycoproteomic and Single-Protein Glycomic Analyses Reveal Zwitterionic N-Glycans on Natural and Recombinant Proteins Derived From Insect Cells., Mol Cell Proteomics, PMID 40334746

PXD051436 Dataset with its publication pending (from iProX)
Dataset title: Quantitative Site-specific N-glycosylation Analysis Reveals IgG Glyco-signatures for Pancreatic Cancer Diagnosis
Possible reference: Jin, Y. et al. (2024) Quantitative site-specific N-glycosylation analysis reveals IgG glyco-signatures for pancreatic cancer diagnosis., Clin Proteomics, PMID 39734184

PXD051431 Dataset with its publication pending (from PRIDE)
Dataset title: Pharmacological Targeting of Casein Kinase 1Î´ Suppresses Oncogenic NRAS-Driven Melanoma
Possible reference: Wen, Y. et al. (2024) Pharmacological targeting of casein kinase 1δ suppresses oncogenic NRAS-driven melanoma., Nat Commun, PMID 39572526

PXD051412 Dataset with its publication pending (from PRIDE)
Dataset title: Site-specific identification of UFMylation by remnant VG-immunoprecipitation
Possible reference: Blazev, R. et al. (2025) Site-specific quantification of the in vivo UFMylome reveals myosin modification in ALS., Cell Rep Methods, PMID 40347946

PXD051405 Dataset with its publication pending (from PRIDE)
Dataset title: Spatiotemporal Deciphering of Dynamic Proteome during Liquid-Liquid Phase Separation in Living Cells
Possible reference: Song, S. et al. (2025) Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells., Nat Commun, PMID 40346035

PXD051392 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of fission yeast RNA degradation mutants
Possible reference: Bitton, DA. et al. (2015) Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast., Genome Res, PMID 25883323

PXD051378 Dataset with its publication pending (from PRIDE)
Dataset title: DNA-Protein Crosslinks Promote cGAS-STING-driven Premature Aging and Embryonic Lethality
Possible reference: Tomaskovic, I. et al. (2026) DNA-protein cross-links promote cGAS-STING-driven premature aging and embryonic lethality., Science, PMID 41610251

PXD051369 Dataset with its publication pending (from PRIDE)
Dataset title: Unraveling developmental gene regulation in holometabolous insects through comparative transcriptomics and proteomics
Possible reference: Wilkens, M. et al. (2025) Unraveling developmental gene regulation in holometabolous insects through comparative transcriptomics and proteomics., Commun Biol, PMID 40596634

PXD051367 no publication (from MassIVE)
Dataset title: Comparative analysis of plasma protein dynamics in female patients with ST-elevation myocardial infarction and Takotsubo syndrome
Possible reference: Hussain, S. et al. (2024) Comparative Analysis of Plasma Protein Dynamics in Women with ST-Elevation Myocardial Infarction and Takotsubo Syndrome., Cells, PMID 39513871

PXD051349 Dataset with its publication pending (from iProX)
Dataset title: Exosomes derived from syncytia induced by SARS-2-S promote the proliferation and metastasis of hepatocellular carcinoma cells
Possible reference: Li, H. et al. (2024) Exosomes derived from syncytia induced by SARS-2-S promote the proliferation and metastasis of hepatocellular carcinoma cells., Front Cell Infect Microbiol, PMID 39844837

PXD051347 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics profiling of the honeybee parasite Tropilaelpas mercedesae across post-embryonic development
Possible reference: Wei, Q. et al. (2024) Proteomics profiling of the honeybee parasite Tropilaelaps mercedesae across post-embryonic development., Sci Data, PMID 38750068

PXD051328 Dataset with its publication pending (from iProX)
Dataset title: Fluorescence imaging sheds light on the immune evasion mechanisms of hepatic stellate cells mediated by superoxide anion
Possible reference: Mao, Y. et al. (2024) Fluorescence imaging sheds light on the immune evasion mechanisms of hepatic stellate cells mediated by superoxide anion., Commun Biol, PMID 38730013

PXD051289 Dataset with its publication pending (from iProX)
Dataset title: GAPDH K251 Succinylation Induced by Tobacco Smoking Coordinates Glycolysis and Glutamine Metabolism to Promote NSCLC Progression
Possible reference: Wang, K. et al. (2025) Tobacco Smoking Rewires Cell Metabolism by Inducing GAPDH Succinylation to Promote Lung Cancer Progression., Cancer Res, PMID 40366632

PXD051284 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of mice modeling NAFLD and after treatment with a novel chrysin derivative
Possible reference: Zhang, R. et al. (2024) Synthesis and biological evaluation of the novel chrysin prodrug for non-alcoholic fatty liver disease treatment., Front Pharmacol, PMID 38708081

PXD051282 Dataset with its publication pending (from iProX)
Dataset title: Urinary proteomic analysis of HGSOC
Possible reference: Ni, M. et al. (2024) Candidate prognostic biomarkers and prediction models for high-grade serous ovarian cancer from urinary proteomics., J Proteomics, PMID 38925351

PXD051276 no publication (from MassIVE)
Dataset title: Metabolomics reveals the importance of metabolites in Mussaenda pubescens for antioxidant properties and quality traits
Possible reference: Zhou, C. et al. (2024) Metabolomics reveals the importance of metabolites in Mussaenda pubescens for antioxidant properties and quality traits., Physiol Plant, PMID 38628104

PXD051275 Dataset with its publication pending (from PRIDE)
Dataset title: Selective Mitochondrial Respiratory Complex I Subunit Deficiency Causes Tumor Immunogenicity
Possible reference: Liang, J. et al. (2023) Selective Mitochondrial Respiratory Complex I Subunit Deficiency Causes Tumor Immunogenicity., bioRxiv, PMID 37873273

PXD051267 Dataset with its publication pending (from PRIDE)
Dataset title: Ubiquitin E3 ligases UBR4, UBR5 and HUWE1 protect human genome integrity by targeting cancer-associated APOBEC3 deaminases for degradation
Possible reference: Schwartz, I. et al. (2026) Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity., Nat Commun, PMID 41554709

PXD051262 no publication (from MassIVE)
Dataset title: Liver and Pancreatic-Targeted Interleukin-22 as a Therapeutic for Metabolic Dysfunction-Associated Steatohepatitis
Possible reference: Sajiir, H. et al. (2024) Liver and pancreatic-targeted interleukin-22 as a therapeutic for metabolic dysfunction-associated steatohepatitis., Nat Commun, PMID 38811532

PXD051254 Dataset with its publication pending (from iProX)
Dataset title: Urine proteome uncover common mechanism between mucopolysaccharidosis type I and II
Possible reference: Yuan, X. et al. (2025) Urine proteome uncovers common mechanisms between mucopolysaccharidosis types I and II., Clin Biochem, PMID 40939753

PXD051246 Dataset with its publication pending (from PRIDE)
Dataset title: Neutrophil-derived migrasomes are an essential part of the coagulation system
Possible reference: Jiang, D. et al. (2024) Neutrophil-derived migrasomes are an essential part of the coagulation system., Nat Cell Biol, PMID 38997457

PXD051238 Dataset with its publication pending (from PRIDE)
Dataset title: Neutrophil-derived migrasomes are an essential part of the coagulation system
Possible reference: Jiang, D. et al. (2024) Neutrophil-derived migrasomes are an essential part of the coagulation system., Nat Cell Biol, PMID 38997457

PXD051231 Dataset with its publication pending (from PRIDE)
Dataset title: Neutrophil-derived migrasomes are an essential part of the coagulation system
Possible reference: Jiang, D. et al. (2024) Neutrophil-derived migrasomes are an essential part of the coagulation system., Nat Cell Biol, PMID 38997457

PXD051229 Dataset with its publication pending (from PRIDE)
Dataset title: Neutrophil-derived migrasomes are an essential part of the coagulation system
Possible reference: Jiang, D. et al. (2024) Neutrophil-derived migrasomes are an essential part of the coagulation system., Nat Cell Biol, PMID 38997457

PXD051224 Dataset with its publication pending (from PRIDE)
Dataset title: Copper(I)-Nitrene Platform for Chemoproteomics Profiling of Methionine
Possible reference: Sahu, S. et al. (2024) Copper(I)-nitrene platform for chemoproteomic profiling of methionine., Nat Commun, PMID 38762540

PXD051223 Dataset with its publication pending (from PRIDE)
Dataset title: metabolic tuning of mixed purple phototrophic bacteria biofilms in photoheterotrophic conditions
Possible reference: D�az-Rullo Edreira, S. et al. (2024) Elucidating metabolic tuning of mixed purple phototrophic bacteria biofilms in photoheterotrophic conditions through microbial photo-electrosynthesis., Commun Biol, PMID 39557963

PXD051206 Dataset with its publication pending (from PRIDE)
Dataset title: Defining the heterogeneous molecular landscape of lung cancer cell responses to epigenetic inhibition
Possible reference: Lin, C. et al. (2024) Defining the heterogeneous molecular landscape of lung cancer cell responses to epigenetic inhibition., bioRxiv, PMID 38853901

PXD051202 Dataset with its publication pending (from PRIDE)
Dataset title: The SPFH complex HflK-HflC regulates aerobic respiration in bacteria
Possible reference: P�rez-L�pez, MI. et al. (2025) The SPFH complex HflK-HflC regulates aerobic respiration in bacteria., PLoS Biol, PMID 40193326

PXD051182 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring the early molecular pathogenesis of osteoarthritis using differential network analysis of human synovial fluid
Possible reference: Shay, JW. et al. (2016) Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015., BMC Genomics, PMID 27454254

PXD051171 Dataset with its publication pending (from iProX)
Dataset title: GlycoIP: An Integrated Platform for the Simultaneous Profiling of Intact N- and O-glycopeptides from Human Semen
Possible reference: Yan, G. et al. (2025) GlycoIP: an integrated platform for simultaneous and site-specific N/O-glycosylation analysis of human semen., Front Chem, PMID 40458655

PXD051146 Dataset with its publication pending (from PRIDE)
Dataset title: Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER-Phagy
Possible reference: Prieto-Garcia, C. et al. (2024) Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy., Science, PMID 39541449

PXD051144 no publication (from MassIVE)
Dataset title: Proteomics analysis of mesenchymal stem cells treated with dimethyl fumarate
Possible reference: Adelipour, M. et al. (2024) Evaluation of the effect of dimethyl fumarate on human bone marrow-derived mesenchymal stem cells using bottom-up proteomics., Biochimie, PMID 37931793

PXD051130 Dataset with its publication pending (from PRIDE)
Dataset title: Netrin-1 engineered endothelial cell exosomes induce the formation of pre-regenerative niche to accelerate peripheral nerve repair
Possible reference: Huang, J. et al. (2024) Netrin-1-engineered endothelial cell exosomes induce the formation of pre-regenerative niche to accelerate peripheral nerve repair., Sci Adv, PMID 38941462

PXD051129 Dataset with its publication pending (from jPOST)
Dataset title: Mitochondria inside acute myeloid leukemia cells hydrolyze ATP to resist chemotherapy
Possible reference: Hagen, JT. et al. (2024) Acute myeloid leukemia mitochondria hydrolyze ATP to resist chemotherapy., bioRxiv, PMID 38659944

PXD051128 Dataset with its publication pending (from PRIDE)
Dataset title: GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies
Possible reference: Benbarche, S. et al. (2024) GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies., Mol Cell, PMID 38688280

PXD051119 Dataset with its publication pending (from iProX)
Dataset title: RH3 enhances antiviral defense by facilitating small RNA loading into Argonaute 2
Possible reference: Huang, J. et al. (2025) RH3 enhances antiviral defense by facilitating small RNA loading into Argonaute 2 at endoplasmic reticulum-chloroplast membrane contact sites., Nat Commun, PMID 40000658

PXD051118 Dataset with its publication pending (from iProX)
Dataset title: Remoulding probiotics for effective treatment of type 2 diabetes via oral administration
Possible reference: Ji, H. et al. (2025) Remolding probiotics for effective treatment of type 2 diabetes via oral administration., Biomaterials, PMID 39577036

PXD051080 Dataset with its publication pending (from iProX)
Dataset title: TMT-Based Quantitative Proteomic Profiling of Human Esophageal Cancer Cells Reveals the Potential Mechanism and Potential Therapeutic Targets Associated with Radio-Resistance
Possible reference: Gao, A. et al. (2025) TMT-Based Quantitative Proteomic Profiling of Human Esophageal Cancer Cells Reveals the Potential Mechanism and Potential Therapeutic Targets Associated With Radioresistance., Proteomics Clin Appl, PMID 39375892

PXD051075 Dataset with its publication pending (from PRIDE)
Dataset title: Conventional cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure
Possible reference: Michael, ARM. et al. (2024) Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure., Nat Commun, PMID 39358380

PXD051063 Dataset with its publication pending (from PRIDE)
Dataset title: Comana monomorpha caterpillar venom proteomics
Possible reference: Goudarzi, MH. et al. (2024) Phylogeny, envenomation syndrome, and membrane permeabilising venom produced by Australia's electric caterpillar Comana monomorpha., Sci Rep, PMID 38898081

PXD051062 Dataset with its publication pending (from PRIDE)
Dataset title: A comparative analysis of digestion methods for bile proteomics: the key to unlocking biliary biomarker potential in liver transplantation
Possible reference: Thorne, AM. et al. (2024) Comparative Analysis of Digestion Methods for Bile Proteomics: The Key to Unlocking Biliary Biomarker Potential., Anal Chem, PMID 39186690

PXD051048 Dataset with its publication pending (from iProX)
Dataset title: The Transcription factor FgSfp1 orchestrates mycotoxin deoxynivalenol biosynthesis in Fusarium graminearum
Possible reference: Sun, S. et al. (2024) The transcription factor FgSfp1 orchestrates mycotoxin deoxynivalenol biosynthesis in Fusarium graminearum., Commun Biol, PMID 39604708

PXD051022 Dataset with its publication pending (from PRIDE)
Dataset title: Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.
Possible reference: Burnett, LE. et al. (2024) Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice., PLoS Biol, PMID 38857283

PXD050983 Dataset with its publication pending (from PRIDE)
Dataset title: Fam134c and Fam134b shape axonal endoplasmic reticulum architecture in vivo.
Possible reference: Iavarone, F. et al. (2024) Fam134c and Fam134b shape axonal endoplasmic reticulum architecture in vivo., EMBO Rep, PMID 39039299

PXD050980 Dataset with its publication pending (from PRIDE)
Dataset title: Resting skeletal muscle reduces ATP turnover during hibernation
Possible reference: De Napoli, C. et al. (2025) Reduced ATP turnover during hibernation in relaxed skeletal muscle., Nat Commun, PMID 39747078

PXD050943 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic Integrity of Tape-Stripped Stratum Corneum Samples Endures Higher Temperatures
Possible reference: Azimi, A. et al. (2025) Proteomic integrity of tape-stripped stratum corneum samples endures higher temperatures., J Proteomics, PMID 39369955

PXD050937 Dataset with its publication pending (from PRIDE)
Dataset title: Fission yeast Caprin protein is required for efficient heterochromatin establishment.
Possible reference: Zhang, H. et al. (2025) Fission yeast Caprin protein is required for efficient heterochromatin establishment., PLoS Genet, PMID 40063661

PXD050927 no publication (from MassIVE)
Dataset title: Salinity-induced photorespiration in poplar vascular tissues facilitates nitrogen reallocation
Possible reference: Wilhelmi, MDMR. et al. (2025) Salinity-Induced Photorespiration in Populus Vascular Tissues Facilitate Nitrogen Reallocation., Plant Cell Environ, PMID 39351842

PXD050923 Dataset with its publication pending (from jPOST)
Dataset title: Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease
Possible reference: Sakarin, S. et al. (2024) Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease., PeerJ, PMID 38708342

PXD050922 no publication (from MassIVE)
Dataset title: An accessible workflow for high sensitivity proteomics using Parallel Accumulation - Serial Fragmentation (PASEF)
Possible reference: Skowronek, P. et al. (2025) An accessible workflow for high-sensitivity proteomics using parallel accumulation-serial fragmentation (PASEF)., Nat Protoc, PMID 39825144

PXD050921 Dataset with its publication pending (from PRIDE)
Dataset title: SWI/SNF is a gatekeeper of chromatin access at enhancer networks controlling triple-negative breast cancer progression
Possible reference: M�ldrup, RIJ. et al. (2025) SWI/SNF Functions as a Gatekeeper of Enhancer Chromatin Access to Control Progression of Mesenchymal Triple-Negative Breast Cancer., Cancer Res, PMID 40928937

PXD050919 no publication (from MassIVE)
Dataset title: Intracellular IL-23R is necessary for mitotic spindle formation and viability in AML
Possible reference: Duong, N. et al. (2026) Intracellular IL-23R is necessary for mitotic spindle formation and viability in AML., Leukemia, PMID 41998300

PXD050905 no publication (from MassIVE)
Dataset title: Synthetic genomes unveil the effects of synonymous recoding
Possible reference: Nyerges, A. et al. (2024) Synthetic genomes unveil the effects of synonymous recoding., bioRxiv, PMID 38915524

PXD050880 Dataset with its publication pending (from iProX)
Dataset title: High antimony resistance strain Enterobacter sp. Z1 mediates biomineralization of antimony trioxide
Possible reference: Zhou, Z. et al. (2025) High antimony resistance strain Enterobacter sp. Z1 mediates biomineralization of antimony trioxide., Environ Int, PMID 39721567

PXD050877 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted proteomic approach for quantification of Collagen type I and type III in formalin-fixed paraffin-embedded tissue
Possible reference: Rosin, NL. et al. (2024) Targeted proteomic approach for quantification of collagen type I and type III in formalin-fixed paraffin-embedded tissue., Sci Rep, PMID 39090134

PXD050870 no publication (from MassIVE)
Dataset title: Single-cell m6A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation
Possible reference: Tegowski, M. et al. (2024) Single-cell m6A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation., Nat Neurosci, PMID 39317796

PXD050860 Dataset with its publication pending (from jPOST)
Dataset title: Comparative Proteomic Analysis of Dental Pulp from Supernumerary and Normal Permanent Teeth
Possible reference: Lertruangpanya, K. et al. (2024) Comparative proteomic analysis of dental pulp from supernumerary and normal permanent teeth., Clin Oral Investig, PMID 38758416

PXD050857 Dataset with its publication pending (from PRIDE)
Dataset title: The use of omics technologies in creating LBP and postbiotics based on the Limosilactobacillus fermentum U-21
Possible reference: Odorskaya, MV. et al. (2024) The use of omics technologies in creating LBP and postbiotics based on the Limosilactobacillus fermentum U-21., Front Microbiol, PMID 38919499

PXD050853 Dataset with its publication pending (from PRIDE)
Dataset title: Increased response to mitochondrial uncoupling for lipid oxidation and reduced lipid synthesis in AMPKÎ±2-/- myotubes
Possible reference: Skagen, C. et al. (2025) Reduced lipid and glucose oxidation and reduced lipid synthesis in AMPKα2-/- myotubes., Arch Physiol Biochem, PMID 39781899

PXD050844 Dataset with its publication pending (from PRIDE)
Dataset title: PARP4 interacts with hnRNPM to regulate splicing during lung cancer progression
Possible reference: Lee, YF. et al. (2024) PARP4 interacts with hnRNPM to regulate splicing during lung cancer progression., Genome Med, PMID 39034402

PXD050806 Dataset with its publication pending (from PRIDE)
Dataset title: Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER-Phagy
Possible reference: Prieto-Garcia, C. et al. (2024) Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy., Science, PMID 39541449

PXD050801 Dataset with its publication pending (from PRIDE)
Dataset title: Chemoproteomics reveals immunogenic and tumor-associated cell surface substrates of ectokinase CK2Î±
Possible reference: Delaveris, CS. et al. (2024) Chemoproteomics reveals immunogenic and tumor-associated cell surface substrates of ectokinase CK2α., bioRxiv, PMID 38562834

PXD050798 Dataset with its publication pending (from PRIDE)
Dataset title: Combining multiomics to analyze the molecular mechanism of hair follicle cycle change in cashmere goats from Inner Mongolia.
Possible reference: Zhang, C. et al. (2024) Combining multiomics to analyze the molecular mechanism of hair follicle cycle change in cashmere goats from Inner Mongolia., Front Vet Sci, PMID 39036798

PXD050786 no publication (from MassIVE)
Dataset title: Post-translational Regulation of the Response to Different Exercise Modes in Muscle
Possible reference: Pataky, MW. et al. (2025) Aerobic and resistance exercise-regulated phosphoproteome and acetylproteome modifications in human skeletal muscle., Nat Commun, PMID 40595512

PXD050769 Dataset with its publication pending (from PRIDE)
Dataset title: FLAG-BMAL1 Immunoprecipitation followed by LC MS/MS in mESCs
Possible reference: Zhang, Q. et al. (2013) Histone modification mapping in human brain reveals aberrant expression of histone H3 lysine 79 dimethylation in neural tube defects., Neurobiol Dis, PMID 23376398

PXD050758 Dataset with its publication pending (from PRIDE)
Dataset title: Pregnancy alters fatty acid metabolism, glucose regulation, and detoxification of the liver in synchrony with biomechanical property changes
Possible reference: Guo, J. et al. (2024) Pregnancy alters fatty acid metabolism, glucose regulation, and detoxification of the liver in synchrony with biomechanical property changes., Heliyon, PMID 39506943

PXD050757 Dataset with its publication pending (from iProX)
Dataset title: Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation
Possible reference: Liu, W. et al. (2025) Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation., Mol Cell, PMID 40015272

PXD050755 Dataset with its publication pending (from PRIDE)
Dataset title: Secretome analysis of HSPD1 knockdown in A549 lung cancer cells
Possible reference: Aluksanasuwan, S. et al. (2024) Knockdown of heat shock protein family D member 1 (HSPD1) in lung cancer cell altered secretome profile and cancer-associated fibroblast induction., Biochim Biophys Acta Mol Cell Res, PMID 38663552

PXD050749 no publication (from MassIVE)
Dataset title: Deep, Unbiased and Quantitative mass spectrometry-based plasma proteome analysis of personalized response to mRNA COVID-19 vaccine
Possible reference: Huang, T. et al. (2025) Deep, Unbiased, and Quantitative Mass Spectrometry-Based Plasma Proteome Analysis of Individual Responses to mRNA COVID-19 Vaccine., J Proteome Res, PMID 39904632

PXD050747 Dataset with its publication pending (from PRIDE)
Dataset title: Xenogeneic-free culture of human intestinal stem cells on functional polymer-coated substrates for scalable, clinical-grade stem cell therapy
Possible reference: Park, S. et al. (2024) Xenogeneic-free culture of human intestinal stem cells on functional polymer-coated substrates for scalable, clinical-grade stem cell therapy., Nat Commun, PMID 39622824

PXD050734 Dataset with its publication pending (from PRIDE)
Dataset title: Crosslinking of Ly6a metabolically reprogram CD8 T cells for cancer immunotherapy.
Possible reference: Maliah, A. et al. (2024) Crosslinking of Ly6a metabolically reprograms CD8 T cells for cancer immunotherapy., Nat Commun, PMID 39333093

PXD050733 no publication (from MassIVE)
Dataset title: SDS22 coordinates the assembly of holoenzymes from nascent protein phosphatase-1
Possible reference: Cao, X. et al. (2024) SDS22 coordinates the assembly of holoenzymes from nascent protein phosphatase-1., Nat Commun, PMID 38918402

PXD050708 Dataset with its publication pending (from jPOST)
Dataset title: Data Independent Acquisition Mass Spectrometry Enhanced Personalized Glycosylation Profiling of Haptoglobin in Hepatocellular Carcinoma
Possible reference: Pradita, T. et al. (2024) Data Independent Acquisition Mass Spectrometry Enhanced Personalized Glycosylation Profiling of Haptoglobin in Hepatocellular Carcinoma., J Proteome Res, PMID 38994555

PXD050707 no publication (from MassIVE)
Dataset title: Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response
Possible reference: H�fer, S. et al. (2025) Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response., Mol Syst Biol, PMID 39838187

PXD050685 Dataset with its publication pending (from PRIDE)
Dataset title: Redirecting the pioneering function of FOXA1 with covalent small molecules
Possible reference: Won, SJ. et al. (2024) Redirecting the pioneering function of FOXA1 with covalent small molecules., bioRxiv, PMID 38562719

PXD050684 Dataset with its publication pending (from PRIDE)
Dataset title: The Interferon-inducible NAMPT acts as a protein phosphoribosylase to restrict viral infection
Possible reference: Zhang, S. et al. (2023) The Interferon-inducible NAMPT acts as a protein phosphoribosylase to restrict viral infection., bioRxiv, PMID 37905103

PXD050676 Dataset with its publication pending (from PRIDE)
Dataset title: Systems-level Plant Responses Reveal Pseudomonas-Mediated Growth Promotion in Brachypodium Under Nitrogen Limitation
Possible reference: Sanow, S. et al. (2026) Systems-Level Plant Responses Reveal Pseudomonas-Mediated Growth Promotion in Brachypodium Under Nitrogen Limitation., Plant Cell Environ, PMID 42178962

PXD050653 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of mouse liver lesions at all three stages of Echinococcus granulosus infection
Possible reference: Jiang, N. et al. (2024) Proteomic analysis of mouse liver lesions at all three stages of Echinococcus granulosus infection., PLoS Negl Trop Dis, PMID 39625960

PXD050636 Dataset with its publication pending (from iProX)
Dataset title: Palmitoylation licenses RIPK1 cytotoxicity in the TNF pathway
Possible reference: Zhang, N. et al. (2024) Palmitoylation licenses RIPK1 kinase activity and cytotoxicity in the TNF pathway., Mol Cell, PMID 39471814

PXD050616 no publication (from MassIVE)
Dataset title: Interplay between beta-propeller subunits WDR26 and muskelin regulates the CTLH E3 ligase supramolecular complex
Possible reference: Maitland, MER. et al. (2024) Interplay between β-propeller subunits WDR26 and muskelin regulates the CTLH E3 ligase supramolecular complex., Commun Biol, PMID 39702571

PXD050606 Dataset with its publication pending (from iProX)
Dataset title: The plant-specific protein IQD22 interacts with calmodulins to facilitate hypoxia-induced ethanolic fermentation
Possible reference: Zhao, S. et al. (2025) The plant-specific protein IQD22 interacts with calcium sensors to activate anaerobic respiration during hypoxia in Arabidopsis., Mol Plant, PMID 40652330

PXD050597 Dataset with its publication pending (from PRIDE)
Dataset title: Dental calculus formation rate: the role of salivary proteome and metaproteome
Possible reference: Cai, W. et al. (2025) Dental Calculus Formation Rate: The Role of Salivary Proteome and Metaproteome., J Clin Periodontol, PMID 39953744

PXD050593 Dataset with its publication pending (from jPOST)
Dataset title: Changes in Protein Fluxes in Skeletal Muscle During Sequential Stages of Muscle Regeneration After Acute Injury in Male Mice
Possible reference: Bizieff, A. et al. (2024) Changes in protein fluxes in skeletal muscle during sequential stages of muscle regeneration after acute injury in male mice., Sci Rep, PMID 38849371

PXD050563 Dataset with its publication pending (from jPOST)
Dataset title: Degron-based targeted protein degradation systems in mice
Possible reference: Xu, J. et al. (2025) METTL3 uncouples chromatin accessibility from transcription during retinal development., Stem Cell Reports, PMID 41135527

PXD050561 no publication (from MassIVE)
Dataset title: A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology
Possible reference: Zhang, Y. et al. (2024) A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology., bioRxiv, PMID 36945530

PXD050551 Dataset with its publication pending (from iProX)
Dataset title: Phosphoproteomics of postharvest blueberries softening
Possible reference: Sun, L. et al. (2024) Phosphoproteomic Analysis Indicates Phosphorylated Proteins in Response to Postharvest Blueberries Fruit Softening during Shelf Life., J Agric Food Chem, PMID 39257137

PXD050541 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of melanotic schwannoma
Possible reference: R�hrich, M. et al. (2016) Methylation-based classification of benign and malignant peripheral nerve sheath tumors., Acta Neuropathol, PMID 26857854

PXD050510 Dataset with its publication pending (from iProX)
Dataset title: In situ chemoproteomic profiling reveals itaconate inhibits de novo purine biosynthesis in pathogens
Possible reference: Liu, Z. et al. (2024) In situ chemoproteomic profiling reveals itaconate inhibits de novo purine biosynthesis in pathogens., Cell Rep, PMID 39277862

PXD050500 Dataset with its publication pending (from PRIDE)
Dataset title: A complete telomere-to-telomere genome of bread wheat presents insights into the evolution, transcriptome, and proteome of a hexaploid genome
Possible reference: Liu, S. et al. (2025) A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat., Nat Genet, PMID 40195562

PXD050493 Dataset with its publication pending (from PRIDE)
Dataset title: A High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid
Possible reference: Ulmer, LD. et al. (2024) High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid., J Proteome Res, PMID 38968604

PXD050492 Dataset with its publication pending (from jPOST)
Dataset title: Changes in Protein Fluxes in Skeletal Muscle During Sequential Stages of Muscle Regeneration After Acute Injury in Male Mice
Possible reference: Bizieff, A. et al. (2024) Changes in protein fluxes in skeletal muscle during sequential stages of muscle regeneration after acute injury in male mice., Sci Rep, PMID 38849371

PXD050472 Dataset with its publication pending (from jPOST)
Dataset title: Sperm proteins in the coral Acropora digitifera
Possible reference: Morita, M. et al. (2024) Conservation of Protein Kinase A Substrates in the Cnidarian Coral Spermatozoa Among Animals and Their Molecular Evolution., J Mol Evol, PMID 38662235

PXD050454 no publication (from MassIVE)
Dataset title: Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules
Possible reference: Ashkarran, AA. et al. (2024) Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules., bioRxiv, PMID 38496642

PXD050430 Dataset with its publication pending (from iProX)
Dataset title: Proteomic Analysis of Moorella thermoacetica-g-C3N4 Nanocomposite system for Artificial Photosynthesis
Possible reference: Shen, J. et al. (2024) Proteomic and metabolic analysis of Moorella thermoacetica-g-C3N4 nanocomposite system for artificial photosynthesis., Talanta, PMID 38941811

PXD050423 Dataset with its publication pending (from PRIDE)
Dataset title: Prey killing without invasion by Bdellovibrio bacteriovorus defective for a MIDAS-family adhesin
Possible reference: Tyson, J. et al. (2024) Prey killing without invasion by Bdellovibrio bacteriovorus defective for a MIDAS-family adhesin., Nat Commun, PMID 38594280

PXD050418 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Insights into Psychrophile Growth in Perchlorate-Amended Subzero Conditions: Implications for Martian Life Detection
Possible reference: Gentilhomme, AS. et al. (2025) Proteomic Insights into Psychrophile Growth in Perchlorate-Amended Subzero Conditions: Implications for Martian Life Detection., Astrobiology, PMID 39960803

PXD050403 no publication (from MassIVE)
Dataset title: Immuno-Oncologic Profiling by Stage-Dependent Transcriptome and Proteome Analyses of Spontaneously Regressing Canine Cutaneous Histiocytoma
Possible reference: Loriani Fard, AK. et al. (2024) Immuno-oncologic profiling by stage-dependent transcriptome and proteome analyses of spontaneously regressing canine cutaneous histiocytoma., PeerJ, PMID 39619201

PXD050401 Dataset with its publication pending (from PRIDE)
Dataset title: GFI1B and LSD1 repress myeloid traits during megakaryocyte differentiation
Possible reference: Venhuizen, J. et al. (2024) GFI1B and LSD1 repress myeloid traits during megakaryocyte differentiation., Commun Biol, PMID 38548886

PXD050388 Dataset with its publication pending (from iProX)
Dataset title: Immunoregulatory role of the gut microbiota in inflammatory depression
Possible reference: Rook, GA. et al. (2014) Microbiota, immunoregulatory old friends and psychiatric disorders., Adv Exp Med Biol, PMID 24997041

PXD050360 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of vascular tissue from critical limb ischemia mouse models treated with Etrinabdione
Possible reference: García-Martín, A. et al. (2024) Etrinabdione (VCE-004.8), a B55α activator, promotes angiogenesis and arteriogenesis in critical limb ischemia., J Transl Med, PMID 39506809

PXD050356 Dataset with its publication pending (from PRIDE)
Dataset title: NRVM Conditioned Media Proteomics
Possible reference: Blackwood, EA. et al. (2020) Proteomic analysis of the cardiac myocyte secretome reveals extracellular protective functions for the ER stress response., J Mol Cell Cardiol, PMID 32339566

PXD050348 Dataset with its publication pending (from PRIDE)
Dataset title: Venom evolution of 15 neotropical ants
Possible reference: Menk, JJ. et al. (2023) Antimicrobial Peptide Arsenal Predicted from the Venom Gland Transcriptome of the Tropical Trap-Jaw Ant Odontomachus chelifer., Toxins (Basel), PMID 37235379

PXD050341 no publication (from MassIVE)
Dataset title: Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap)
Possible reference: Forrester, MT. et al. (2024) Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap)., bioRxiv, PMID 38585928

PXD050328 Dataset with its publication pending (from PRIDE)
Dataset title: HDAC inhibitors activate lipid peroxidation and ferroptosis in gastric cancer
Possible reference: Jenke, R. et al. (2024) HDAC inhibitors activate lipid peroxidation and ferroptosis in gastric cancer., Biochem Pharmacol, PMID 38705532

PXD050315 Dataset with its publication pending (from PRIDE)
Dataset title: System-level characterization of engineered and evolved formatotrophic E. coli strains
Possible reference: Yilmaz, S. et al. (2025) System-level characterization of engineered and evolved formatotrophic E. coli strains., Synth Syst Biotechnol, PMID 40166614

PXD050300 Dataset with its publication pending (from PRIDE)
Dataset title: Cardiac Fibroblast Foxm1 Deficiency Prevents Pressure Overload-Induced Cardiac Remodeling via the Usp10/p38Î³ MAPK Axis
Possible reference: Song, S. et al. (2026) Cardiac fibroblast Foxm1 deficiency prevents pressure overload-induced cardiac remodeling via the Usp10/MKK6-p38γ MAPK axis., Cell Death Differ, PMID 41198967

PXD050293 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of High dose of TCM in osteoporosis rat
Possible reference: Chu, S. et al. (2021) Effects and Mechanism of Zishen Jiangtang Pill on Diabetic Osteoporosis Rats Based on Proteomic Analysis., Evid Based Complement Alternat Med, PMID 34608397

PXD050281 Dataset with its publication pending (from PRIDE)
Dataset title: Cardiac Fibroblast Foxm1 Deficiency Prevents Pressure Overload-Induced Cardiac Remodeling via the Usp10/p38Î³ MAPK Axis
Possible reference: Song, S. et al. (2026) Cardiac fibroblast Foxm1 deficiency prevents pressure overload-induced cardiac remodeling via the Usp10/MKK6-p38γ MAPK axis., Cell Death Differ, PMID 41198967

PXD050266 no publication (from MassIVE)
Dataset title: Polyamines sustain epithelial regeneration of aged intestine
Possible reference: Minetti, A. et al. (2025) Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis., Nat Cell Biol, PMID 41286441

PXD050249 Dataset with its publication pending (from PRIDE)
Dataset title: Transcription factors induce differential splicing of duplicated ribosomal protein genes during meiosis
Possible reference: Petibon, C. et al. (2025) Transcription factors induce differential splicing of duplicated ribosomal protein genes during meiosis., Nucleic Acids Res, PMID 39817510

PXD050197 no publication (from MassIVE)
Dataset title: Oligonucleotide-mediated proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ.
Possible reference: Tsue, AF. et al. (2023) Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ., bioRxiv, PMID 36711823

PXD050196 no publication (from MassIVE)
Dataset title: Directed Evolution of Genetically Encoded LYTACs for Cell-Mediated Delivery
Possible reference: Yang, JL. et al. (2023) Directed Evolution of Genetically Encoded LYTACs for Cell-Mediated Delivery., bioRxiv, PMID 38014030

PXD050186 no publication (from MassIVE)
Dataset title: Retinal cells derived from patients with DRAM2-dependent CORD21 dystrophy exhibit key lysosomal enzyme deficiency and lysosomal content accumulation
Possible reference: Tsikandelova, R. et al. (2024) Retinal cells derived from patients with DRAM2-dependent CORD21 dystrophy exhibit key lysosomal enzyme deficiency and lysosomal content accumulation., Stem Cell Reports, PMID 38964324

PXD050174 no publication (from MassIVE)
Dataset title: mRNA-LNP HIV-1 trimer boosters elicit precursors to bnAbs
Possible reference: Xie, Z. et al. (2024) mRNA-LNP HIV-1 trimer boosters elicit precursors to broad neutralizing antibodies., Science, PMID 38753770

PXD050163 no publication (from MassIVE)
Dataset title: Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates
Possible reference: Steichen, JM. et al. (2024) Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates., Science, PMID 38753769

PXD050159 Dataset with its publication pending (from PRIDE)
Dataset title: An Integrated Proteomics Approach Identifies Phosphorylation Sites on Host and Viral Proteins that Regulate West Nile Virus Infection
Possible reference: Walter, Z. et al. (2025) An integrated proteomics approach identifies phosphorylation sites on viral and host proteins that regulate West Nile virus infection., Cell Rep, PMID 40381193

PXD050156 Dataset with its publication pending (from PRIDE)
Dataset title: Highly potent quinoxalinediones inhibit Î±âhemolysin and ameliorate lung infections by Staphylococcus aureus
Possible reference: Shekhar, A. et al. (2025) Highly potent quinoxalinediones inhibit α-hemolysin and ameliorate Staphylococcus aureus lung infections., Cell Host Microbe, PMID 40168998

PXD050154 Dataset with its publication pending (from PRIDE)
Dataset title: Impact of Surfactants on Cumulative Trypsin Activity for Bottom-up Proteome Analysis
Possible reference: Nickerson, JL. et al. (2024) Impact of Surfactants on Cumulative Trypsin Activity in Bottom-Up Proteome Analysis., J Proteome Res, PMID 38973097

PXD050153 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of secretion of transmembrane effectors by the type IV b secretion system of Legionella pneumophila
Possible reference: Malmsheimer, S. et al. (2024) The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors., bioRxiv, PMID 38559167

PXD050150 no publication (from MassIVE)
Dataset title: Tight regulation of a nuclear HAPSTR1-HUWE1 pathway essential for mammalian life
Possible reference: Amici, DR. et al. (2024) Tight regulation of a nuclear HAPSTR1-HUWE1 pathway essential for mammalian life., Life Sci Alliance, PMID 38453366

PXD050149 Dataset with its publication pending (from PRIDE)
Dataset title: Metabolic regulation of host defense against influenza virus infection through sensing oxaloacetate
Possible reference: Jin, S. et al. (2025) Oxaloacetate sensing promotes innate immune antiviral defence against influenza virus infection., Nat Microbiol, PMID 40983701

PXD050139 Dataset with its publication pending (from PRIDE)
Dataset title: Implications of O-glycan modifications in the hinge region of a plant-produced SARS-CoV-2-IgA antibody on functionality
Possible reference: Uetz, P. et al. (2024) Implications of O-glycan modifications in the hinge region of a plant-produced SARS-CoV-2-IgA antibody on functionality., Front Bioeng Biotechnol, PMID 38511130

PXD050137 Dataset with its publication pending (from PRIDE)
Dataset title: Microbial consortia driving lignocellulose transformation in agricultural woodchip bioreactors
Possible reference: Schiml, VC. et al. (2024) Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors., Appl Environ Microbiol, PMID 39526802

PXD050122 Dataset with its publication pending (from iProX)
Dataset title: YAP maintains the dynamics of TDP-43 condensates and antagonizes TDP-43 pathology
Possible reference: Zhang, J. et al. (2025) YAP maintains the dynamics of TDP-43 condensates and antagonizes TDP-43 pathological aggregates., Nat Cell Biol, PMID 40542195

PXD050099 Dataset with its publication pending (from jPOST)
Dataset title: The trajectory of vesicular proteomic signatures from HBV-HCC by chitosan-magnetic bead-based separation and DIA-proteomic analysis
Possible reference: Cao, L. et al. (2024) The trajectory of vesicular proteomic signatures from HBV-HCC by chitosan-magnetic bead-based separation and DIA-proteomic analysis., J Extracell Vesicles, PMID 39207047

PXD050098 Dataset with its publication pending (from jPOST)
Dataset title: Hydrophilic interaction chromatography coupled to ultraviolet photodissociation affords identification, localization, and relative quantitation of glycans on intact glycoproteins
Possible reference: James, VK. et al. (2024) Hydrophilic Interaction Chromatography Coupled to Ultraviolet Photodissociation Affords Identification, Localization, and Relative Quantitation of Glycans on Intact Glycoproteins., J Proteome Res, PMID 39312773

PXD050095 Dataset with its publication pending (from PRIDE)
Dataset title: Functional Effects of Extracellular Vesicles Altered by a Per- and Polyfluoroalkyl Substance Mixture: Liver Cell Proteomic Expression Alterations
Possible reference: Carberry, CK. et al. (2026) Functional effects of extracellular vesicles altered by a per- and polyfluoroalkyl substance mixture: In vitro liver cytotoxicity and proteomic expression alterations., PLoS One, PMID 41849429

PXD050087 Dataset with its publication pending (from PRIDE)
Dataset title: Purification of time-resolved insulin granules reveals proteomic and lipidomic changes during granule aging
Possible reference: Neukam, M. et al. (2024) Purification of time-resolved insulin granules reveals proteomic and lipidomic changes during granule aging., Cell Rep, PMID 38421874

PXD050038 no publication (from MassIVE)
Dataset title: A Protein Phosphatase 1 specific phosphatase targeting peptide (PhosTAP) to identify the PP1 phosphatome
Possible reference: Choy, MS. et al. (2024) A protein phosphatase 1 specific phosphatase targeting peptide (PhosTAP) to identify the PP1 phosphatome., Proc Natl Acad Sci U S A, PMID 39446389

PXD049996 Dataset with its publication pending (from PRIDE)
Dataset title: Proinsulin degradation and presentation of a proinsulin B-chain autoantigen involves ER-associated protein degradation (ERAD)-enzyme UBE2G2
Possible reference: Cremer, T. et al. (2024) Proinsulin degradation and presentation of a proinsulin B-chain autoantigen involves ER-associated protein degradation (ERAD)-enzyme UBE2G2., PLoS One, PMID 38787820

PXD049995 Dataset with its publication pending (from PRIDE)
Dataset title: TblncRNA-23, a long non-coding RNA transcribed by RNA polymerase I, regulates developmental changes in Trypanosoma brucei
Possible reference: Galili-Kostin, B. et al. (2025) TblncRNA-23, a long non-coding RNA transcribed by RNA polymerase I, regulates developmental changes in Trypanosoma brucei., Nat Commun, PMID 40251171

PXD049992 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic characteristics in degenerated and regenerative mouse retina
Possible reference: Wang, X. et al. (2024) Comparative proteomic analysis of regenerative mechanisms in mouse retina to identify markers for neuro-regeneration in glaucoma., Sci Rep, PMID 39366989

PXD049969 Dataset with its publication pending (from PRIDE)
Dataset title: Influence of Different Sample Preparation Approaches on Proteoform Identification by Top-Down Proteomics
Possible reference: Kaulich, PT. et al. (2024) Influence of different sample preparation approaches on proteoform identification by top-down proteomics., Nat Methods, PMID 39438734

PXD049968 no publication (from MassIVE)
Dataset title: Thylakoid Protein FPB1 Synergistically Cooperates with PAM68 to Promote CP47 Biogenesis and Photosystem II Assembly
Possible reference: Zhang, L. et al. (2024) Thylakoid protein FPB1 synergistically cooperates with PAM68 to promote CP47 biogenesis and Photosystem II assembly., Nat Commun, PMID 38600073

PXD049966 Dataset with its publication pending (from PRIDE)
Dataset title: Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming
Possible reference: Wu, X. et al. (2024) Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming., Nat Cancer, PMID 38519786

PXD049965 no publication (from MassIVE)
Dataset title: Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques.
Possible reference: Conforti, JM. et al. (2024) Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques., bioRxiv, PMID 38559195

PXD049721 no publication (from MassIVE)
Dataset title: Honey bee arginine kinase is involved in Deformed Wing Virus infection
Possible reference: Becchimanzi, A. et al. (2025) Deformed wing virus coopts the host arginine kinase to enhance its fitness in honey bees (Apis mellifera)., BMC Biol, PMID 39800727

PXD049720 Dataset with its publication pending (from jPOST)
Dataset title: Glutathione S-transferase omega class 1 (GSTO1)-associated large extracellular vesicles involves in tumor-associated macrophage-mediated cisplatin resistance in bladder cancer
Possible reference: Pan, YC. et al. (2024) Glutathione S-transferase omega class 1 (GSTO1)-associated large extracellular vesicles are involved in tumor-associated macrophage-mediated cisplatin resistance in bladder cancer., Mol Oncol, PMID 38750006

PXD049719 Dataset with its publication pending (from jPOST)
Dataset title: Glutathione S-transferase omega class 1 (GSTO1)-associated large extracellular vesicles involves in tumor-associated macrophage-mediated cisplatin resistance in bladder cancer
Possible reference: Pan, YC. et al. (2024) Glutathione S-transferase omega class 1 (GSTO1)-associated large extracellular vesicles are involved in tumor-associated macrophage-mediated cisplatin resistance in bladder cancer., Mol Oncol, PMID 38750006

PXD049712 Dataset with its publication pending (from iProX)
Dataset title: The combined effect of sodium alginate (SA) and bovine serum albumin (BSA) improved the cryopreservation quality of boar sperm through the PI3K-AKT pathway
Possible reference: Wang, J. et al. (2025) Sodium alginate and bovine serum albumin co-combined improved the cryopreservation quality of boar sperm through the PI3K-AKT pathway., Reprod Fertil Dev, PMID 39998932

PXD049709 Dataset with its publication pending (from jPOST)
Dataset title: Proteome analysis of mouse oocyte pronuclei
Possible reference: Ogushi, S. et al. (2017) Reconstitution of the oocyte nucleolus in mice through a single nucleolar protein, NPM2., J Cell Sci, PMID 28600324

PXD049480 Dataset with its publication pending (from PRIDE)
Dataset title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF
Possible reference: Magnitov, MD. et al. (2025) ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF., Mol Cell, PMID 39708805

PXD049479 Dataset with its publication pending (from PRIDE)
Dataset title: Vibrio coralliilyticus T6SS comparative proteomics
Possible reference: Mass, S. et al. (2024) The coral pathogen Vibrio coralliilyticus uses a T6SS to secrete a group of novel anti-eukaryotic effectors that contribute to virulence., PLoS Biol, PMID 39226241

PXD049478 Dataset with its publication pending (from PRIDE)
Dataset title: Protein aggregation is a consequence of the dormancy-inducing membrane toxin TisB in Escherichia coli
Possible reference: Leinberger, FH. et al. (2024) Protein aggregation is a consequence of the dormancy-inducing membrane toxin TisB in Escherichia coli., mSystems, PMID 39377584

PXD049477 Dataset with its publication pending (from PRIDE)
Dataset title: Fasting boosts breast cancer therapy via glucocorticoid activation.
Possible reference: Padr�o, N. et al. (2026) Fasting boosts breast cancer therapy efficacy via glucocorticoid activation., Nature, PMID 41372410

PXD049473 Dataset with its publication pending (from PRIDE)
Dataset title: An outer membrane porin-lipoprotein complex modulates elongasome movement to establish cell curvature in Rhodospirillum rubrum
Possible reference: P�hl, S. et al. (2024) An outer membrane porin-lipoprotein complex modulates elongasome movement to establish cell curvature in Rhodospirillum rubrum., Nat Commun, PMID 39223154

PXD049470 Dataset with its publication pending (from jPOST)
Dataset title: Ascorbic acid deficiency promote metabolic remodeling and pulmonary fibrosis that leads to respiratory failure in Sod1 and Akr1a double-knockout mice
Possible reference: Osaki, T. et al. (2025) Ascorbic acid deficiency promotes metabolic remodeling and pulmonary fibrosis that leads to respiratory failure in Sod1 and Akr1a double-knockout mice., Redox Biol, PMID 40616948

PXD049468 Dataset with its publication pending (from iProX)
Dataset title: An antifouling membrane-fusogenic liposome for effective intracellular delivery in vivo
Possible reference: Kong, H. et al. (2024) An antifouling membrane-fusogenic liposome for effective intracellular delivery in vivo., Nat Commun, PMID 38769317

PXD049459 Dataset with its publication pending (from iProX)
Dataset title: Proteomic sequencing of ADAM17 deficiency mouse
Possible reference: Sommer, A. et al. (2016) Phosphatidylserine exposure is required for ADAM17 sheddase function., Nat Commun, PMID 27161080

PXD049433 Dataset with its publication pending (from PRIDE)
Dataset title: Proximity labeling proteomics reveals Kv1.3 potassium channel immune interactors in microglia.
Possible reference: Bowen, CA. et al. (2024) Proximity Labeling Proteomics Reveals Kv1.3 Potassium Channel Immune Interactors in Microglia., Mol Cell Proteomics, PMID 38936775

PXD049427 Dataset with its publication pending (from PRIDE)
Dataset title: Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan
Possible reference: Ryu, HY. et al. (2024) Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan., Res Sq, PMID 38562857

PXD049423 Dataset with its publication pending (from jPOST)
Dataset title: Mechanism of αKtx12 peptide on hippocampus
Possible reference: Beraldo-Neto, E. et al. (2024) Unraveling neuroprotection with Kv1.3 potassium channel blockade by a scorpion venom peptide., Sci Rep, PMID 39537765

PXD049409 Dataset with its publication pending (from PRIDE)
Dataset title: O-GlcNAcylation of RUNX1 promotes its stability and PDGF-BB-mediated resistance to CDK4/6 inhibitors in breast cancer
Possible reference: Zhou, S. et al. (2025) Stabilization of RUNX1 Induced by O-GlcNAcylation Promotes PDGF-BB-Mediated Resistance to CDK4/6 Inhibitors in Breast Cancer., Cancer Res, PMID 39937190

PXD049391 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular mechanism of Î²-arrestin-2 pre-activation by phosphatidylinositol 4,5-bisphosphate
Possible reference: Kim, K. et al. (2024) Molecular mechanism of β-arrestin-2 pre-activation by phosphatidylinositol 4,5-bisphosphate., EMBO Rep, PMID 39242774

PXD049383 Dataset with its publication pending (from PRIDE)
Dataset title: Clinical implications and molecular features of extracellular matrix networks in soft tissue sarcomas
Possible reference: Pankova, V. et al. (2024) Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas., Clin Cancer Res, PMID 38810090

PXD049373 Dataset with its publication pending (from PRIDE)
Dataset title: Clinical implications and molecular features of extracellular matrix networks in soft tissue sarcomas
Possible reference: Pankova, V. et al. (2024) Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas., Clin Cancer Res, PMID 38810090

PXD049369 Dataset with its publication pending (from PRIDE)
Dataset title: Helical superstructures between amyloid and collagen VI in heart derived fibrils from a patient with Light Chain Amyloidosis
Possible reference: Schulte, T. et al. (2024) Helical superstructures between amyloid and collagen in cardiac fibrils from a patient with AL amyloidosis., Nat Commun, PMID 39069558

PXD049353 no publication (from MassIVE)
Dataset title: Senescence of endothelial cells promotes phenotypic changes in adventitial fibroblasts: possible implications for vascular aging
Possible reference: Sarad, K. et al. (2025) Senescence of endothelial cells promotes phenotypic changes in adventitial fibroblasts: possible implications for vascular aging., Mol Cell Biochem, PMID 38743322

PXD049352 Dataset with its publication pending (from PRIDE)
Dataset title: Photoreceptor-induced LHL4 protects photosystem II in Chlamydomonas reinhardtii
Possible reference: Dannay, M. et al. (2025) Photoreceptor-induced LHL4 protects the photosystem II monomer in Chlamydomonas reinhardtii., Proc Natl Acad Sci U S A, PMID 39946539

PXD049330 Dataset with its publication pending (from PRIDE)
Dataset title: Alkylamine-tethered molecules recruit FBXO22 for targeted protein degradation
Possible reference: Kagiou, C. et al. (2024) Alkylamine-tethered molecules recruit FBXO22 for targeted protein degradation., Nat Commun, PMID 38926334

PXD049317 no publication (from MassIVE)
Dataset title: The co-chaperone DNAJA2 buffers proteasomal degradation of cytosolic proteins with missense mutations
Possible reference: Baker, HA. et al. (2025) The co-chaperone DNAJA2 buffers proteasomal degradation of cytosolic proteins with missense mutations., J Cell Sci, PMID 39618332

PXD049316 Dataset with its publication pending (from PRIDE)
Dataset title: The RBPome of influenza A virus mRNA reveals a role for TDP-43 in viral replication
Possible reference: Dupont, M. et al. (2024) The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication., Nucleic Acids Res, PMID 38686810

PXD049313 Dataset with its publication pending (from jPOST)
Dataset title: Bioinformatics-Guided Identification and Quantification of Biomarkers of Crotalus atrox Envenomation and its Neutralization by Antivenom
Possible reference: Bala, AA. et al. (2025) Bioinformatics-Guided Identification and Quantification of Biomarkers of Crotalus atrox Envenoming and Its Neutralization by Antivenom., Mol Cell Proteomics, PMID 40147718

PXD049307 no publication (from MassIVE)
Dataset title: Substrate recognition principles for PP2A-B55
Possible reference: Kruse, T. et al. (2024) Substrate recognition principles for the PP2A-B55 protein phosphatase., bioRxiv, PMID 38370611

PXD049301 Dataset with its publication pending (from PRIDE)
Dataset title: Helical superstructures between amyloid and collagen VI in heart derived fibrils from a patient with Light Chain Amyloidosis
Possible reference: Schulte, T. et al. (2024) Helical superstructures between amyloid and collagen in cardiac fibrils from a patient with AL amyloidosis., Nat Commun, PMID 39069558

PXD049267 Dataset with its publication pending (from iProX)
Dataset title: Lysine Acylations in Bacillus thuringiensis
Possible reference: Liu, T. et al. (2024) Characterization of diverse lysine acylations in Bacillus thuringiensis: Substrate profiling and functional exploration., Proteomics, PMID 38491406

PXD049235 Dataset with its publication pending (from PRIDE)
Dataset title: PKM2 functions as a histidine kinase to phosphorylate PGAM1 to increase glycolysis shunts in cancer
Possible reference: Wang, Y. et al. (2024) PKM2 functions as a histidine kinase to phosphorylate PGAM1 and increase glycolysis shunts in cancer., EMBO J, PMID 38750259

PXD049216 no publication (from MassIVE)
Dataset title: LC-MS based Proteomics Analysis of aneuploid cells
Possible reference: Gemoll, T. et al. (2012) Protein profiling of genomic instability in endometrial cancer., Cell Mol Life Sci, PMID 21739232

PXD049214 no publication (from MassIVE)
Dataset title: HDX-MS of murine urokinase plasminogen activator and variants
Possible reference: Kromann-Hansen, T. et al. (2018) Ligand binding modulates the structural dynamics and activity of urokinase-type plasminogen activator: A possible mechanism of plasminogen activation., PLoS One, PMID 29420634

PXD049210 Dataset with its publication pending (from PRIDE)
Dataset title: Mass spectrometry analysis of the testicular interstitial fluid exosome
Possible reference: Han, D. et al. (2023) Altered transcriptomic and metabolomic profiles of testicular interstitial ﬂuid during aging in mice., Theriogenology, PMID 36773384

PXD049200 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic characterization and comparison of the infective and adult life stage secretomes from Necator Americanus and Ancylostoma ceylanicum
Possible reference: Wong, Y. et al. (2025) Proteomic characterization and comparison of the infective and adult life stage secretomes from Necator americanus and Ancylostoma ceylanicum., PLoS Negl Trop Dis, PMID 39832284

PXD049166 Dataset with its publication pending (from iProX)
Dataset title: An Integrated Multi-Omics Profiling Landscape of Organizing Pneumonia
Possible reference: Tang, Y. et al. (2024) Integrated multi-omics profiling landscape of organising pneumonia., Clin Transl Med, PMID 39083563

PXD049141 Dataset with its publication pending (from iProX)
Dataset title: [HPP-2.0] Dynamic phosphotyrosine-dependent signaling profiling in living cells by two-dimensional proximity proteomics
Possible reference: Kong, Q. et al. (2022) Dynamic Phosphotyrosine-Dependent Signaling Profiling in Living Cells by Two-Dimensional Proximity Proteomics., J Proteome Res, PMID 36280823

PXD049136 Dataset with its publication pending (from PRIDE)
Dataset title: Widespread prevalence of a post-translational modification in activation of an essential bacterial DNA damage response
Possible reference: Kamat, A. et al. (2024) Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria., PLoS Biol, PMID 38466718

PXD049110 Dataset with its publication pending (from PRIDE)
Dataset title: Sequential Glycosylations at the Multibasic Cleavage Site of SARS-CoV-2 Spike Protein Regulate Viral Activation, Assembly, and Infection
Possible reference: Wang, S. et al. (2024) Sequential glycosylations at the multibasic cleavage site of SARS-CoV-2 spike protein regulate viral activity., Nat Commun, PMID 38755139

PXD049092 Dataset with its publication pending (from PRIDE)
Dataset title: Roles of Mettl14 in mouse limb bud development
Possible reference: Katoku-Kikyo, N. et al. (2025) METTL14 regulates chondrogenesis through the GDF5-RUNX-extracellular matrix gene axis during limb development., Nat Commun, PMID 40307229

PXD049085 Dataset with its publication pending (from PRIDE)
Dataset title: Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing
Possible reference: Jensvold, ZD. et al. (2024) Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing., bioRxiv, PMID 38313255

PXD049069 Dataset with its publication pending (from iProX)
Dataset title: FBXO7 Ubiquitinates PRMT1 to Suppress Serine Synthesis and Tumor Growth in HCC
Possible reference: Luo, L. et al. (2024) FBXO7 ubiquitinates PRMT1 to suppress serine synthesis and tumor growth in hepatocellular carcinoma., Nat Commun, PMID 38839752

PXD049058 Dataset with its publication pending (from iProX)
Dataset title: Dysregulated RBM24 phosphorylation impairs APOE translation underlying stress-induced cardiovascular disease
Possible reference: Yang, H. et al. (2024) Dysregulated RBM24 phosphorylation impairs APOE translation underlying psychological stress-induced cardiovascular disease., Nat Commun, PMID 39580475

PXD049046 Dataset with its publication pending (from PRIDE)
Dataset title: A deterministic, c-di-GMP-dependent genetic program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis
Possible reference: P�rez-Burgos, M. et al. (2024) A deterministic, c-di-GMP-dependent program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis., Nat Commun, PMID 39019889

PXD049023 Dataset with its publication pending (from iProX)
Dataset title: Characteristics of changes in plasma proteome profiling after sleeve gastrectomy
Possible reference: Zhang, Y. et al. (2024) Characteristics of changes in plasma proteome profiling after sleeve gastrectomy., Front Endocrinol (Lausanne), PMID 38375199

PXD049022 Dataset with its publication pending (from PRIDE)
Dataset title: The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerant Staphylococcus aureu
Possible reference: Wu, W. et al. (2024) The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin-tolerant Staphylococcus aureus., mSystems, PMID 38534138

PXD049015 Dataset with its publication pending (from jPOST)
Dataset title: Involvement of Glucosamine 6 phosphate isomerase 2 (GNPDA2) Overproduction in Î²-Amyloid and Tau P301L-driven pathomechanisms
Possible reference: Lachén-Montes, M. et al. (2024) Involvement of Glucosamine 6 Phosphate Isomerase 2 (GNPDA2) Overproduction in β-Amyloid- and Tau P301L-Driven Pathomechanisms., Biomolecules, PMID 38672412

PXD049003 Dataset with its publication pending (from PRIDE)
Dataset title: Deciphering Staphylococcus aureus-host dynamics using dual Activity-based protein profiling of ATP-interacting proteins
Possible reference: Ahator, SD. et al. (2024) Deciphering Staphylococcus aureus-host dynamics using dual activity-based protein profiling of ATP-interacting proteins., mSystems, PMID 38656122

PXD048995 Dataset with its publication pending (from iProX)
Dataset title: Hypoxia promotes histone H3K9 lactylation to enhance LAMC2 transcription in esophageal squamous cell carcinoma
Possible reference: Zang, Y. et al. (2024) Hypoxia promotes histone H3K9 lactylation to enhance LAMC2 transcription in esophageal squamous cell carcinoma., iScience, PMID 38989468

PXD048981 Dataset with its publication pending (from PRIDE)
Dataset title: Lack of phosphatidylinositol 3-kinase VPS34 in regulatory T cells leads to a fatal lymphoproliferative disorder without affecting their development
Possible reference: Courreges, CJF. et al. (2024) Lack of phosphatidylinositol 3-kinase VPS34 in regulatory T cells leads to a fatal lymphoproliferative disorder without affecting their development., Front Immunol, PMID 39664390

PXD048964 Dataset with its publication pending (from PRIDE)
Dataset title: Site-specific N-glycoproteomic analysis of four M2 macrophage subtypes derived from human THP-1 cells
Possible reference: Li, P. et al. (2026) Site-specific N-glycoproteomic analysis of four M2 macrophage subtypes derived from human THP-1 cells., Chem Commun (Camb), PMID 41532413

PXD048962 Dataset with its publication pending (from iProX)
Dataset title: Serum-derived exosome proteomics unveils the distinct and adjustable of the dampness constitution in traditional Chinese medicine
Possible reference: Wu, W. et al. (2025) Serum-derived exosome proteomics unveils the distinct and adjustable nature of the dampness constitution in traditional Chinese medicine., J Ethnopharmacol, PMID 40784529

PXD048959 Dataset with its publication pending (from iProX)
Dataset title: Optimizing and integrating depletion and precipitation methods for plasma proteomics through data-independent acquisition-mass spectrometry
Possible reference: Zhou, Y. et al. (2024) Optimizing and integrating depletion and precipitation methods for plasma proteomics through data-independent acquisition-mass spectrometry., J Chromatogr B Analyt Technol Biomed Life Sci, PMID 38382157

PXD048956 Dataset with its publication pending (from iProX)
Dataset title: Functional study of EYA1 in glioma formation and progression
Possible reference: Wei, T. et al. (2025) Protein phosphatase EYA1 regulates the dephosphorylation and turnover of BCL2L12 to promote glioma development., Int J Biol Sci, PMID 39897043

PXD048947 Dataset with its publication pending (from iProX)
Dataset title: The mechanism of tigecycline resistance in Acinetobacter baumannii under sub-minimal inhibitory concentration tigecycline
Possible reference: Liu, C. et al. (2024) The Mechanism of Tigecycline Resistance in Acinetobacter baumannii under Sub-Minimal Inhibitory Concentrations of Tigecycline., Int J Mol Sci, PMID 38339095

PXD048931 Dataset with its publication pending (from PRIDE)
Dataset title: Degradome analysis to identify direct substrates of small-molecule protein degraders
Possible reference: Jochem, M. et al. (2025) Degradome analysis to identify direct protein substrates of small-molecule degraders., Cell Chem Biol, PMID 39536762

PXD048915 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanism of Jianxin granules in the Treatment of Heart Failure Based on Proteomics and Metabolomics
Possible reference: Yongzhong, C. et al. (2024) Mechanism of jianxin granules in the treatment of heart failure based on proteomics and metabolomics., Chin Med, PMID 39605071

PXD048911 no publication (from MassIVE)
Dataset title: Coupling microdroplet-based sample preparation, multiplexed isobaric labeling, and nanoflow peptide fractionation for deep proteome profiling of tissue microenvironment
Possible reference: Veličković, M. et al. (2023) Coupling microdroplet-based sample preparation, multiplexed isobaric labeling, and nanoflow peptide fractionation for deep proteome profiling of tissue microenvironment., bioRxiv, PMID 36993277

PXD048909 Dataset with its publication pending (from PRIDE)
Dataset title: CTDP1 and RPB7 Stabilize Pol II and Permit Reinitiation
Possible reference: Zheng, H. et al. (2025) CTDP1 and RPB7 stabilize Pol II and permit reinitiation., Nat Commun, PMID 40038320

PXD048893 Dataset with its publication pending (from jPOST)
Dataset title: Volatile communication in plants relies on a KAI2-mediated signaling pathway
Possible reference: Stirling, SA. et al. (2024) Volatile communication in plants relies on a KAI2-mediated signaling pathway., Science, PMID 38513014

PXD048875 Dataset with its publication pending (from PRIDE)
Dataset title: Protein composition of the chicken egg tooth.
Possible reference: Sachslehner, AP. et al. (2025) The Epithelial Egg Tooth of the Chicken Shares Protein Markers with the Embryonic Subperiderm and Feathers., J Dev Biol, PMID 41562861

PXD048870 Dataset with its publication pending (from PRIDE)
Dataset title: Identifying cellular RNA-binding proteins during infection uncovers a role for MKRN2 in influenza mRNA trafficking.
Possible reference: Bonazza, S. et al. (2024) Identifying cellular RNA-binding proteins during infection uncovers a role for MKRN2 in influenza mRNA trafficking., PLoS Pathog, PMID 38753876

PXD048866 Dataset with its publication pending (from PRIDE)
Dataset title: Mouse tumor cell SCC7/SCC7-M LC-MS
Possible reference: Wang, J. et al. (2024) Chemopreventive effect of modified zeng-sheng-ping on oral squamous cell carcinoma by regulating tumor associated macrophages through targeting tnf alpha induced protein 6., BMC Complement Med Ther, PMID 39068492

PXD048861 Dataset with its publication pending (from PRIDE)
Dataset title: GID/CTLH E3 ligase complex control cell fate programs for sexual development of Plasmodium falciparum
Possible reference: Marapana, DS. et al. (2026) GID/CTLH E3 ligase complex control cell fate programs for sexual development of Plasmodium falciparum., Nat Commun, PMID 41986327

PXD048855 Dataset with its publication pending (from iProX)
Dataset title: Unravelling Intracellular Protein Corona Components of Nanoplas-tics via Photocatalytic Protein Proximity Labeling
Possible reference: Zhang, Z. et al. (2024) Unraveling Intracellular Protein Corona Components of Nanoplastics via Photocatalytic Protein Proximity Labeling., Anal Chem, PMID 38471057

PXD048849 Dataset with its publication pending (from PRIDE)
Dataset title: Detection of structure-specific interactions of Rab GTPases
Possible reference: Holfeld, A. et al. (2024) Systematic identification of structure-specific protein-protein interactions., Mol Syst Biol, PMID 38702390

PXD048833 Dataset with its publication pending (from PRIDE)
Dataset title: Human aneuploid cells depend on the RAF/MEK/ERK pathway for overcoming increased DNA damage
Possible reference: Zerbib, J. et al. (2024) Human aneuploid cells depend on the RAF/MEK/ERK pathway for overcoming increased DNA damage., Nat Commun, PMID 39251587

PXD048820 Dataset with its publication pending (from iProX)
Dataset title: Cpt1a drives Lipid remodeling in Primed-to-Na�ve Pluripotency Transition
Possible reference: Ma, Z. et al. (2024) Cpt1a Drives primed-to-na�ve pluripotency transition through lipid remodeling., Commun Biol, PMID 39349670

PXD048799 Dataset with its publication pending (from PRIDE)
Dataset title: GlPRMT5 inhibits GlPP2C1 via symmetric dimethylation and regulates the biosynthesis of secondary metabolites in Ganoderma lucidum
Possible reference: Wang, Z. et al. (2024) GlPRMT5 inhibits GlPP2C1 via symmetric dimethylation and regulates the biosynthesis of secondary metabolites in Ganoderma lucidum., Commun Biol, PMID 38418849

PXD048744 Dataset with its publication pending (from iProX)
Dataset title: protein malonylation sites in Hepatocarcinoma cells
Possible reference: Lally, JSV. et al. (2019) Inhibition of Acetyl-CoA Carboxylase by Phosphorylation or the Inhibitor ND-654 Suppresses Lipogenesis and Hepatocellular Carcinoma., Cell Metab, PMID 30244972

PXD048737 Dataset with its publication pending (from PRIDE)
Dataset title: MS-CETSA Target Identification of MMV000848
Possible reference: Wirjanata, G. et al. (2024) Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development., Cell Chem Biol, PMID 38593807

PXD048714 Dataset with its publication pending (from PRIDE)
Dataset title: Fonsecaea pedrosoi response to zinc deprivation
Possible reference: Santos, TAO. et al. (2024) Zinc Starvation Induces Cell Wall Remodeling and Activates the Antioxidant Defense System in Fonsecaea pedrosoi., J Fungi (Basel), PMID 38392790

PXD048711 Dataset with its publication pending (from PRIDE)
Dataset title: CemR atypical response regulator impacts energy conversion in Campylobacteria
Possible reference: Noszka, M. et al. (2024) CemR atypical response regulator impacts energy conversion in Campylobacteria., mSystems, PMID 38980050

PXD048706 Dataset with its publication pending (from iProX)
Dataset title: Integrated multi-omics analysis reveals osteokines involved in global regulation
Possible reference: Liang, W. et al. (2024) An integrated multi-omics analysis reveals osteokines involved in global regulation., Cell Metab, PMID 38574738

PXD048703 Dataset with its publication pending (from iProX)
Dataset title: Identification of O-GlcNAc proteins and glycosites using bioorthogonal ligation-tryptic cleavage strategy
Possible reference: Xiong, Y. et al. (2024) Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation., Natl Sci Rev, PMID 39534244

PXD048693 Dataset with its publication pending (from PRIDE)
Dataset title: CRISPR screen for protein inclusion formation uncovers a role for SRRD in the regulation of intermediate filament dynamics and aggresome assembly
Possible reference: Sweeney, KM. et al. (2024) CRISPR screen for protein inclusion formation uncovers a role for SRRD in the regulation of intermediate filament dynamics and aggresome assembly., PLoS Genet, PMID 38315730

PXD048682 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial calcium uniporter complex controls T‑cell‑mediated immune responses
Possible reference: Shumanska, M. et al. (2025) Mitochondrial calcium uniporter complex controls T-cell-mediated immune responses., EMBO Rep, PMID 39623165

PXD048658 Dataset with its publication pending (from PRIDE)
Dataset title: Aging aggravates aortic aneurysm and dissection via the miR-1204-MYLK signaling axis
Possible reference: Liu, ZL. et al. (2024) Aging aggravates aortic aneurysm and dissection via miR-1204-MYLK signaling axis in mice., Nat Commun, PMID 39013850

PXD048652 Dataset with its publication pending (from PRIDE)
Dataset title: Global, neuronal, and beta-cell specific deletion of the insulin inhibitory receptor (inceptor) improves glucose homeostasis in diet-induced obese male mice
Possible reference: Grandl, G. et al. (2024) Global, neuronal or β cell-specific deletion of inceptor improves glucose homeostasis in male mice with diet-induced obesity., Nat Metab, PMID 38418586

PXD048650 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial calcium uniporter complex controls T-cell-mediated immune responses
Possible reference: Shumanska, M. et al. (2025) Mitochondrial calcium uniporter complex controls T-cell-mediated immune responses., EMBO Rep, PMID 39623165

PXD048648 Dataset with its publication pending (from PRIDE)
Dataset title: Metabolic engineering of Saccharomyces cerevisiae and role of transcription factor Znf1
Possible reference: Songdech, P. et al. (2020) Overexpression of Transcription Factor ZNF1 of Glycolysis Improves Bioethanol Productivity under High Glucose Concentration and Enhances Acetic Acid Tolerance of Saccharomyces cerevisiae., Biotechnol J, PMID 32196937

PXD048636 Dataset with its publication pending (from iProX)
Dataset title: Alterations in Placental Proteomics Induced by Intrauterine Hyperglycemia
Possible reference: Ren, ZR. et al. (2024) Sex-Specific Alterations in Placental Proteomics Induced by Intrauterine Hyperglycemia., J Proteome Res, PMID 38470452

PXD048632 Dataset with its publication pending (from PRIDE)
Dataset title: MACSPI Enables Tissue-Selective Proteomic and Interactomic Analyses in Multicellular Organisms
Possible reference: Huang, S. et al. (2024) MACSPI enables tissue-selective proteomic and interactomic analyses in multicellular organisms., Proc Natl Acad Sci U S A, PMID 38753516

PXD048592 Dataset with its publication pending (from iProX)
Dataset title: KDF1 interacting protein in the ameloblast cell line
Possible reference: Liu, H. et al. (2024) KDF1 promotes ameloblast differentiation by inhibiting the IKK/IκB/NF-κB axis., J Cell Physiol, PMID 39300779

PXD048587 Dataset with its publication pending (from iProX)
Dataset title: EFHD2 Suppresses Intestinal Inflammation by Blocking Intestinal Epithelial Cell TNFR1 Internalization and Cell Death
Possible reference: Wu, J. et al. (2024) EFHD2 suppresses intestinal inflammation by blocking intestinal epithelial cell TNFR1 internalization and cell death., Nat Commun, PMID 38346956

PXD048581 Dataset with its publication pending (from iProX)
Dataset title: Antimicrobial activity and multi-targeted mechanism of action of suberanilic acid against methicillin-resistant Staphylococcus aureus
Possible reference: Wen, J. et al. (2024) Antibacterial Activity and Multi-Targeted Mechanism of Action of Suberanilic Acid Isolated from Pestalotiopsis trachycarpicola DCL44: An Endophytic Fungi from Ageratina adenophora., Molecules, PMID 39275053

PXD048574 Dataset with its publication pending (from iProX)
Dataset title: Transcription factor ZNF263 enhances EGFR-targeted therapeutic response and reduces residual disease in lung adenocarcinoma
Possible reference: Liang, J. et al. (2024) Transcription factor ZNF263 enhances EGFR-targeted therapeutic response and reduces residual disease in lung adenocarcinoma., Cell Rep, PMID 38335093

PXD048573 Dataset with its publication pending (from iProX)
Dataset title: Phenol degrading manganese oxidizing Pseudomonas AN-1
Possible reference: Qiao, A. et al. (2024) Can xenobiotics support the growth of Mn(II)-oxidizing bacteria (MnOB)? A case of phenol-utilizing bacteria Pseudomonas sp. AN-1., J Hazard Mater, PMID 38521035

PXD048554 Dataset with its publication pending (from jPOST)
Dataset title: The N-acetylglucosaminyltransferase Radical Fringe contributes to defects in JAG1-dependent turnover and signaling of NOTCH3 CADASIL mutants
Possible reference: Suzuki, S. et al. (2024) The N-acetylglucosaminyltransferase Radical fringe contributes to defects in JAG1-dependent turnover and signaling of NOTCH3 CADASIL mutants., J Biol Chem, PMID 39303912

PXD048553 Dataset with its publication pending (from PRIDE)
Dataset title: A new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Possible reference: Reinhard, J. et al. (2024) MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress., EMBO J, PMID 38491296

PXD048539 Dataset with its publication pending (from jPOST)
Dataset title: hnRNPA2B1 represses the disassembly of arsenite-induced stress granules and is essential for male fertility
Possible reference: Wang, X. et al. (2024) hnRNPA2B1 represses the disassembly of arsenite-induced stress granules and is essential for male fertility., Cell Rep, PMID 38363675

PXD048533 Dataset with its publication pending (from jPOST)
Dataset title: Comprehensive analysis of O-linked glycans on Notch receptors using mass spectrometry
Possible reference: Harvey, BM. et al. (2016) Mapping Sites of O-Glycosylation and Fringe Elongation on Drosophila Notch., J Biol Chem, PMID 27268051

PXD048511 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of serum small extracellular vesicles identifies diagnostic biomarkers for neuroblastoma
Possible reference: Cheng, J. et al. (2024) Proteomic analysis of serum small extracellular vesicles identifies diagnostic biomarkers for neuroblastoma., Front Oncol, PMID 39228987

PXD048503 Dataset with its publication pending (from PRIDE)
Dataset title: ERLIN1 and ERLIN2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway
Possible reference: Veronese, M. et al. (2024) ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway., Life Sci Alliance, PMID 38782601

PXD048484 Dataset with its publication pending (from iProX)
Dataset title: Simultaneous identification of O-GlcNAc sites and N-glycosites by a two-step enzymatic release strategy
Possible reference: Xiong, Y. et al. (2024) Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation., Natl Sci Rev, PMID 39534244

PXD048469 no publication (from MassIVE)
Dataset title: Uncovering missing glycans and unexpected fragments with pGlycoNovo: a full-range Y-ion dynamic searching strategy for site-specific glycosylation analysis across species
Possible reference: Zeng, WF. et al. (2024) Uncovering missing glycans and unexpected fragments with pGlycoNovo for site-specific glycosylation analysis across species., Nat Commun, PMID 39277585

PXD048432 Dataset with its publication pending (from iProX)
Dataset title: Proteome of B. subtilis with and without sodium nitrate
Possible reference: Xia, L. et al. (2024) Enhancing surfactin production in Bacillus subtilis: Insights from proteomic analysis of nitrate-induced overproduction and strategies for combinatorial metabolic engineering., Bioresour Technol, PMID 38417461

PXD048429 Dataset with its publication pending (from iProX)
Dataset title: The Small Extracellular Vesicle-Mediated Intercellular Transformation of CXCR1-Low to CXCR1-High Tumor Cells Promotes the Progression of Head and Neck Squamous Cell Carcinoma
Possible reference: Xu, Q. et al. (2024) The small extracellular vesicle-mediated intercellular transformation of CXCR1Low to CXCR1High tumour cells promotes the progression of head and neck squamous cell carcinoma., J Extracell Vesicles, PMID 38545803

PXD048425 Dataset with its publication pending (from iProX)
Dataset title: USP36 variant confers resistance to EGFR-TKIs
Possible reference: Guan, S. et al. (2024) Germline USP36 Mutation Confers Resistance to EGFR-TKIs by Upregulating MLLT3 Expression in Patients with Non-Small Cell Lung Cancer., Clin Cancer Res, PMID 38261467

PXD048423 Dataset with its publication pending (from iProX)
Dataset title: Spindle apparatus coiled-coil protein 1 (SPDL1) serves as a novel prognostic biomarker in triple-negative breast cancer
Possible reference: Yang, XY. et al. (2024) Spindle apparatus coiled-coil protein 1 (SPDL1) serves as a novel prognostic biomarker in triple-negative breast cancer., Proteomics Clin Appl, PMID 38316615

PXD048382 Dataset with its publication pending (from PRIDE)
Dataset title: An inhibitory segment within G-patch activators tunes Prp43-ATPase activity during ribosome assembly
Possible reference: Portugal-Calisto, D. et al. (2024) An inhibitory segment within G-patch activators tunes Prp43-ATPase activity during ribosome assembly., Nat Commun, PMID 39578461

PXD048378 Dataset with its publication pending (from PRIDE)
Dataset title: Regional differences in the small intestinal proteome of control mice and of mice lacking lysosomal acid lipase
Possible reference: Bianco, V. et al. (2024) Regional Differences in the Small Intestinal Proteome of Control Mice and of Mice Lacking Lysosomal Acid Lipase., J Proteome Res, PMID 38422518

PXD048368 Dataset with its publication pending (from iProX)
Dataset title: Proteomics analysis of Pseudoduganella aquatica HC52-OMVs
Possible reference: Park, Y. et al. (2024) Alleviation of H2O2 toxicity by extracellular catalases in the phycosphere of Microcystis aeruginosa., Harmful Algae, PMID 39003030

PXD048366 no publication (from MassIVE)
Dataset title: The primate-specific Nedd4-1-NE localizes to late endosomes in response to amino acids to suppress autophagy
Possible reference: Kefalas, G. et al. (2025) The primate-specific Nedd4-1(NE) localizes to late endosomes in response to amino acids to suppress autophagy., Nat Commun, PMID 40102426

PXD048365 Dataset with its publication pending (from jPOST)
Dataset title: Inhibitory effect of S-Allylmercaptocysteine on TLR4-mediated inflammation in mammary epithelial cells
Possible reference: Takashima, M. et al. (2024) S-allylmercaptocysteine inhibits TLR4-mediated inflammation through enhanced formation of inhibitory MyD88 splice variant in mammary epithelial cells., Sci Rep, PMID 39609525

PXD048356 no publication (from MassIVE)
Dataset title: Calorie restriction and rapamycin distinctly mitigate aging-associated protein phosphorylation changes in mouse muscles
Possible reference: Ataman, M. et al. (2024) Calorie restriction and rapamycin distinctly mitigate aging-associated protein phosphorylation changes in mouse muscles., Commun Biol, PMID 39127848

PXD048346 Dataset with its publication pending (from PRIDE)
Dataset title: Pupylation-based proximity labelling reveals regulatory factors in cellulose biosynthesis in Arabidopsis
Possible reference: Zheng, S. et al. (2025) Pupylation-based proximity labeling reveals regulatory factors in cellulose biosynthesis in Arabidopsis., Nat Commun, PMID 39833163

PXD048331 Dataset with its publication pending (from PRIDE)
Dataset title: Global analysis of protein lysine lactylation profiles in the marine bacterium Photobacterium damselae
Possible reference: Yu, Y. et al. (2025) Global analysis of protein lysine lactylation profiles in the marine bacterium Photobacterium damselae subsp. damselae., Front Microbiol, PMID 40600136

PXD048292 no publication (from MassIVE)
Dataset title: The TRIP12 E3 Ligase Induces Interaction Between the SWI/SNF Component BRG1 and Beta-catenin to Promote Wnt Signaling
Possible reference: Kassel, S. et al. (2025) The TRIP12 E3 ligase induces SWI/SNF component BRG1-β-catenin interaction to promote Wnt signaling., Nat Commun, PMID 40473626

PXD048290 Dataset with its publication pending (from PRIDE)
Dataset title: Transposable elements drive regulatory and functional innovation of F box genes
Possible reference: Almeida, MV. et al. (2025) Transposable Elements Drive Regulatory and Functional Innovation of F-box Genes., Mol Biol Evol, PMID 40279373

PXD048284 Dataset with its publication pending (from jPOST)
Dataset title: Volatile communication in plants relies on a KAI2-mediated signaling pathway
Possible reference: Stirling, SA. et al. (2024) Volatile communication in plants relies on a KAI2-mediated signaling pathway., Science, PMID 38513014

PXD048272 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping in silico genetic networks of tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities
Possible reference: Takemon, Y. et al. (2024) Mapping in silico genetic networks of the KMT2D tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities., Genome Med, PMID 39578878

PXD048264 Dataset with its publication pending (from PRIDE)
Dataset title: Exaptation of an evolutionary constraint enables behavioural control over the composition of secreted venom in giant centipedes
Possible reference: Schendel, V. et al. (2025) Exaptation of an evolutionary constraint enables behavioural control over the composition of secreted venom in a giant centipede., Nat Ecol Evol, PMID 39496866

PXD048258 no publication (from MassIVE)
Dataset title: A mechanism that transduces lysosomal damage signals to stress granule formation for cell survival
Possible reference: Duran, J. et al. (2024) A mechanism that transduces lysosomal damage signals to stress granule formation for cell survival., bioRxiv, PMID 38617306

PXD048243 Dataset with its publication pending (from iProX)
Dataset title: Thermal proteome profiling reveals fructose-1,6-bisphosphate as a phosphate donor to activate phosphoglycerate mutase 1
Possible reference: Zhang, Y. et al. (2024) Thermal proteome profiling reveals fructose-1,6-bisphosphate as a phosphate donor to activate phosphoglycerate mutase 1., Nat Commun, PMID 39414782

PXD048239 Dataset with its publication pending (from PRIDE)
Dataset title: Salt stress in freshwater anaerobic methane-oxidizing archaea
Possible reference: Echeveste Medrano, MJ. et al. (2024) Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress., ISME J, PMID 39030685

PXD048234 Dataset with its publication pending (from iProX)
Dataset title: O-GlcNAcylation of E3 ubiquitin ligase SKP2 promotes hepatocellular carcinoma proliferation
Possible reference: Feng, Z. et al. (2024) O-GlcNAcylation of E3 ubiquitin ligase SKP2 promotes hepatocellular carcinoma proliferation., Oncogene, PMID 38396292

PXD048217 Dataset with its publication pending (from iProX)
Dataset title: The mechanisms of chitosan to enhance the biological control efficacy of Wickerhamomyces anomalus against blue mold decay of grapes
Possible reference: Guo, S. et al. (2025) Effect of volatile compounds produced by Wickerhamomyces anomalus induced with chitosan against blue mold disease in table grapes., Int J Biol Macromol, PMID 40118422

PXD048216 Dataset with its publication pending (from PRIDE)
Dataset title: S-palmitoylation of MAP kinase is essential for fungal virulence
Possible reference: Duan, Y. et al. (2024) S-palmitoylation of MAP kinase is essential for fungal virulence., mBio, PMID 39470248

PXD048184 Dataset with its publication pending (from PRIDE)
Dataset title: Asp23-controlled cell wall imbalance promotes membrane vesicles biogenesis in Staphylococcus aureus
Possible reference: Li, J. et al. (2024) Alkaline shock protein 23 (Asp23)-controlled cell wall imbalance promotes membrane vesicle biogenesis in Staphylococcus aureus., J Extracell Vesicles, PMID 39193667

PXD048156 Dataset with its publication pending (from iProX)
Dataset title: Histone-like transcription factor Hfl1p in Candida albicans harmonizes nuclear and mitochondrial genomic network in regulation of energy metabolism and filamentation development
Possible reference: She, X. et al. (2024) Histone-like transcription factor Hfl1p in Candida albicans harmonizes nuclear and mitochondrial genomic network in regulation of energy metabolism and filamentation development., Virulence, PMID 39370643

PXD048142 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome Changes Induced by Hydrogen Peroxide in Sugarcane Plants
Possible reference: Trentin, AR. et al. (2015) Proteome readjustments in the apoplastic space of Arabidopsis thaliana ggt1 mutant leaves exposed to UV-B radiation., Front Plant Sci, PMID 25852701

PXD048127 Dataset with its publication pending (from iProX)
Dataset title: Genetic code expansion reveals site-specific lactylation in living cells reshapes protein function
Possible reference: Shao, C. et al. (2025) Genetic code expansion reveals site-specific lactylation in living cells reshapes protein functions., Nat Commun, PMID 39779673

PXD048122 Dataset with its publication pending (from iProX)
Dataset title: Metaproteomics analysis of shower hoses biofilm
Possible reference: Yao, M. et al. (2025) Unveiling the influence of heating temperature on biofilm formation in shower hoses through multi-omics., Water Res, PMID 39481332

PXD048103 Dataset with its publication pending (from iProX)
Dataset title: Phosphorylation proteomics of JEV infected macrophages
Possible reference: Rees, A. et al. (2026) DAMP Laden Extracellular Vesicles From the Airways of Patients With Severe SARS-CoV-2 Respiratory Infection Compromise Inflammation and Cellular Metabolism., J Extracell Vesicles, PMID 42204964

PXD048093 Dataset with its publication pending (from PRIDE)
Dataset title: The proteome sequencing of ectopic and paired eutopic endometria
Possible reference: Liu, F. et al. (2021) Endometrial stromal cell proteomic analysis reveals LIM and SH3 protein 1 (LASP1) plays important roles in the progression of adenomyosis., Mol Hum Reprod, PMID 33543750

PXD048068 Dataset with its publication pending (from iProX)
Dataset title: A LINC00472-encoded polypeptide impedes migration and proliferation through modulation of the HDAC2/SP1 axis in non-small cell lung cancer cells
Possible reference: Xu, L. et al. (2025) A LINC00472-encoded polypeptide impedes migration and proliferation through modulation of the HDAC2/SP1 axis in non-small cell lung cancer cells., Cancer Cell Int, PMID 40671075

PXD048065 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of diapause and non-diapause stages of Loxostege sticticalis
Possible reference: Shao, L. et al. (2024) Comparative Proteomics and Metabonomics Analysis of Different Diapause Stages Revealed a New Regulation Mechanism of Diapause in Loxostege sticticalis (Lepidoptera: Pyralidae)., Molecules, PMID 39124877

PXD048063 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of plasma exosomes reveals S100A8 as a novel biomarker for Alzheimer’s disease: a preliminary study
Possible reference: Zhang, Y. et al. (2024) Proteomics of plasma-derived extracellular vesicles reveals S100A8 as a novel biomarker for Alzheimer's disease: A preliminary study., J Proteomics, PMID 39159863

PXD048056 Dataset with its publication pending (from PRIDE)
Dataset title: Monocarboxylate transporters facilitate succinate uptake into brown adipocytes
Possible reference: Reddy, A. et al. (2023) Monocarboxylate transporters facilitate succinate uptake into brown adipocytes., bioRxiv, PMID 36909624

PXD048049 no publication (from MassIVE)
Dataset title: Dark respiration optimizes photosynthesis carbon yield in cyanobacteria
Possible reference: Xie, N. et al. (2024) Phosphoketolase and KDPG aldolase metabolisms modulate photosynthetic carbon yield in cyanobacteria., Plant Cell, PMID 39471324

PXD048035 Dataset with its publication pending (from PRIDE)
Dataset title: Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies
Possible reference: He, H. et al. (2024) Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies., Nat Commun, PMID 39406738

PXD048024 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular-Level Architecture of Chlamydomonas reinhardtii’s Glycoprotein-Rich Cell Wall
Possible reference: Poulhazan, A. et al. (2024) Molecular-level architecture of Chlamydomonas reinhardtii's glycoprotein-rich cell wall., Nat Commun, PMID 38307857

PXD048016 Dataset with its publication pending (from PRIDE)
Dataset title: Optimization of protein identifications by exploring several crhomatographic and search engine parameters
Possible reference: Muth, T. et al. (2015) Navigating through metaproteomics data: a logbook of database searching., Proteomics, PMID 25778831

PXD047990 Dataset with its publication pending (from jPOST)
Dataset title: Global proteome of the saprophytic strain Leptospira biflexa
Possible reference: Nascimento Filho, EG. et al. (2024) Global proteome of the saprophytic strain Leptospira biflexa and comparative analysis with pathogenic strain Leptospira interrogans uncover new pathogenesis mechanisms., J Proteomics, PMID 38364905

PXD047982 Dataset with its publication pending (from iProX)
Dataset title: Characterization of Testicular O-glycoproteome during Spermatogenesis in Mice
Possible reference: Liu, Q. et al. (2025) Global characterization of mouse testis O-glycoproteome landscape during spermatogenesis., Nat Commun, PMID 40102425

PXD047978 Dataset with its publication pending (from iProX)
Dataset title: Delineation of renal protein profiles in aristolochic acid I-induced nephrotoxicity in mice by label-free quantitative proteomics
Possible reference: Liu, X. et al. (2024) Delineation of renal protein profiles in aristolochic acid I-induced nephrotoxicity in mice by label-free quantitative proteomics., Front Pharmacol, PMID 38783935

PXD047909 no publication (from MassIVE)
Dataset title: Zika Virus NS1 Drives Tunneling Nanotube Formation for Mitochondrial Transfer, Enhanced Survival, Interferon Evasion, and Stealth Transmission in Trophoblasts
Possible reference: Mysorekar, I. et al. (2023) Zika Virus NS1 Drives Tunneling Nanotube Formation for Mitochondrial Transfer, Enhanced Survival, Interferon Evasion, and Stealth Transmission in Trophoblasts., Res Sq, PMID 38106210

PXD047891 Dataset with its publication pending (from iProX)
Dataset title: PARylation of 14-3-3 proteins control the virulence of Magnaporthe oryzae
Possible reference: Gao, X. et al. (2024) PARylation of 14-3-3 proteins controls the virulence of Magnaporthe oryzae., Nat Commun, PMID 39277621

PXD047872 Dataset with its publication pending (from PRIDE)
Dataset title: Investigating HMGB1 as a Potential Serum Biomarker for Early Diabetic Nephropathy Monitoring by Quantitative Proteomics
Possible reference: Peng, R. et al. (2024) Investigating HMGB1 as a potential serum biomarker for early diabetic nephropathy monitoring by quantitative proteomics., iScience, PMID 38303703

PXD047866 Dataset with its publication pending (from PRIDE)
Dataset title: Substrate identification and specificity profiling of deubiquitylases against endogenously-generated ubiquitin-protein conjugates
Possible reference: Rossio, V. et al. (2023) Substrate identification and specificity profiling of deubiquitylases against endogenously-generated ubiquitin-protein conjugates., bioRxiv, PMID 38187689

PXD047864 Dataset with its publication pending (from PRIDE)
Dataset title: Inflammation causes insulin resistance via IRF3-mediated reduction in FAHFA levels
Possible reference: Yan, S. et al. (2024) Inflammation causes insulin resistance in mice via interferon regulatory factor 3 (IRF3)-mediated reduction in FAHFA levels., Nat Commun, PMID 38816388

PXD047859 Dataset with its publication pending (from PRIDE)
Dataset title: Enhanced Staphylococcus aureus vaccine protection by uncoupling of the alpha-toxin-ADAM10 interaction
Possible reference: Tomaszewski, KL. et al. (2024) Enhanced Staphylococcus aureus protection by uncoupling of the α-toxin-ADAM10 interaction during murine neonatal vaccination., Nat Commun, PMID 39379345

PXD047841 Dataset with its publication pending (from PRIDE)
Dataset title: Parallel control of cold-triggered adipocyte thermogenesis by UCP1 and CKB
Possible reference: Rahbani, JF. et al. (2024) Parallel control of cold-triggered adipocyte thermogenesis by UCP1 and CKB., Cell Metab, PMID 38272036

PXD047837 Dataset with its publication pending (from PRIDE)
Dataset title: ATM Inhibition Exploits Checkpoint Defects and ATM-Dependent Double Strand Break Repair in TP53-Mutant Glioblastoma
Possible reference: Laverty, DJ. et al. (2024) ATM inhibition exploits checkpoint defects and ATM-dependent double strand break repair in TP53-mutant glioblastoma., Nat Commun, PMID 38906885

PXD047810 Dataset with its publication pending (from iProX)
Dataset title: Phosphoproteomics profiling of sorafenib-resistant HCC patient-derived xenografts reveals potential therapeutic strategies
Possible reference: Li, F. et al. (2025) Phosphoproteomics profiling of sorafenib-resistant hepatocellular carcinoma patient-derived xenografts reveals potential therapeutic strategies., iScience, PMID 39886465

PXD047809 Dataset with its publication pending (from iProX)
Dataset title: Enhancing Tendon Regeneration: Investigating the Impact of Topography on the Secretome of Adipose-Derived Stem Cells
Possible reference: Long, Q. et al. (2025) Enhancing Tendon Regeneration: Investigating the Impact of Topography on the Secretome of Adipose-Derived Stem Cells., Adv Sci (Weinh), PMID 40091553

PXD047799 no publication (from MassIVE)
Dataset title: Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics
Possible reference: Eckert, S. et al. (2025) Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics., Nat Biotechnol, PMID 38714896

PXD047795 Dataset with its publication pending (from PRIDE)
Dataset title: Nitrogen signaling factor triggers a respiration-like gene expression program
Possible reference: Ohsawa, S. et al. (2024) Nitrogen signaling factor triggers a respiration-like gene expression program in fission yeast., EMBO J, PMID 39256560

PXD047793 Dataset with its publication pending (from PRIDE)
Dataset title: A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer
Possible reference: Lapcik, P. et al. (2024) A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer., Sci Data, PMID 39025866

PXD047788 Dataset with its publication pending (from PRIDE)
Dataset title: Schizophrenia risk gene ZNF804A controls ribosome localization and synaptogenesis in developing human neurons
Possible reference: Sichlinger, L. et al. (2026) Schizophrenia risk gene ZNF804A controls ribosome localization and synaptogenesis in developing human neurons., Sci Adv, PMID 42160410

PXD047764 no publication (from MassIVE)
Dataset title: Outer membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly
Possible reference: Potapova, A. et al. (2024) Outer membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly., mBio, PMID 38206049

PXD047757 no publication (from MassIVE)
Dataset title: Automated workflow for BioID improves reproducibility and identification of protein-protein interactions
Possible reference: Cirri, E. et al. (2024) Optimized Automated Workflow for BioID Improves Reproducibility and Identification of Protein-Protein Interactions., J Proteome Res, PMID 39231529

PXD047750 Dataset with its publication pending (from PRIDE)
Dataset title: Immunopeptidomics identification of Listeria monocytogenes T cell epitopes in mice
Possible reference: Gul, A. et al. (2024) Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice., Mol Cell Proteomics, PMID 39147027

PXD047749 Dataset with its publication pending (from PRIDE)
Dataset title: Preclinical study with a CD40 agonist on patient-derived xenograft mice for the treatment of B-cell acute lymphoblastic leukemia
Possible reference: Bellaye, PS. et al. (2025) CD40 Agonist on Patient-Derived Xenograft Mice for the Treatment of B-Cell Acute Lymphoblastic Leukemia., Clin Cancer Res, PMID 39540842

PXD047740 Dataset with its publication pending (from iProX)
Dataset title: AKAP1/PKA-mediated GRP75 phosphorylation at MAMs sequesters GRP75 outside the mitochondria to protect cancer cells against ferroptosis
Possible reference: Liu, H. et al. (2025) AKAP1/PKA-mediated GRP75 phosphorylation at mitochondria-associated endoplasmic reticulum membranes protects cancer cells against ferroptosis., Cell Death Differ, PMID 39537840

PXD047719 no publication (from MassIVE)
Dataset title: Native Top-Down Mass Spectrometry for Characterizing Sarcomeric Proteins Directly from Cardiac Tissue Lysate
Possible reference: Chapman, EA. et al. (2024) Native Top-Down Mass Spectrometry for Characterizing Sarcomeric Proteins Directly from Cardiac Tissue Lysate., J Am Soc Mass Spectrom, PMID 38422011

PXD047707 Dataset with its publication pending (from PRIDE)
Dataset title: Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression
Possible reference: Lobo, V. et al. (2024) Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression., Sci Data, PMID 38866801

PXD047700 Dataset with its publication pending (from PRIDE)
Dataset title: HYPK controls stability and catalytic activity of the N-terminal acetyltransferase A in Arabidopsis thaliana
Possible reference: Gong, X. et al. (2024) HYPK controls stability and catalytic activity of the N-terminal acetyltransferase A in Arabidopsis thaliana., Cell Rep, PMID 38363676

PXD047680 no publication (from MassIVE)
Dataset title: Small-scale Serial Size Exclusion Chromatography (s3SEC) for High Sensitivity Top-down Proteomics of Large Proteoforms
Possible reference: Rogers, HT. et al. (2024) Small-Scale Serial Size Exclusion Chromatography (s3SEC) for High Sensitivity Top-Down Proteomics of Large Proteoforms., Anal Chem, PMID 38315630

PXD047676 no publication (from MassIVE)
Dataset title: Phosphoproteomics of dried blood collected on Mitra devices
Possible reference: Foster, MW. et al. (2025) Mass spectrometry-based quantification of proteins and post-translational modifications in dried blood: longitudinal sampling of patients with sepsis in Tanzania., bioRxiv, PMID 40492198

PXD047674 Dataset with its publication pending (from PRIDE)
Dataset title: Mass spectrometry-based proteomic profiling of exosomal proteins in diabetic and non-diabetic ischemic stroke patients: a case-control study
Possible reference: Qadri, S. et al. (2024) Mass spectrometry-based proteomic profiling of extracellular vesicle proteins in diabetic and non-diabetic ischemic stroke patients: a case-control study., Front Mol Biosci, PMID 38948080

PXD047668 Dataset with its publication pending (from PRIDE)
Dataset title: CSB promotes transcription-coupled repair of DNA-protein crosslinks
Possible reference: Carnie, CJ. et al. (2024) Transcription-coupled repair of DNA-protein cross-links depends on CSA and CSB., Nat Cell Biol, PMID 38600235

PXD047666 no publication (from MassIVE)
Dataset title: Proteomics of dried blood collected on Mitra devices
Possible reference: Foster, MW. et al. (2025) Mass spectrometry-based quantification of proteins and post-translational modifications in dried blood: longitudinal sampling of patients with sepsis in Tanzania., bioRxiv, PMID 40492198

PXD047661 no publication (from MassIVE)
Dataset title: Proteostasis perturbation of N-Myc by HSP70 inhibition improves treatment in neuroendocrine prostate cancer
Possible reference: Xu, P. et al. (2024) Proteostasis perturbation of N-Myc leveraging HSP70 mediated protein turnover improves treatment of neuroendocrine prostate cancer., Nat Commun, PMID 39103353

PXD047659 no publication (from MassIVE)
Dataset title: Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics
Possible reference: Chang, YC. et al. (2024) Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics., Cell Rep, PMID 38795348

PXD047658 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of hepatic inclusions and fibrinogen biogenesis by SEL1L-HRD1 ERAD
Possible reference: Song, Z. et al. (2024) Regulation of hepatic inclusions and fibrinogen biogenesis by SEL1L-HRD1 ERAD., Nat Commun, PMID 39455574

PXD047650 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation of secretomes derived from human dermal and adipose tissue mesenchymal stem/stromal cells for skin wound healing: Not as effective as cells
Possible reference: Zomer, HD. et al. (2024) Evaluation of secretomes derived from human dermal and adipose tissue mesenchymal stem/stromal cells for skin wound healing: not as effective as cells., Stem Cell Res Ther, PMID 38229157

PXD047646 Dataset with its publication pending (from jPOST)
Dataset title: A Rapid One-pot Workflow for Sensitive Microscale Phosphoproteomics
Possible reference: Muneer, G. et al. (2024) A Rapid One-Pot Workflow for Sensitive Microscale Phosphoproteomics., J Proteome Res, PMID 39038167

PXD047641 Dataset with its publication pending (from PRIDE)
Dataset title: NeoDisc: A neoantigen discovery pipeline for the development of personalized cancer immunotherapy
Possible reference: Huber, F. et al. (2025) A comprehensive proteogenomic pipeline for neoantigen discovery to advance personalized cancer immunotherapy., Nat Biotechnol, PMID 39394480

PXD047603 Dataset with its publication pending (from PRIDE)
Dataset title: Overactive mitochondrial DNA replication disrupts perinatal cardiac maturation
Possible reference: Landoni, JC. et al. (2024) Overactive mitochondrial DNA replication disrupts perinatal cardiac maturation., Nat Commun, PMID 39277581

PXD047594 Dataset with its publication pending (from PRIDE)
Dataset title: FERONIA controls ABA-mediated seed germination via the regulation of the kinase activity of CARK1
Possible reference: Wang, X. et al. (2024) FERONIA controls ABA-mediated seed germination via the regulation of CARK1 kinase activity., Cell Rep, PMID 39412988

PXD047591 Dataset with its publication pending (from iProX)
Dataset title: SM1702 cold-adaptation proteome
Possible reference: Xu, WY. et al. (2024) Increase of ATP synthesis and amino acids absorption contributes to cold adaptation in Antarctic bacterium Poseidonibacter antarcticus SM1702T., Extremophiles, PMID 39576362

PXD047571 Dataset with its publication pending (from PRIDE)
Dataset title: Insights from multi-omic modelling of neurodegeneration in Xeroderma Pigmentosum using an induced pluripotent stem cell system
Possible reference: Badja, C. et al. (2024) Insights from multi-omic modeling of neurodegeneration in xeroderma pigmentosum using an induced pluripotent stem cell system., Cell Rep, PMID 38805398

PXD047569 Dataset with its publication pending (from PRIDE)
Dataset title: The PRC1 and PRC2 proximal interactome
Possible reference: Zijlmans, DW. et al. (2025) PRC1 and PRC2 proximal interactome in mouse embryonic stem cells., Cell Rep, PMID 40053453

PXD047560 no publication (from MassIVE)
Dataset title: Comparison of glioblastoma cell culture platforms based on transcriptional similarity with paired tissue
Possible reference: Park, J. et al. (2024) Comparison of Glioblastoma Cell Culture Platforms Based on Transcriptional Similarity with Paired Tissue., Pharmaceuticals (Basel), PMID 38675489

PXD047537 Dataset with its publication pending (from PRIDE)
Dataset title: Synthetically primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Possible reference: Dvořák, P. et al. (2024) Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose., Nat Commun, PMID 38531855

PXD047519 Dataset with its publication pending (from iProX)
Dataset title: Mesenteric Adipose-Derived Exosomal TINAGL1 Enhances Intestinal Fibrosis in Crohn's Disease via SMAD4
Possible reference: Chen, Y. et al. (2025) Mesenteric adipose-derived exosomal TINAGL1 enhances intestinal fibrosis in Crohn's Disease via SMAD4., J Adv Res, PMID 38750695

PXD047513 no publication (from MassIVE)
Dataset title: Comparison of glycopeptide to released glycan abundances and the influence of glycopeptide charge state on N-linked glycosylation of IgG antibodies
Possible reference: Remoroza, CA. et al. (2024) Comparison of N-Glycopeptide to Released N-Glycan Abundances and the Influence of Glycopeptide Mass and Charge States on N-Linked Glycosylation of IgG Antibodies., J Proteome Res, PMID 38450643

PXD047503 Dataset with its publication pending (from PRIDE)
Dataset title: FET fusion oncoproteins enrich SWI/SNF complex subtypes and interaction partners
Possible reference: Lind�n, M. et al. (2025) FET fusion oncoproteins enrich SWI/SNF complex subtypes and interaction partners., Cell Mol Biol Lett, PMID 40988026

PXD047477 Dataset with its publication pending (from iProX)
Dataset title: Calciprotein particle-activated endothelial cells aggravate smooth muscle cell calcification via paracrine signalling
Possible reference: Feenstra, L. et al. (2025) Calciprotein particle-activated endothelial cells aggravate smooth muscle cell calcification via paracrine signalling., Cell Mol Life Sci, PMID 40287595

PXD047466 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics reveals oxygen-induced adaptations in Caldalkalibacillus thermarum TA2.A1 chemostat cultures
Possible reference: de Jong, SI. et al. (2024) Quantitative proteomics reveals oxygen-induced adaptations in Caldalkalibacillus thermarum TA2.A1 microaerobic chemostat cultures., Front Microbiol, PMID 39529675

PXD047464 Dataset with its publication pending (from PRIDE)
Dataset title: Bioactive decellularized extracellular matrix-based hydrogel supports human adipose tissue-derived stem cell maintenance and fibrocartilage phenotype
Possible reference: Josino, R. et al. (2023) Bioactive decellularized extracellular matrix-based hydrogel supports human adipose tissue-derived stem cell maintenance and fibrocartilage phenotype., Front Bioeng Biotechnol, PMID 38260748

PXD047434 no publication (from MassIVE)
Dataset title: IER3IP1-mutations cause microcephaly by selective inhibition of ER-Golgi transport
Possible reference: Anitei, M. et al. (2024) IER3IP1-mutations cause microcephaly by selective inhibition of ER-Golgi transport., Cell Mol Life Sci, PMID 39115595

PXD047433 Dataset with its publication pending (from iProX)
Dataset title: The Proteome of chicken cecum inoculated with Salmonella enterica serovar Enteritidis
Possible reference: Wang, Y. et al. (2025) Transcriptomic and proteomic analysis reveals the mechanism of chicken cecum response to Salmonella enterica serovar Enteritidis inoculation., iScience, PMID 39845417

PXD047422 Dataset with its publication pending (from PRIDE)
Dataset title: Structural Host Virus Interactome Profiling of Intact Infected Cells
Possible reference: Bogdanow, B. et al. (2025) Structural host-virus interactome profiling of intact infected cells., Nat Commun, PMID 40691152

PXD047419 Dataset with its publication pending (from PanoramaPublic)
Dataset title: Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics
Possible reference: Chang, YC. et al. (2024) Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics., Cell Rep, PMID 38795348

PXD047412 Dataset with its publication pending (from PRIDE)
Dataset title: A Spatiotemporal Proteomic Map of Human Adipogenesis
Possible reference: Klingelhuber, F. et al. (2024) A spatiotemporal proteomic map of human adipogenesis., Nat Metab, PMID 38565923

PXD047403 Dataset with its publication pending (from jPOST)
Dataset title: Bioinformatics-Guided Identification and Quantification of Biomarkers in Exposomic of Crotalus atrox Venom and its Neutralization by Antivenom
Possible reference: Bala, AA. et al. (2025) Bioinformatics-Guided Identification and Quantification of Biomarkers of Crotalus atrox Envenoming and Its Neutralization by Antivenom., Mol Cell Proteomics, PMID 40147718

PXD047396 Dataset with its publication pending (from PRIDE)
Dataset title: Reprogramming neuroblastoma by diet-enhanced polyamine depletion
Possible reference: Cherkaoui, S. et al. (2024) Reprogramming neuroblastoma by diet-enhanced polyamine depletion., bioRxiv, PMID 38260457

PXD047364 Dataset with its publication pending (from iProX)
Dataset title: Granzyme A can be modified by 4-OI
Possible reference: Gong, W. et al. (2024) 4-Octyl itaconate blocks GSDMB-mediated pyroptosis and restricts inflammation by inactivating granzyme A., Cell Prolif, PMID 38982510

PXD047348 no publication (from MassIVE)
Dataset title: Itaconate modulates immune responses via inhibition of peroxiredoxins
Possible reference: Paulenda, T. et al. (2025) Itaconate modulates immune responses via inhibition of peroxiredoxin 5., Nat Metab, PMID 40251412

PXD047339 Dataset with its publication pending (from PRIDE)
Dataset title: A novel strategy to generate immunocytokines with activity-on-demand using small molecule inhibitors
Possible reference: Rotta, G. et al. (2024) A novel strategy to generate immunocytokines with activity-on-demand using small molecule inhibitors., EMBO Mol Med, PMID 38448543

PXD047337 Dataset with its publication pending (from PRIDE)
Dataset title: ANDROGEN DRIVES MELANOMA INVASIVENESS AND METASTATIC SPREAD BY INDUCING TUMORIGENIC FUCOSYLATION: Fucoproteomics
Possible reference: Liu, Q. et al. (2024) Androgen drives melanoma invasiveness and metastatic spread by inducing tumorigenic fucosylation., Nat Commun, PMID 38326303

PXD047335 Dataset with its publication pending (from PRIDE)
Dataset title: ANDROGEN DRIVES MELANOMA INVASIVENESS AND METASTATIC SPREAD BY INDUCING TUMORIGENIC FUCOSYLATION: Phosphoproteomics
Possible reference: Liu, Q. et al. (2024) Androgen drives melanoma invasiveness and metastatic spread by inducing tumorigenic fucosylation., Nat Commun, PMID 38326303

PXD047328 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles secreted by 3D tumor organoids are enriched for immune regulatory signaling biomolecules compared to conventional 2D glioblastoma cell systems
Possible reference: Schuster, M. et al. (2024) Extracellular vesicles secreted by 3D tumor organoids are enriched for immune regulatory signaling biomolecules compared to conventional 2D glioblastoma cell systems., Front Immunol, PMID 38726003

PXD047325 Dataset with its publication pending (from PRIDE)
Dataset title: MCT1-governed pyruvate metabolism is essential for antibody class-switch recombination through H3K27 acetylation
Possible reference: Chi, W. et al. (2024) MCT1-governed pyruvate metabolism is essential for antibody class-switch recombination through H3K27 acetylation., Nat Commun, PMID 38167945

PXD047314 Dataset with its publication pending (from iProX)
Dataset title: Application of Label-Free Quantitative Proteomics in saliva of periodontitis
Possible reference: Bostanci, N. et al. (2018) Targeted Proteomics Guided by Label-free Quantitative Proteome Analysis in Saliva Reveal Transition Signatures from Health to Periodontal Disease., Mol Cell Proteomics, PMID 29610270

PXD047312 Dataset with its publication pending (from iProX)
Dataset title: Comparative proteomic analysis of vancomycin-sensitive and vancomycin-intermediate resistant Staphylococcus aureus
Possible reference: Hu, J. et al. (2024) Comparative proteomic analysis of vancomycin-sensitive and vancomycin-intermediate resistant Staphylococcus aureus., Eur J Clin Microbiol Infect Dis, PMID 37985551

PXD047283 Dataset with its publication pending (from jPOST)
Dataset title: Subcutaneous white adipose tissue independently regulates burn-induced hypermetabolism via immune-adipose crosstalk
Possible reference: Knuth, CM. et al. (2024) Subcutaneous white adipose tissue independently regulates burn-induced hypermetabolism via immune-adipose crosstalk., Cell Rep, PMID 38117653

PXD047271 Dataset with its publication pending (from PRIDE)
Dataset title: Changes in FUS interactome in motor neurons upon ALS-related mutation
Possible reference: Alirzayeva, H. et al. (2024) ALS-FUS mutations cause abnormal PARylation and histone H1.2 interaction, leading to pathological changes., Cell Rep, PMID 39167487

PXD047266 Dataset with its publication pending (from PRIDE)
Dataset title: High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells
Possible reference: Rega, C. et al. (2025) High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells., Nat Commun, PMID 40089461

PXD047265 Dataset with its publication pending (from PRIDE)
Dataset title: EEF1D stabilized by SRSF9 promotes colorectal cancer via enhancing the proliferation and metastasis
Possible reference: Wang, R. et al. (2024) EEF1D stabilized by SRSF9 promotes colorectal cancer via enhancing the proliferation and metastasis., Int J Cancer, PMID 38771720

PXD047252 Dataset with its publication pending (from PRIDE)
Dataset title: Tracing active members in microbial communities by BONCAT and click chemistry-based enrichment of newly synthesised proteins
Possible reference: Hellwig, P. et al. (2024) Tracing active members in microbial communities by BONCAT and click chemistry-based enrichment of newly synthesized proteins., ISME Commun, PMID 39736848

PXD047242 Dataset with its publication pending (from jPOST)
Dataset title: Site-specific SUMOylation proteomics in Arabidopsis
Possible reference: Sang, T. et al. (2024) Highly sensitive site-specific SUMOylation proteomics in Arabidopsis., Nat Plants, PMID 39294263

PXD047235 Bhosale SD, Moulder R, Suomi T, et al (2024) Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk. iScience 110048. https://doi.org/https://doi.org/10.1016/j.isci.2024.110048 (from PanoramaPublic)
Dataset title: Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk
Possible reference: Bhosale, SD. et al. (2024) Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk., iScience, PMID 38883825

PXD047226 Dataset with its publication pending (from PRIDE)
Dataset title: VAP spatially stabilizes dendritic mitochondria to locally support synaptic plasticity
Possible reference: Bapat, O. et al. (2024) VAP spatially stabilizes dendritic mitochondria to locally support synaptic plasticity., Nat Commun, PMID 38177103

PXD047219 no publication (from MassIVE)
Dataset title: Computationally designed sensors detect Ras activity and signaling effectors at subcellular resolution
Possible reference: Zhang, JZ. et al. (2024) Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution., Nat Biotechnol, PMID 38273065

PXD047183 Dataset with its publication pending (from PRIDE)
Dataset title: A noncanonical role of roX RNAs in autosomal epigenetic repression
Possible reference: Li, J. et al. (2025) A noncanonical role of roX RNAs in autosomal epigenetic repression., Nat Commun, PMID 39747148

PXD047178 Dataset with its publication pending (from PRIDE)
Dataset title: DPP8/9 processing of human AK2 unmasks an IAP binding motif
Possible reference: Lapacz, KJ. et al. (2025) DPP8/9 processing of human AK2 unmasks an IAP binding motif., EMBO Rep, PMID 40312560

PXD047173 Dataset with its publication pending (from PRIDE)
Dataset title: An inhibitory segment within G-patch activators tunes Prp43-ATPase activity during ribosome assembly
Possible reference: Portugal-Calisto, D. et al. (2024) An inhibitory segment within G-patch activators tunes Prp43-ATPase activity during ribosome assembly., Nat Commun, PMID 39578461

PXD047170 Dataset with its publication pending (from jPOST)
Dataset title: Site-specific SUMOylation proteomics in Arabidopsis
Possible reference: Sang, T. et al. (2024) Highly sensitive site-specific SUMOylation proteomics in Arabidopsis., Nat Plants, PMID 39294263

PXD047167 Dataset with its publication pending (from PRIDE)
Dataset title: A single gene mutation underpins metabolic adaptation and acquisition of filamentous competence in the emerging fungal pathogen Candida auris
Possible reference: Deng, Y. et al. (2024) A single gene mutation underpins metabolic adaptation and acquisition of filamentous competence in the emerging fungal pathogen Candida auris., PLoS Pathog, PMID 38976759

PXD047144 no publication (from MassIVE)
Dataset title: Hepatic SerpinA1 Improves Energy and Glucose Metabolism through Regulation of Preadipocyte Proliferation and UCP1 Expression
Possible reference: Okagawa, S. et al. (2024) Hepatic SerpinA1 improves energy and glucose metabolism through regulation of preadipocyte proliferation and UCP1 expression., Nat Commun, PMID 39532838

PXD047124 Dataset with its publication pending (from PRIDE)
Dataset title: Post-translational regulation of photosynthetic activity via the TOR kinase in plants.
Possible reference: D'Alessandro, S. et al. (2024) Posttranslational regulation of photosynthetic activity via the TOR kinase in plants., Sci Adv, PMID 38896607

PXD047109 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring the secretome of Corynebacterium glutamicum ATCC 13032
Possible reference: Balasubramanian, S. et al. (2024) Exploring the secretome of Corynebacterium glutamicum ATCC 13032., Front Bioeng Biotechnol, PMID 38415189

PXD047097 Dataset with its publication pending (from PRIDE)
Dataset title: The long-chain flavodoxin FldX1 improves the biodegradation of 4-hydroxyphenylacetate and 3-hydroxyphenylacetate and counteracts the oxidative stress associated to aromatic catabolism in Paraburkholderia xenovorans
Possible reference: Rodr�guez-Castro, L. et al. (2024) The long-chain flavodoxin FldX1 improves the biodegradation of 4-hydroxyphenylacetate and 3-hydroxyphenylacetate and counteracts the oxidative stress associated to aromatic catabolism in Paraburkholderia xenovorans., Biol Res, PMID 38561836

PXD047087 Dataset with its publication pending (from jPOST)
Dataset title: Comprehensive identification of Ubiquitin-like 3 (UBL3)-interacting proteins in mouse brain
Possible reference: Ageta, H. et al. (2024) Comprehensive identification of ubiquitin-like 3 (UBL3)-interacting proteins in the mouse brain., Mol Brain, PMID 39148092

PXD047081 Dataset with its publication pending (from iProX)
Dataset title: Activity-based protein profiling reveals Hydroxysafflor yellow A binds to malate dehydrogenase 1 against myocardial ischemia reperfusion injury by maintaining mitochondrial functional homeostasis
Possible reference: Zhao, F. et al. (2025) Hydroxysafflor yellow A ameliorates myocardial ischemia/reperfusion injury by promoting MDH1-mediated mitochondrial metabolic homeostasis., Phytomedicine, PMID 40513321

PXD047067 Dataset with its publication pending (from iProX)
Dataset title: A skin organoid-based infection platform identifies an inhibitor specific for HFMD
Possible reference: Li, J. et al. (2025) A skin organoid-based infection platform identifies an inhibitor specific for HFMD., Nat Commun, PMID 40082449

PXD047065 Dataset with its publication pending (from PRIDE)
Dataset title: TIHAMAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics Analysis
Possible reference: Chen, CW. et al. (2024) TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and�N-glycoproteomics., Mol Cell Proteomics, PMID 38608839

PXD047045 Dataset with its publication pending (from PRIDE)
Dataset title: Novel brain-penetrant inhibitor of G9a methylase blocks Alzheimer’s disease proteopathology for precision medication
Possible reference: Xie, L. et al. (2023) Novel brain-penetrant inhibitor of G9a methylase blocks Alzheimer's disease proteopathology for precision medication., medRxiv, PMID 37961307

PXD047042 no publication (from MassIVE)
Dataset title: In vivo mapping of protein-protein interactions of schizophrenia risk factors generates an interconnected disease network.
Possible reference: McClatchy, DB. et al. (2023) In vivo mapping of protein-protein interactions of schizophrenia risk factors generates an interconnected disease network., bioRxiv, PMID 38168169

PXD047034 no publication (from MassIVE)
Dataset title: Calorie restriction and rapamycin distinctly restore non-canonical ORF translation in the muscles of aging mice
Possible reference: Mittal, N. et al. (2024) Calorie restriction and rapamycin distinctly restore non-canonical ORF translation in the muscles of aging mice., NPJ Regen Med, PMID 39300171

PXD047029 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted mass spectrometry analyses of somatic mutations in colorectal cancer specimens using differential ion mobility
Possible reference: Wu, Z. et al. (2024) Targeted Mass Spectrometry Analyses of Somatic Mutations in Colorectal Cancer Specimens Using Differential Ion Mobility., J Proteome Res, PMID 38153093

PXD047024 Dataset with its publication pending (from PRIDE)
Dataset title: An Immunological Synapse Formation Between T Regulatory Cells and Cancer-Associated Fibroblasts Promotes Tumour Development
Possible reference: Varveri, A. et al. (2024) Immunological synapse formation between T regulatory cells and cancer-associated fibroblasts promotes tumour development., Nat Commun, PMID 38862534

PXD047022 Dataset with its publication pending (from PRIDE)
Dataset title: A common gene signature of the right ventricle in failing rat and human hearts
Possible reference: Deshpande, A. et al. (2021) SH3-Binding Glutamic Acid Rich-Deficiency Augments Apoptosis in Neonatal Rat Cardiomyocytes., Int J Mol Sci, PMID 34681711

PXD047009 Dataset with its publication pending (from PRIDE)
Dataset title: Exosomes define a local and systemic communication network in healthy pancreas and in pancreatic ductal adenocarcinoma
Possible reference: Adem, B. et al. (2024) Exosomes define a local and systemic communication network in healthy pancreas and pancreatic ductal adenocarcinoma., Nat Commun, PMID 38383468

PXD046999 Dataset with its publication pending (from PRIDE)
Dataset title: Spatial characterization and stratification of colorectal adenomas by Deep Visual Proteomics
Possible reference: Kabatnik, S. et al. (2024) Spatial characterization and stratification of colorectal adenomas by deep visual proteomics., iScience, PMID 39252972

PXD046976 Dataset with its publication pending (from PRIDE)
Dataset title: Differential contributions of interferon classes to driving host inflammatory responses and restricting virus progeny production
Possible reference: Lum, KK. et al. (2024) Differential Contributions of Interferon Classes to Host Inflammatory Responses and Restricting Virus Progeny Production., J Proteome Res, PMID 38564653

PXD046971 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphorylation regulates viral biomolecular condensates to promote infectious progeny production
Possible reference: Grams, N. et al. (2024) Phosphorylation regulates viral biomolecular condensates to promote infectious progeny production., EMBO J, PMID 38177504

PXD046963 Dataset with its publication pending (from PRIDE)
Dataset title: KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism
Possible reference: Yheskel, M. et al. (2024) KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons., Nucleic Acids Res, PMID 38597673

PXD046959 no publication (from MassIVE)
Dataset title: Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics-2
Possible reference: Lee, CY. et al. (2024) Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics., Mol Syst Biol, PMID 38177929

PXD046955 Dataset with its publication pending (from PRIDE)
Dataset title: Human SKI component SKIV2L regulates telomeric DNA-RNA hybrids and prevents telomere fragility
Possible reference: Herrera-Moyano, E. et al. (2024) Human SKI component SKIV2L regulates telomeric DNA-RNA hybrids and prevents telomere fragility., iScience, PMID 39493885

PXD046941 Dataset with its publication pending (from PRIDE)
Dataset title: Landscape of protein-protein-interactions during hepatitis C virus assembly and release
Possible reference: Matthaei, A. et al. (2024) Landscape of protein-protein interactions during hepatitis C virus assembly and release., Microbiol Spectr, PMID 38230952

PXD046931 Dataset with its publication pending (from iProX)
Dataset title: PARP5A and RNF146 phase separation restrains RIPK1-dependent necroptosis
Possible reference: Hou, S. et al. (2024) PARP5A and RNF146 phase separation restrains RIPK1-dependent necroptosis., Mol Cell, PMID 38272024

PXD046926 Dataset with its publication pending (from PRIDE)
Dataset title: Cryo-EM structure of the extracellular domain of murine Thrombopoietin Receptor in complex with Thrombopoietin.
Possible reference: Sarson-Lawrence, KTG. et al. (2024) Cryo-EM structure of the extracellular domain of murine Thrombopoietin Receptor in complex with Thrombopoietin., Nat Commun, PMID 38326297

PXD046925 no publication (from MassIVE)
Dataset title: Cross-talks between Metabolic and Translational Controls during Beige Adipocyte Differentiation
Possible reference: Youn, D. et al. (2025) Cross-talks between Metabolic and Translational Controls during Beige Adipocyte Differentiation., Nat Commun, PMID 40204764

PXD046907 Dataset with its publication pending (from jPOST)
Dataset title: Acute exposure to ultraviolet radiation targets proteins involved in collagen fibrillogenesis
Possible reference: Platt, CI. et al. (2024) Acute exposure to ultraviolet radiation targets proteins involved in collagen fibrillogenesis., Front Physiol, PMID 38559576

PXD046904 Dataset with its publication pending (from PRIDE)
Dataset title: MeCP2 Represses the Activity of Topoisomerase IIÎ² in Long Neuronal Genes
Possible reference: Nettles, SA. et al. (2023) MeCP2 represses the activity of topoisomerase IIβ in long neuronal genes., Cell Rep, PMID 38096051

PXD046881 Dataset with its publication pending (from iProX)
Dataset title: Quantitative proteomics based on TMT revealed the response of PK15 cells infected PEDV wild strain
Possible reference: Lv, Y. et al. (2024) Quantitative proteomics based on TMT revealed the response of PK15�cells infected PEDV wild strain., Microb Pathog, PMID 38142905

PXD046869 no publication (from MassIVE)
Dataset title: Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity
Possible reference: Yu, Y. et al. (2024) Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity., Elife, PMID 38240316

PXD046866 Rocio Prisby, Alessandra Luchini, Lance A. Liotta, Caroline Solazzo. Wheat-based glues in conservation and cultural heritage: (dis)solving the proteome of flour and starch pastes and their adhering properties. https://doi.org/10.1021/acs.jproteome.3c00804 (from MassIVE)
Dataset title: Wheat-based glues in conservation and cultural heritage: (dis)solving the proteome of flour and starch pastes and their adhering properties
Possible reference: Prisby, R. et al. (2024) Wheat-Based Glues in Conservation and Cultural Heritage: (Dis)solving the Proteome of Flour and Starch Pastes and Their Adhering Properties., J Proteome Res, PMID 38574199

PXD046826 no publication (from MassIVE)
Dataset title: Multiomics characterization of a less invasive microfluidic-based cell sorting technique
Possible reference: Choudhury, FK. et al. (2024) Multiomics Characterization of a Less Invasive Microfluidic-Based Cell Sorting Technique., J Proteome Res, PMID 38417049

PXD046806 no publication (from MassIVE)
Dataset title: The dilated cardiomyopathy-associated RNA Binding Motif Protein 20 regulates long pre-mRNAs in neurons
Possible reference: Di Bartolomei, G. et al. (2026) Dilated cardiomyopathy-associated RNA-binding motif protein 20 regulates long pre-mRNAs in neurons., Elife, PMID 41524378

PXD046802 Dataset with its publication pending (from PRIDE)
Dataset title: DIA-based phosphoproteomics identifies early phosphorylation events in response to EGTA and mannitol in Arabidopsis
Possible reference: Sang, T. et al. (2024) DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis., Mol Cell Proteomics, PMID 38901673

PXD046800 Dataset with its publication pending (from iProX)
Dataset title: Lactylome and Proteome of Human Hypertrophic Scar Tissues
Possible reference: Zhang, E. et al. (2024) Integrative Analysis of Lactylome and Proteome of Hypertrophic Scar To Identify Pathways or Proteins Associated with Disease Development., J Proteome Res, PMID 39012622

PXD046793 Dataset with its publication pending (from PRIDE)
Dataset title: LPS-Stimulated Mouse Macrophage RNA Binding Protein Domain Enrichment and Analysis
Possible reference: Li, Y. et al. (2024) Fibroblastic reticular cell-derived exosomes are a promising therapeutic approach for septic acute kidney injury., Kidney Int, PMID 38163633

PXD046762 Dataset with its publication pending (from iProX)
Dataset title: Proteomic and Phosphoproteomic of Cipangopaludina chinensis
Possible reference: Liu, G. et al. (2024) Proteomics and phosphoproteomics reveal novel proteins involved in Cipangopaludina chinensis carcasses., Front Chem, PMID 39268005

PXD046759 Dataset with its publication pending (from PRIDE)
Dataset title: Role of the Yersinia pestis Phospholipase D (Ymt) in the Initial Aggregation Step of Biofilm Formation in the Flea
Possible reference: Jarrett, CO. et al. (2024) Role of the Yersinia pestis phospholipase D (Ymt) in the initial aggregation step of biofilm formation in the flea., mBio, PMID 38722159

PXD046748 Dataset with its publication pending (from PRIDE)
Dataset title: Histone modification profile of Pristionchus pacificus
Possible reference: Werner, MS. et al. (2018) Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation., Genome Res, PMID 30232198

PXD046738 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling comparison for plasma from patients with acute ischemic stroke under rt-PA treatment
Possible reference: Bateman, RM. et al. (2016) 36th International Symposium on Intensive Care and Emergency Medicine : Brussels, Belgium. 15-18 March 2016., Crit Care, PMID 27885969

PXD046721 no publication (from MassIVE)
Dataset title: The ALPHA Phase 1 Study: Pulmonary ArteriaL Hypertension Treated with CardiosPHere-Derived Allogeneic Stem Cells
Possible reference: Lewis, MI. et al. (2024) The ALPHA phase 1 study: pulmonary ArteriaL hypertension treated with CardiosPHere-Derived allogeneic stem cells., EBioMedicine, PMID 38092579

PXD046716 Dataset with its publication pending (from iProX)
Dataset title: Local Delivery of Dual Stem Cell-derived Exosomes using an Electrospun Nanofibrous Platform for the Treatment of Traumatic Brain Injury
Possible reference: Li, J. et al. (2024) Local Delivery of Dual Stem Cell-Derived Exosomes Using an Electrospun Nanofibrous Platform for the Treatment of Traumatic Brain Injury., ACS Appl Mater Interfaces, PMID 38980910

PXD046701 Dataset with its publication pending (from PRIDE)
Dataset title: Insights from multi-omic modelling of neurodegeneration in Xeroderma Pigmentosum using an induced pluripotent stem cell system
Possible reference: Badja, C. et al. (2024) Insights from multi-omic modeling of neurodegeneration in xeroderma pigmentosum using an induced pluripotent stem cell system., Cell Rep, PMID 38805398

PXD046689 Dataset with its publication pending (from iProX)
Dataset title: MANF facilitates breast cancer cell survival under glucose starvation via PRKN-mediated mitophagy regulation
Possible reference: Xiong, Z. et al. (2025) MANF facilitates breast cancer cell survival under glucose-starvation conditions via PRKN-mediated mitophagy regulation., Autophagy, PMID 39147386

PXD046687 Dataset with its publication pending (from iProX)
Dataset title: Expression of stress responsive genes enables Limosilactobacillus reuteri
Possible reference: Josephs-Spaulding, J. et al. (2024) Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning., mSystems, PMID 38349131

PXD046683 Dataset with its publication pending (from iProX)
Dataset title: Comparative proteomics and N-glycoproteomics reveal the effects of different plasma protein enrichment technologies
Possible reference: Tian, H. et al. (2025) Comparative Proteomics and N-Glycoproteomics Reveal the Effects of Different Plasma Protein Enrichment Technologies., J Proteome Res, PMID 39668702

PXD046680 Dataset with its publication pending (from iProX)
Dataset title: Mapping start codons of small open reading frames by N-terminomics approach
Possible reference: Peng, M. et al. (2024) Mapping Start Codons of Small Open Reading Frames by N-Terminomics Approach., Mol Cell Proteomics, PMID 39419446

PXD046676 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling comparison for plasma from patients with acute ischemic stroke under rt-PA treatment
Possible reference: Bateman, RM. et al. (2016) 36th International Symposium on Intensive Care and Emergency Medicine : Brussels, Belgium. 15-18 March 2016., Crit Care, PMID 27885969

PXD046668 no publication (from MassIVE)
Dataset title: A mammalian-specific Alex3/Galphaq protein complex regulating mitochondrial dynamics, dendritic complexity, and neuronal survival
Possible reference: Izquierdo-Villalba, I. et al. (2024) A mammalian-specific Alex3/Gαq protein complex regulates mitochondrial trafficking, dendritic complexity, and neuronal survival., Sci Signal, PMID 38320000

PXD046662 Dataset with its publication pending (from PRIDE)
Dataset title: Chloroquine Target Identification with MS-CETSA
Possible reference: Gao, P. et al. (2022) Identification of antimalarial targets of chloroquine by a combined deconvolution strategy of ABPP and MS-CETSA., Mil Med Res, PMID 35698214

PXD046646 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Landscape of Endoplasmic Reticulum Remodeling During Neurogenesis via Combinatorial Selective ER-phagy
Possible reference: Hoyer, MJ. et al. (2023) Combinatorial selective ER-phagy remodels the ER during neurogenesis., bioRxiv, PMID 37425907

PXD046642 Dataset with its publication pending (from PRIDE)
Dataset title: MK4815 Target Identification with MS-CETSA
Possible reference: Wirjanata, G. et al. (2024) Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development., Cell Chem Biol, PMID 38593807

PXD046638 Dataset with its publication pending (from PRIDE)
Dataset title: Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough
Possible reference: Marbehan, X. et al. (2024) Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough., Front Microbiol, PMID 38463485

PXD046637 Dataset with its publication pending (from PRIDE)
Dataset title: Proteogenomic Characterization Reveals Tumorigenesis and Progression of Lung Adenocarcinoma Manifested as Subsolid Nodules
Possible reference: Su, H. et al. (2025) Proteogenomic characterization reveals tumorigenesis and progression of lung cancer manifested as subsolid nodules., Nat Commun, PMID 40069142

PXD046631 Dataset with its publication pending (from PRIDE)
Dataset title: Lysine lactylation of mouse ischemia reperfusion heart
Possible reference: Wang, L. et al. (2025) Serpina3k lactylation protects from cardiac ischemia reperfusion injury., Nat Commun, PMID 39856050

PXD046597 no publication (from MassIVE)
Dataset title: Itaconate modulates immune responses via inhibition of peroxiredoxin 5
Possible reference: Paulenda, T. et al. (2025) Itaconate modulates immune responses via inhibition of peroxiredoxin 5., Nat Metab, PMID 40251412

PXD046596 Dataset with its publication pending (from PRIDE)
Dataset title: Spatial proteomics of skeletal muscle using thin cryosections reveals metabolic adaption at the muscle-tendon transition zone
Possible reference: Schmidt, L. et al. (2024) Spatial proteomics of skeletal muscle using thin cryosections reveals metabolic adaptation at the muscle-tendon transition zone., Cell Rep, PMID 38900641

PXD046590 no publication (from MassIVE)
Dataset title: Human Keratinocyte Responses to Woodsmoke
Possible reference: Lin, LW. et al. (2021) Woodsmoke Extracts Cross-Link Proteins and Induce Cornified Envelope Formation without Stimulating Keratinocyte Terminal Differentiation., Toxicol Sci, PMID 34086961

PXD046575 Dataset with its publication pending (from PRIDE)
Dataset title: MMV665806 Target Identification with MS-CETSA
Possible reference: Wirjanata, G. et al. (2024) Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development., Cell Chem Biol, PMID 38593807

PXD046571 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of the ubiquitin-modified proteome identifies novel host determinants of Kaposi’s sarcoma herpesvirus lytic reactivation
Possible reference: Causey, A. et al. (2025) Analysis of the ubiquitin-modified proteome identifies novel host factors in Kaposi's sarcoma herpesvirus lytic reactivation., J Virol, PMID 39636148

PXD046569 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic profiling of extracellular vesicles of the Lactiplantibacillus plantarum strains
Possible reference: Chernova, OA. et al. (2024) Structure of Extracellular Vesicles and Their Effect on Bacterial Biofilms Change with the Development of Antibiotic Resistance in the Probiotic Strain Lactiplantibacillus plantarum 8p-a3., Dokl Biol Sci, PMID 39400899

PXD046538 Dataset with its publication pending (from PRIDE)
Dataset title: MMV000848 Target Identification with MS-CETSA
Possible reference: Wirjanata, G. et al. (2024) Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development., Cell Chem Biol, PMID 38593807

PXD046501 Dataset with its publication pending (from PRIDE)
Dataset title: Poss_Pronobis BioID2 Zebrafish Interaction Proteomics
Possible reference: Pronobis, MI. et al. (2021) In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration., Elife, PMID 33764296

PXD046498 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of P granules Z granules and Mutator foci in C.elegans
Possible reference: Suen, KM. et al. (2023) Expansion microscopy reveals subdomains in C. elegans germ granules., Life Sci Alliance, PMID 36750365

PXD046457 Dataset with its publication pending (from PRIDE)
Dataset title: A SIRT7-dependent acetylation switch regulates early B-cell differentiation and lineage commitment through PAX5
Possible reference: Gamez-Garcia, A. et al. (2024) A SIRT7-dependent acetylation switch regulates early B cell differentiation and lineage commitment through Pax5., Nat Immunol, PMID 39424985

PXD046448 Dataset with its publication pending (from PRIDE)
Dataset title: The CDK Pho85 inhibits Whi7 Start repressor to promote cell cycle entry in budding yeast
Possible reference: Ros-Carrero, C. et al. (2024) The CDK Pho85 inhibits Whi7 Start repressor to promote cell cycle entry in budding yeast., EMBO Rep, PMID 38233717

PXD046445 Dataset with its publication pending (from PRIDE)
Dataset title: (N)1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting
Possible reference: Mulroney, TE. et al. (2024) N1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting., Nature, PMID 38057663

PXD046422 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of GITR and OX40 signaling complexes
Possible reference: Zhang, Y. et al. (2026) [SOX4 drives the differentiation of CD4+T cells toward an immunosuppressive phenotype]., Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi, PMID 41620962

PXD046414 Dataset with its publication pending (from PRIDE)
Dataset title: Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics
Possible reference: Delhaye, L. et al. (2024) Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics., Cell Rep Methods, PMID 38986614

PXD046413 Dataset with its publication pending (from PRIDE)
Dataset title: Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics
Possible reference: Delhaye, L. et al. (2024) Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics., Cell Rep Methods, PMID 38986614

PXD046412 Dataset with its publication pending (from PRIDE)
Dataset title: Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics
Possible reference: Delhaye, L. et al. (2024) Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics., Cell Rep Methods, PMID 38986614

PXD046411 no publication (from MassIVE)
Dataset title: Mapping the immunopeptidome of several SARS-CoV-2 antigens across common HLA haplotypes
Possible reference: Braun, A. et al. (2024) Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes., Nat Commun, PMID 39214998

PXD046409 Dataset with its publication pending (from iProX)
Dataset title: Integrated transcriptomics, proteomics and functional analysis to characterize the tissue-specific small extracellular vesicle network of breast cancer
Possible reference: Shen, L. et al. (2023) Integrated transcriptomics, proteomics, and functional analysis to characterize the tissue-specific small extracellular vesicle network of breast cancer., MedComm (2020), PMID 38053815

PXD046408 Dataset with its publication pending (from iProX)
Dataset title: Multi-omic Analyses Identified a Novel Biomarker in Abnormal Uterine Bleeding with Ovulatory Dysfunction
Possible reference: Zhao, Y. et al. (2024) Multi-omic analyses identified SFRP4 as a novel biomarker in abnormal uterine bleeding with ovulatory dysfunction., Heliyon, PMID 39286067

PXD046405 Dataset with its publication pending (from PRIDE)
Dataset title: Position-specific N- and O-glycosylation of the reactive centre loop impacts neutrophil elastase-mediated proteolysis of corticosteroid-binding globulin
Possible reference: Chernykh, A. et al. (2024) Position-specific N- and O-glycosylation of the reactive center loop impacts neutrophil elastase-mediated proteolysis of corticosteroid-binding globulin., J Biol Chem, PMID 38042488

PXD046404 Dataset with its publication pending (from iProX)
Dataset title: In-depth Profiling of 4-hydroxy-2-nonenal Modification via Reversible Thiazolidine Chemistry
Possible reference: Wang, J. et al. (2024) In-Depth Profiling of 4-Hydroxy-2-nonenal Modification via Reversible Thiazolidine Chemistry., Anal Chem, PMID 38502245

PXD046385 Dataset with its publication pending (from PRIDE)
Dataset title: Ribosomal Protein SA (RPSA) is required for localized translation and sarcomere maintenance
Possible reference: Haddad, R. et al. (2024) Localized translation and sarcomere maintenance requires ribosomal protein SA in mice., J Clin Invest, PMID 38743494

PXD046382 Dataset with its publication pending (from PRIDE)
Dataset title: Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology
Possible reference: Zhu, Y. et al. (2024) Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies., Nat Commun, PMID 38632225

PXD046380 Dataset with its publication pending (from PRIDE)
Dataset title: Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates ageing in mice
Possible reference: Sirozh, O. et al. (2024) Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates aging in mice., Mol Cell, PMID 38521064

PXD046358 Dataset with its publication pending (from PRIDE)
Dataset title: The virulence regulator VirB from Shigella flexneri uses a CTPdependent switch mechanism to activate gene expression
Possible reference: Jakob, S. et al. (2024) The virulence regulator VirB from Shigella flexneri uses a CTP-dependent switch mechanism to activate gene expression., Nat Commun, PMID 38182620

PXD046355 Dataset with its publication pending (from PRIDE)
Dataset title: Bile proteome reveals biliary regeneration during normothermic preservation of human donor livers
Possible reference: Thorne, AM. et al. (2023) Bile proteome reveals biliary regeneration during normothermic preservation of human donor livers., Nat Commun, PMID 38036513

PXD046354 Dataset with its publication pending (from PRIDE)
Dataset title: Deep Visual Proteomics and spatial transcriptomics reveal the landscape of tumor malignancy in borderline ovarian cancer
Possible reference: Schweizer, L. et al. (2025) Spatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression., Cancer Cell, PMID 40578359

PXD046344 Dataset with its publication pending (from iProX)
Dataset title: SLC4A7 suppresses the oncogenesis of lung adenocarcinoma by reducing lactate transport and protein lactylation
Possible reference: Yan, H. et al. (2025) SLC4A7 suppresses lung adenocarcinoma oncogenesis by reducing lactate transport and protein lactylation., Int J Oncol, PMID 40084702

PXD046335 Dataset with its publication pending (from PRIDE)
Dataset title: The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics
Possible reference: Sherman, DJ. et al. (2023) The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics., bioRxiv, PMID 37873239

PXD046333 Dataset with its publication pending (from PRIDE)
Dataset title: Remodeling of the gastric environment in Helicobacter pylori-induced atrophic gastritis
Possible reference: Shuman, JHB. et al. (2024) Remodeling of the gastric environment in Helicobacter pylori-induced atrophic gastritis., mSystems, PMID 38059647

PXD046319 Dataset with its publication pending (from PRIDE)
Dataset title: Pathogenic phosphorylation of linear ubiquitin machinery causes inflammasome sensor degradation [Human]
Possible reference: Yu, Y. et al. (2025) Pathogenic phosphorylation of linear ubiquitin machinery causes inflammasome sensor degradation., Cell Rep, PMID 40944911

PXD046297 Dataset with its publication pending (from iProX)
Dataset title: BIN2 Inhibition Suppress Cancer Progression and Protect Ovarian function through Downregulating HDAC1 Phosphorylation
Possible reference: Li, CR. et al. (2024) BIN2 inhibition suppress ovarian cancer progression meanwhile protect ovarian function through downregulating HDAC1 and RPS6 phosphorylation respectively., Clin Transl Med, PMID 39412213

PXD046282 Dataset with its publication pending (from jPOST)
Dataset title: Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2 complexes
Possible reference: Homma, MK. et al. (2024) Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexes., Life Sci Alliance, PMID 37907238

PXD046277 Dataset with its publication pending (from PRIDE)
Dataset title: Pharmacological Targeting of Casein Kinase 1Î´ Suppresses Oncogenic NRAS-Driven Melanoma
Possible reference: Wen, Y. et al. (2024) Pharmacological targeting of casein kinase 1δ suppresses oncogenic NRAS-driven melanoma., Nat Commun, PMID 39572526

PXD046264 Dataset with its publication pending (from PRIDE)
Dataset title: Proteolysis Targeting Chimeras With Reduced Off-targets
Possible reference: Nguyen, TM. et al. (2024) Proteolysis-targeting chimeras with reduced off-targets., Nat Chem, PMID 38110475

PXD046263 Dataset with its publication pending (from PRIDE)
Dataset title: Repression of pattern-triggered immunity by the hypoxia response program
Possible reference: Mooney, BC. et al. (2024) Hypoxia represses pattern-triggered immune responses in Arabidopsis., Plant Physiol, PMID 39158089

PXD046260 Dataset with its publication pending (from PRIDE)
Dataset title: Predicting the efficacy of glucocorticoids in pediatric primary immune thrombocytopenia using plasma proteomics
Possible reference: Cao, Q. et al. (2023) Predicting the efficacy of glucocorticoids in pediatric primary immune thrombocytopenia using plasma proteomics., Front Immunol, PMID 38162645

PXD046256 Dataset with its publication pending (from PRIDE)
Dataset title: Global, neuronal, and beta-cell specific deletion of the insulin inhibitory receptor (inceptor) improves glucose homeostasis in diet-induced obese male mice
Possible reference: Grandl, G. et al. (2024) Global, neuronal or β cell-specific deletion of inceptor improves glucose homeostasis in male mice with diet-induced obesity., Nat Metab, PMID 38418586

PXD046243 Dataset with its publication pending (from PRIDE)
Dataset title: A synthetically methylotrophic Escherichia coli as a chassis for bioproduction
Possible reference: Reiter, MA. et al. (2024) A synthetic methylotrophic Escherichia coli as a chassis for bioproduction from methanol., Nat Catal, PMID 38828428

PXD046240 no publication (from MassIVE)
Dataset title: Shotgun proteomics of thyroid carcinoma exosomes: insight into the role of exosomal proteins in carcinogenesis and thyroid homeostasis
Possible reference: Surman, M. et al. (2024) Shotgun proteomics of thyroid carcinoma exosomes - Insight into the role of exosomal proteins in carcinogenesis and thyroid homeostasis., Biochim Biophys Acta Gen Subj, PMID 39025337

PXD046237 Dataset with its publication pending (from PRIDE)
Dataset title: Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling
Possible reference: L� Qu�, K. et al. (2024) Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling., NPJ Syst Biol Appl, PMID 38997321

PXD046229 no publication (from MassIVE)
Dataset title: Fully defined NGN2 neuron protocol reveals diverse signatures of neuronal maturation
Possible reference: Shan, X. et al. (2024) Fully defined NGN2 neuron protocol reveals diverse signatures of neuronal maturation., Cell Rep Methods, PMID 39255791

PXD046219 Dataset with its publication pending (from PRIDE)
Dataset title: Differential Protein Expression and Metabolite Profiling in Glaucoma: Insights from a Multi-Omics Analysis
Possible reference: Mok, JH. et al. (2024) Differential protein expression and metabolite profiling in glaucoma: Insights from a multi-omics analysis., Biofactors, PMID 38818964

PXD046218 Dataset with its publication pending (from jPOST)
Dataset title: Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease
Possible reference: Sakarin, S. et al. (2024) Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease., PeerJ, PMID 38708342

PXD046200 no publication (from MassIVE)
Dataset title: Signatures of Cysteine Oxidation on Structural and Contractile Proteins Are Associated with Physical Performance and Muscle Function in Older Adults
Possible reference: Day, NJ. et al. (2023) Signatures of Cysteine Oxidation on Muscle Structural and Contractile Proteins Are Associated with Physical Performance and Muscle Function in Older Adults: Study of Muscle, Mobility and Aging (SOMMA)., medRxiv, PMID 37986748

PXD046198 Dataset with its publication pending (from iProX)
Dataset title: hnRNPA1 SUMOylation promotes cold hypersensitivity in chronic inflammatory pain by stabilizing TRPA1 mRNA
Possible reference: Zhang, Q. et al. (2023) hnRNPA1 SUMOylation promotes cold hypersensitivity in chronic inflammatory pain by stabilizing TRPA1 mRNA., Cell Rep, PMID 37943660

PXD046186 Dataset with its publication pending (from iProX)
Dataset title: SP3-induced Timeless transcription contributes to cell proliferation and pemetrexed resistance of A549 cells
Possible reference: Tian, P. et al. (2024) SP3-induced Timeless transcription contributes to cell growth of lung adenocarcinoma cells., PLoS One, PMID 38354174

PXD046179 Dataset with its publication pending (from PRIDE)
Dataset title: Clinical Evaluation of Advanced MALDI-TOF MS for Carbapenemase Subtyping in Gram-negative Isolates
Possible reference: Cheon, DH. et al. (2025) Clinical evaluation of advanced MALDI-TOF MS for carbapenemase subtyping in Gram-negative isolates., J Clin Microbiol, PMID 39611795

PXD046164 Dataset with its publication pending (from PRIDE)
Dataset title: Protein-protein interactions of the N-terminal region of PRPF40A
Possible reference: Mart�nez-Lumbreras, S. et al. (2024) Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs., Nat Commun, PMID 38719828

PXD046152 Dataset with its publication pending (from PRIDE)
Dataset title: The plastidial protein acetyltransferase GNAT1 interacts with GNAT2 without affecting state transitions
Possible reference: Br�nje, A. et al. (2024) The Plastidial Protein Acetyltransferase GNAT1 Forms a Complex With GNAT2, yet Their Interaction Is Dispensable for State Transitions., Mol Cell Proteomics, PMID 39349166

PXD046137 no publication (from MassIVE)
Dataset title: Self-assembly of nanofilaments in cyanobacteria for protein co-localization
Possible reference: Zedler, JAZ. et al. (2023) Self-Assembly of Nanofilaments in Cyanobacteria for Protein Co-localization., ACS Nano, PMID 38065569

PXD046120 Dataset with its publication pending (from PRIDE)
Dataset title: The deubiquitinase cofactor UAF1 interacts with USP1 and plays an essential role in spermiogenesis
Possible reference: Wang, Z. et al. (2024) The deubiquitinase cofactor UAF1 interacts with USP1 and plays an essential role in spermiogenesis., iScience, PMID 38591005

PXD046119 Dataset with its publication pending (from PRIDE)
Dataset title: Cryo-EM structures of type IV pili complexed with nanobodies reveal immune escape mechanisms
Possible reference: Fernandez-Martinez, D. et al. (2024) Cryo-EM structures of type IV pili complexed with nanobodies reveal immune escape mechanisms., Nat Commun, PMID 38499587

PXD046118 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of Ngo-B interacting proteins
Possible reference: Parajuli, B. et al. (2020) Identification of a glycan cluster in gp120 essential for irreversible HIV-1 lytic inactivation by a lectin-based recombinantly engineered protein conjugate., Biochem J, PMID 33057580

PXD046107 Dataset with its publication pending (from PRIDE)
Dataset title: Polyamine-dependent metabolic shielding regulates U2 snRNP SF3 subcomplex phosphorylation and alternative splicing
Possible reference: Zabala-Letona, A. et al. (2026) Polyamine-dependent metabolic shielding regulates alternative splicing., Nature, PMID 41535471

PXD046064 no publication (from MassIVE)
Dataset title: PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression
Possible reference: Mittal, P. et al. (2024) PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression., Nat Commun, PMID 39181868

PXD046059 Dataset with its publication pending (from jPOST)
Dataset title: Comparative serum proteome profiling of canine benign prostatic hyperplasia before and after castration
Possible reference: Ploypetch, S. et al. (2023) Comparative Serum Proteome Profiling of Canine Benign Prostatic Hyperplasia before and after Castration., Animals (Basel), PMID 38136890

PXD046050 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome along the dorso-ventral axis of the early Drosophila embryo
Possible reference: Gomez, JM. et al. (2024) Differential regulation of the proteome and phosphoproteome along the dorso-ventral axis of the early Drosophila embryo., Elife, PMID 39221782

PXD046048 Dataset with its publication pending (from jPOST)
Dataset title: OGE sensitizes HCC to cisplatin treatment
Possible reference: Chen, JH. et al. (2024) Aqueous Extracts of Ocimum gratissimum Sensitize Hepatocellular Carcinoma Cells to Cisplatin through BRCA1 Inhibition., Int J Mol Sci, PMID 39125994

PXD046038 no publication (from MassIVE)
Dataset title: (N)1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting
Possible reference: Mulroney, TE. et al. (2024) N1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting., Nature, PMID 38057663

PXD046036 Dataset with its publication pending (from PRIDE)
Dataset title: Localized synthesis of molecular chaperones sustains neuronal proteostasis
Possible reference: Kawasaki, F. et al. (2016) Small heat shock proteins mediate cell-autonomous and -nonautonomous protection in a Drosophila model for environmental-stress-induced degeneration., Dis Model Mech, PMID 27483356

PXD046016 Dataset with its publication pending (from iProX)
Dataset title: NAMPT-targeting PROTAC and nicotinic acid co-administration elicits safe and robust anti-tumor efficacy in NAPRT-deficient pan-cancers
Possible reference: Zhu, X. et al. (2024) NAMPT-targeting PROTAC and nicotinic acid co-administration elicit safe and robust anti-tumor efficacy in NAPRT-deficient pan-cancers., Cell Chem Biol, PMID 38906111

PXD046006 Dataset with its publication pending (from PRIDE)
Dataset title: On-target, dual aminopeptidase inhibition provides cross-species antimalarial activity
Possible reference: Edgar, RCS. et al. (2024) On-target, dual aminopeptidase inhibition provides cross-species antimalarial activity., mBio, PMID 38717141

PXD045996 Dataset with its publication pending (from PRIDE)
Dataset title: p38Î³/Î´ activation alters cardiac electrical activity and predisposes to ventricular arrhythmia
Possible reference: Romero-Becerra, R. et al. (2023) p38γ/δ activation alters cardiac electrical activity and predisposes to ventricular arrhythmia., Nat Cardiovasc Res, PMID 39196141

PXD045982 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of cerebrospinal fluid for development of biomarker in medulloblastoma
Possible reference: Low, SYY. et al. (2020) Cerebrospinal fluid cytokines in metastatic group 3 and 4 medulloblastoma., BMC Cancer, PMID 32539808

PXD045974 Dataset with its publication pending (from iProX)
Dataset title: Proteomics analysis of wheat under combined Fusarium crown rot and drought stress
Possible reference: Gao, Y. et al. (2025) Combined Fusarium Crown Rot and Drought Stress Leads to Overlapping and Unique Proteomic Responses in Wheat., Phytopathology, PMID 40923977

PXD045972 Dataset with its publication pending (from iProX)
Dataset title: Chemical Sensors Detect and Resolve Proteome Aggregation in Peripheral Neuropathy induced by Chemotherapeutic Agents
Possible reference: Wang, Z. et al. (2024) Chemical sensors detect and resolve proteome aggregation in peripheral neuropathy cell model induced by chemotherapeutic agents., Bioorg Chem, PMID 38788365

PXD045943 Dataset with its publication pending (from iProX)
Dataset title: iTRAQ proteomic analysis of peaonia ostii ‘Fengdan’ leaf
Possible reference: Zheng, W. et al. (2024) iTRAQ proteome analysis reveals the underling mechanisms of foliage zinc-spraying to improve photosynthetic capacity and seed yields of Peaonia ostii 'Fengdan'., Plant Physiol Biochem, PMID 39217824

PXD045937 Dataset with its publication pending (from iProX)
Dataset title: Proteomic characteristics of serum from mice with alveolar echinococcosis
Possible reference: Zhang, Q. et al. (2025) Preliminary Proteomic and Metabolomic Analyses Reveal Potential Serum Biomarkers for Identifying Alveolar Echinococcosis in Mice., Vet Sci, PMID 40559802

PXD045934 Dataset with its publication pending (from PRIDE)
Dataset title: RHBDL4-triggered downregulation of COPII adaptor protein TMED7 suppresses TLR4-mediated inflammatory signaling
Possible reference: Knopf, JD. et al. (2024) RHBDL4-triggered downregulation of COPII adaptor protein TMED7 suppresses TLR4-mediated inflammatory signaling., Nat Commun, PMID 38453906

PXD045921 Dataset with its publication pending (from PRIDE)
Dataset title: Immunoproximity biotinylation reveals the axon initial segment proteome
Possible reference: Zhang, W. et al. (2023) Immunoproximity biotinylation reveals the axon initial segment proteome., Nat Commun, PMID 38081810

PXD045910 Dataset with its publication pending (from PRIDE)
Dataset title: Physiological variability in mitochondrial rRNA may predispose to metabolic syndrome
Possible reference: Pecina, P. et al. (2024) Haplotype variability in mitochondrial rRNA predisposes to metabolic syndrome., Commun Biol, PMID 39261587

PXD045899 Dataset with its publication pending (from PRIDE)
Dataset title: The Proteomic Landscape of in vitro Cultured Endothelial Cells across Vascular Beds
Possible reference: Groten, SA. et al. (2024) The proteomic landscape of in vitro cultured endothelial cells across vascular beds., Commun Biol, PMID 39143368

PXD045892 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery of molecular glue degraders via isogenic morphological profiling
Possible reference: Ng, A. et al. (2023) Discovery of Molecular Glue Degraders via Isogenic Morphological Profiling., ACS Chem Biol, PMID 38098458

PXD045890 Dataset with its publication pending (from PRIDE)
Dataset title: Calliactis polypus secreted venom
Possible reference: Smith, HL. et al. (2023) Acontia, a Specialised Defensive Structure, Has Low Venom Complexity in Calliactis polypus., Toxins (Basel), PMID 36977109

PXD045888 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamic proximity based interactome of the transcription factor RELA to identify gene-regulatory networks revealed
Possible reference: Leib, L. et al. (2025) The proximity-based protein interactome and regulatory logics of the transcription factor p65 NF-κB/RELA., EMBO Rep, PMID 39753783

PXD045887 Dataset with its publication pending (from PRIDE)
Dataset title: An Intra-Individual Paired Mass Spectrometry dataset for decoding Solar-Induced Proteomic Changes in Facial Skin
Possible reference: Camillo-Andrade, AC. et al. (2024) Intra-Individual Paired Mass Spectrometry Dataset for Decoding Solar-Induced Proteomic Changes in Facial Skin., Sci Data, PMID 38702328

PXD045855 no publication (from MassIVE)
Dataset title: Integrated Immunopeptidomic and Proteomic Analysis of COVID-19 lung biopsies
Possible reference: Yin, S. et al. (2023) Integrated Immunopeptidomic and Proteomic Analysis of COVID-19 lung biopsies., Front Immunol, PMID 37942334

PXD045852 Dataset with its publication pending (from jPOST)
Dataset title: Comparative proteomic profiling represents an inhibition of protein synthesis to regulate osmotic stress in Nile tilapia (Oreochromis niloticus) embryos
Possible reference: Withyachumnarnkul, B. et al. (2024) Comparative proteomic profiling represents an inhibition of protein synthesis to regulate osmotic stress in Nile tilapia (Oreochromis niloticus) embryos., Comp Biochem Physiol Part D Genomics Proteomics, PMID 38061253

PXD045845 Dataset with its publication pending (from PRIDE)
Dataset title: Structural basis for the modulation of MRP2 activity by phosphorylation and drugs
Possible reference: Mazza, T. et al. (2024) Structural basis for the modulation of MRP2 activity by phosphorylation and drugs., Nat Commun, PMID 38438394

PXD045840 Dataset with its publication pending (from PRIDE)
Dataset title: A framework for performing single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology
Possible reference: Srivastava, AK. et al. (2016) Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016., Hum Genomics, PMID 27294413

PXD045836 Dataset with its publication pending (from PRIDE)
Dataset title: Myeloid-derived grancalcin instigates obesity-induced insulin resistance and metabolic inflammation
Possible reference: Su, T. et al. (2024) Myeloid-derived grancalcin instigates obesity-induced insulin resistance and metabolic inflammation in male mice., Nat Commun, PMID 38167327

PXD045833 Dataset with its publication pending (from PRIDE)
Dataset title: CDS2 is a synthetic lethal target in mesenchymal-like cancers
Possible reference: Arnoldus, T. et al. (2025) Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal-like cancers., Nat Genet, PMID 40615674

PXD045808 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of the DLC3 tumor suppressor by a novel phosphoswitch
Possible reference: Frey, Y. et al. (2024) Regulation of the DLC3 tumor suppressor by a novel phosphoswitch., iScience, PMID 39021807

PXD045798 Dataset with its publication pending (from PRIDE)
Dataset title: Secreted and surface proteome and transcriptome of Opisthorchis felineus
Possible reference: Wong, Y. et al. (2023) Secreted and surface proteome and transcriptome of Opisthorchis felineus., Front Parasitol, PMID 39816815

PXD045787 Dataset with its publication pending (from PRIDE)
Dataset title: A brain-enriched circular RNA controls excitatory neurotransmission and restricts sensitivity to aversive stimuli
Possible reference: Giusti, SA. et al. (2024) A brain-enriched circular RNA controls excitatory neurotransmission and restricts sensitivity to aversive stimuli., Sci Adv, PMID 38787942

PXD045773 no publication (from MassIVE)
Dataset title: Generation and Characterization of a Monoclonal Antibody Against an African Swine Fever Virus Protein Encoded by the A137R Gene
Possible reference: Embury-Hyatt, C. et al. (2023) Generation and characterization of a monoclonal antibody against an African swine fever virus protein encoded by the A137R gene., Front Vet Sci, PMID 37929283

PXD045754 Dataset with its publication pending (from PRIDE)
Dataset title: Neuroligin 2 Governs Synaptic Morphology and Function Through RACK1-Cofilin Signaling in Drosophila
Possible reference: Sun, Y. et al. (2023) Neuroligin 2 governs synaptic morphology and function through RACK1-cofilin signaling in Drosophila., Commun Biol, PMID 37853189

PXD045744 Dataset with its publication pending (from jPOST)
Dataset title: DIAPH1-MFN2 interaction regulates mitochondria-SR/ER contact and modulates ischemic/hypoxic stress
Possible reference: Yepuri, G. et al. (2023) DIAPH1-MFN2 interaction regulates mitochondria-SR/ER contact and modulates ischemic/hypoxic stress., Nat Commun, PMID 37903764

PXD045741 Dataset with its publication pending (from PRIDE)
Dataset title: MmoD regulates soluble methane monooxygenase and methanobactin production in Methylosinus trichosporium OB3b
Possible reference: Semrau, JD. et al. (2013) Methanobactin and MmoD work in concert to act as the 'copper-switch' in methanotrophs., Environ Microbiol, PMID 23682956

PXD045724 Dataset with its publication pending (from iProX)
Dataset title: Label-free quantitative proteomic analysis of skin mucus in Fat Greenling (Hexagrammos otakii)
Possible reference: Wei, X. et al. (2024) Mucous cell histopathology and label-free quantitative proteomic analysis of skin mucus in fat greenling (Hexagrammos otakii) infected with Vibrio harveyi., Fish Shellfish Immunol, PMID 38244822

PXD045719 Dataset with its publication pending (from PRIDE)
Dataset title: Microglial Rac1 is essential for experience-dependent brain plasticity and cognitive performance
Possible reference: Socodato, R. et al. (2023) Microglial Rac1 is essential for experience-dependent brain plasticity and cognitive performance., Cell Rep, PMID 37980559

PXD045715 Dataset with its publication pending (from PRIDE)
Dataset title: Chemoproteomics-guided development of SLC15A4 inhibitors with anti-inflammatory activity
Possible reference: Boeszoermenyi, A. et al. (2023) A conformation-locking inhibitor of SLC15A4 with TASL proteostatic anti-inflammatory activity., Nat Commun, PMID 37863876

PXD045712 Dataset with its publication pending (from PRIDE)
Dataset title: Chemoproteomics-guided development of SLC15A4 inhibitors with anti-inflammatory activity
Possible reference: Boeszoermenyi, A. et al. (2023) A conformation-locking inhibitor of SLC15A4 with TASL proteostatic anti-inflammatory activity., Nat Commun, PMID 37863876

PXD045685 Dataset with its publication pending (from jPOST)
Dataset title: Synergistic effects of polymyxin and vancomycin combinations on carbapenem- and polymyxin-resistant Klebsiella pneumoniae and their molecular characteristics
Possible reference: Nwabor, OF. et al. (2023) Synergistic effects of polymyxin and vancomycin combinations on carbapenem- and polymyxin-resistant Klebsiella pneumoniae and their molecular characteristics., Microbiol Spectr, PMID 37905823

PXD045672 no publication (from MassIVE)
Dataset title: Physiological and Cognitive Changes after Treatments of Cyclophosphamide, Methotrexate, and Fluorouracil: Implications of the Gut Microbiome and Depressive-Like Behavior
Possible reference: Corley, C. et al. (2023) Physiological and cognitive changes after treatments of cyclophosphamide, methotrexate, and fluorouracil: implications of the gut microbiome and depressive-like behavior., Front Neurosci, PMID 37869506

PXD045655 Dataset with its publication pending (from PRIDE)
Dataset title: p53 isoforms have a high aggregation propensity, interact with chaperones and lack binding to p53 interaction partners
Possible reference: Brdar, A. et al. (2025) p53 isoforms have a high aggregation propensity, interact with chaperones and lack binding to p53 interaction partners., Elife, PMID 40928972

PXD045652 Dataset with its publication pending (from PRIDE)
Dataset title: BDNF-TrkB signaling orchestrates the buildup process for local sleep
Possible reference: ElGrawani, W. et al. (2024) BDNF-TrkB signaling orchestrates the buildup process of local sleep., Cell Rep, PMID 39046880

PXD045646 no publication (from MassIVE)
Dataset title: Proteomic analysis of PROSER2 overexpressing cells
Possible reference: Lee, YS. et al. (2024) New Function Annotation of PROSER2 in Pancreatic Ductal Adenocarcinoma., J Proteome Res, PMID 38293943

PXD045622 Dataset with its publication pending (from PRIDE)
Dataset title: USP36 stabilizes nucleolar Snail1 to promote ribosome biogenesis and cancer cell survival upon ribotoxic stress
Possible reference: Qin, K. et al. (2023) USP36 stabilizes nucleolar Snail1 to promote ribosome biogenesis and cancer cell survival upon ribotoxic stress., Nat Commun, PMID 37833415

PXD045618 Dataset with its publication pending (from PRIDE)
Dataset title: SCF dynamics regulated by CAND2
Possible reference: Liu, X. et al. (2018) Cand1-Mediated Adaptive Exchange Mechanism Enables Variation in F-Box Protein Expression., Mol Cell, PMID 29499133

PXD045615 Dataset with its publication pending (from jPOST)
Dataset title: Direct Relationship between Protein Expression and Progeny Yield of HSV-1
Possible reference: Nobe, M. et al. (2025) Direct relationship between protein expression and progeny yield of herpes simplex virus 1., mBio, PMID 40323094

PXD045603 no publication (from MassIVE)
Dataset title: STING induces LUBAC synthesis of linear ubiquitin chains to activate NFkB
Possible reference: Chu, Y. et al. (2021) LUBAC and OTULIN regulate autophagy initiation and maturation by mediating the linear ubiquitination and the stabilization of ATG13., Autophagy, PMID 32543267

PXD045599 Dataset with its publication pending (from PRIDE)
Dataset title: Phototropin-Mediated Signaling Kinase regulation in Chlamydomonas reinhardtii
Possible reference: Yuan, Y. et al. (2025) Phototropin connects blue light perception to starch metabolism in green algae., Nat Commun, PMID 40087266

PXD045586 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphorylation of CFP10 modulates Mycobacterium tuberculosis virulence
Possible reference: Malakar, B. et al. (2023) Phosphorylation of CFP10 modulates Mycobacterium tuberculosis virulence., mBio, PMID 37791794

PXD045565 Dataset with its publication pending (from PRIDE)
Dataset title: Cathepsin B Promotes AÎ² Proteotoxicity by Modulating Aging Regulating Mechanisms
Possible reference: Siddiqui, AA. et al. (2024) Cathepsin B promotes Aβ proteotoxicity by modulating aging regulating mechanisms., Nat Commun, PMID 39362844

PXD045562 Dataset with its publication pending (from PRIDE)
Dataset title: Aspartyl-tRNA synthetase 2 orchestrates iron-sulfur metabolism in hematopoietic stem cells via fine-tuning alternative RNA splicing
Possible reference: Gu, X. et al. (2023) Aspartyl-tRNA synthetase 2 orchestrates iron-sulfur metabolism in hematopoietic stem cells via fine-tuning alternative RNA splicing., Cell Rep, PMID 37838946

PXD045561 Dataset with its publication pending (from PRIDE)
Dataset title: Cathepsin B Promotes AÎ² Proteotoxicity by Modulating Aging Regulating Mechanisms
Possible reference: Siddiqui, AA. et al. (2024) Cathepsin B promotes Aβ proteotoxicity by modulating aging regulating mechanisms., Nat Commun, PMID 39362844

PXD045533 no publication (from MassIVE)
Dataset title: Shared and Distinct Mechanisms of UBA1 Inactivation Across Different Diseases
Possible reference: Collins, JC. et al. (2023) Shared and Distinct Mechanisms of UBA1 Inactivation Across Different Diseases., bioRxiv, PMID 37873213

PXD045531 Dataset with its publication pending (from PRIDE)
Dataset title: Cathepsin B Promotes AÎ² Proteotoxicity by Modulating Aging Regulating Mechanisms
Possible reference: Siddiqui, AA. et al. (2024) Cathepsin B promotes Aβ proteotoxicity by modulating aging regulating mechanisms., Nat Commun, PMID 39362844

PXD045525 Dataset with its publication pending (from PRIDE)
Dataset title: Secreted footprint of pluripotency in Man-13 HeSCs
Possible reference: Lewis, PA. et al. (2024) A secreted proteomic footprint for stem cell pluripotency., PLoS One, PMID 38875182

PXD045519 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic biomarkers in seminal plasma as predictors of reproductive potential in azoospermic men
Possible reference: Fietz, D. et al. (2024) Proteomic biomarkers in seminal plasma as predictors of reproductive potential in azoospermic men., Front Endocrinol (Lausanne), PMID 38654926

PXD045503 Dataset with its publication pending (from iProX)
Dataset title: YBX1 promotes homologous recombination and resistance to platinum-induced stress in ovarian cancer by recognizing m5C modification
Possible reference: Meng, H. et al. (2024) YBX1 promotes homologous recombination and resistance to platinum-induced stress in ovarian cancer by recognizing m5C modification., Cancer Lett, PMID 38880223

PXD045499 no publication (from MassIVE)
Dataset title: Staphylococcus aureus LukAB stem domain unlatching influences toxin oligomerization
Possible reference: Ilmain, JK. et al. (2023) Unlatching of the stem domains in the Staphylococcus aureus pore-forming leukocidin LukAB influences toxin oligomerization., J Biol Chem, PMID 37802313

PXD045489 Dataset with its publication pending (from jPOST)
Dataset title: Tyrosinase-based proximity labeling in living cell and in vivo
Possible reference: Zhu, H. et al. (2024) Tyrosinase-Based Proximity Labeling in Living Cells and In Vivo., J Am Chem Soc, PMID 38445591

PXD045483 Dataset with its publication pending (from PRIDE)
Dataset title: Aged gastrocnemius muscle of mice positively responds to a late onset adapted physical training
Possible reference: Cisterna, B. et al. (2023) Aged gastrocnemius muscle of mice positively responds to a late onset adapted physical training., Front Cell Dev Biol, PMID 38020923

PXD045468 Dataset with its publication pending (from PRIDE)
Dataset title: Tamm-Horsfall protein augments neutrophil NETosis
Possible reference: Mercado-Evans, V. et al. (2024) Tamm-Horsfall protein augments neutrophil NETosis during urinary tract infection., bioRxiv, PMID 38370726

PXD045454 Dataset with its publication pending (from PRIDE)
Dataset title: The interactome of histone deacetylase HDA19 in dark-grown Arabidopsis seedlings
Possible reference: V�lez-Berm�dez, IC. et al. (2023) The interactome of histone deacetylase HDA19 in dark-grown Arabidopsis seedlings., Front Plant Sci, PMID 38078106

PXD045452 Dataset with its publication pending (from PRIDE)
Dataset title: The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa
Possible reference: Le Meillour, L. et al. (2023) The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa., R Soc Open Sci, PMID 38026023

PXD045446 Dataset with its publication pending (from PRIDE)
Dataset title: Structure of transcribing RNA polymerase II-Elongin complex
Possible reference: Chen, Y. et al. (2023) Structure of the transcribing RNA polymerase II-Elongin complex., Nat Struct Mol Biol, PMID 37932450

PXD045423 no publication (from MassIVE)
Dataset title: Dynamics of single-cell protein covariation during epithelial-mesenchymal transition
Possible reference: Khan, S. et al. (2024) Dynamics of single-cell protein covariation during epithelial-mesenchymal transition., bioRxiv, PMID 38187715

PXD045415 Dataset with its publication pending (from PRIDE)
Dataset title: DDA1, a novel factor in transcription-coupled repair, modulates CRL4CSA dynamics at DNA damage-stalled RNA polymerase II
Possible reference: Schiffmacher, DL. et al. (2023) DDA1, a novel factor in transcription-coupled repair, modulates CRL4CSA dynamics at DNA damage-stalled RNA polymerase II., Res Sq, PMID 37886519

PXD045411 Dataset with its publication pending (from PRIDE)
Dataset title: Functional analysis of Cdc20 reveals a critical role of CRY box in mitotic checkpoint signaling
Possible reference: Zhang, Y. et al. (2024) Functional analysis of Cdc20 reveals a critical role of CRY box in mitotic checkpoint signaling., Commun Biol, PMID 38337031

PXD045397 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of Human Epileptic Brain Tissue with DIA
Possible reference: Zhou, N. et al. (2025) Discovering molecular drivers of human epileptogenesis through integrative multi-omics profiling., Neurobiol Dis, PMID 41167490

PXD045393 Dataset with its publication pending (from PRIDE)
Dataset title: Multiple phosphorylation sites regulate the activity of the repressor Mig1 in Candida albicans
Possible reference: Ram�rez-Zavala, B. et al. (2023) Multiple phosphorylation sites regulate the activity of the repressor Mig1 in Candida albicans., mSphere, PMID 38010000

PXD045380 Dataset with its publication pending (from PRIDE)
Dataset title: Human cell surface-AAV interactomes identify LRP6 as blood-brain-barrier transcytosis receptor and immune cytokine IL3 as AAV9 binder
Possible reference: Shay, TF. et al. (2024) Human cell surface-AAV interactomes identify LRP6 as blood-brain barrier transcytosis receptor and immune cytokine IL3 as AAV9 binder., Nat Commun, PMID 39245720

PXD045377 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of granulomas from cattle and pigs naturally infected with Mycobacterium tuberculosis complex by MALDI-MSI
Possible reference: Larenas-Mu�oz, F. et al. (2024) Proteomic analysis of granulomas from cattle and pigs naturally infected with Mycobacterium tuberculosis complex by MALDI imaging., Front Immunol, PMID 39021575

PXD045375 Dataset with its publication pending (from iProX)
Dataset title: Integrating physiological features and proteomic analyses provides new insight in blue/red light-treated moso bamboo (Phyllostachys edulis)
Possible reference: Zhang, C. et al. (2024) Integrating Physiological Features and Proteomic Analyses Provides New Insights in Blue/Red Light-Treated Moso Bamboo (Phyllostachys edulis)., J Agric Food Chem, PMID 38780458

PXD045372 no publication (from MassIVE)
Dataset title: Multiomic analysis of PI3K in Atrial Myopathy
Possible reference: Bass-Stringer, S. et al. (2025) Reduced PI3K(p110α) induces atrial myopathy, and PI3K-related lipids are dysregulated in athletes with atrial fibrillation., J Sport Health Sci, PMID 39826614

PXD045328 Dataset with its publication pending (from PRIDE)
Dataset title: Characterizing the secretome of EGFR mutant lung adenocarcinoma
Possible reference: Luu, JK. et al. (2023) Characterizing the secretome of EGFR mutant lung adenocarcinoma., Front Oncol, PMID 38260835

PXD045311 Dataset with its publication pending (from PRIDE)
Dataset title: A comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans
Possible reference: Guilbaud, A. et al. (2023) Discovery adductomics provides a comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans., Nucleic Acids Res, PMID 37843128

PXD045294 Dataset with its publication pending (from iProX)
Dataset title: Phosphoproteomics of rabbit sperm
Possible reference: Wang, C. et al. (2025) Melatonin regulates rabbit sperm motility and kinematics via the MT1/PKC signaling pathway., Anim Biosci, PMID 40045627

PXD045278 N. Pierre, V.A. Huynh-Thu, D. Baiwir, et al., Serum proteome signatures associated with ileal and colonic ulcers in Crohn's disease, Journal of Proteomics (2023), https://doi.org/10.1016/j.jprot.2024.105199 (from PanoramaPublic)
Dataset title: Serum proteome signatures associated with ileal and colonic ulcers in Crohn's disease
Possible reference: Pierre, N. et al. (2024) Serum proteome signatures associated with ileal and colonic ulcers in Crohn's disease., J Proteomics, PMID 38763457

PXD045272 Dataset with its publication pending (from PRIDE)
Dataset title: Tur1 regulates alternative TSS usage in Cryptococcus
Possible reference: Dang, TTV. et al. (2024) Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1., PLoS Biol, PMID 39052688

PXD045270 Dataset with its publication pending (from PRIDE)
Dataset title: TMT-based quantitative proteomics reveals the protective mechanism of Tenuigenin after experimental intracerebral hemorrhage in mice
Possible reference: Wang, P. et al. (2024) TMT-based quantitative proteomics reveals the protective mechanism of tenuigenin after experimental intracerebral hemorrhage in mice., J Ethnopharmacol, PMID 37739103

PXD045256 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of APLN, APLN-DM-expressing cells
Possible reference: Demoures, B. et al. (2025) Repression of apelin Furin cleavage sites provides antimetastatic strategy in colorectal cancer., EMBO Mol Med, PMID 39962271

PXD045248 Dataset with its publication pending (from iProX)
Dataset title: Prediction of glycopeptide fragment mass spectra by deep learning
Possible reference: Yang, Y. et al. (2024) Prediction of glycopeptide fragment mass spectra by deep learning., Nat Commun, PMID 38503734

PXD045246 Dataset with its publication pending (from PRIDE)
Dataset title: Glycoproteomic and Proteomic analysis of Burkholderia cenocepacia reveals glycosylation events within FliF and MotB are dispensable for motility. - FliF DIA
Possible reference: Lewis, JM. et al. (2024) Glycoproteomic and proteomic analysis of Burkholderia cenocepacia reveals glycosylation events within FliF and MotB are dispensable for motility., Microbiol Spectr, PMID 38709084

PXD045244 Dataset with its publication pending (from jPOST)
Dataset title: Secretomic effects of amyloid beta peptides on Alzheimer’s disease related proteins in differentiated SH-SY5Y neuroblastoma cell
Possible reference: Roytrakul, S. et al. (2024) Secretomic changes of amyloid beta peptides on Alzheimer's disease related proteins in differentiated human SH-SY5Y neuroblastoma cells., PeerJ, PMID 39035166

PXD045240 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of pulmonary arteries and lung tissues from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease
Possible reference: Sakarin, S. et al. (2024) Proteomic analysis of pulmonary arteries and lung tissues from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease., PLoS One, PMID 38181036

PXD045239 Dataset with its publication pending (from PRIDE)
Dataset title: Adaptive design of mRNA-loaded extracellular vesicles for targeted immunotherapy of cancer
Possible reference: Dong, S. et al. (2023) Adaptive design of mRNA-loaded extracellular vesicles for targeted immunotherapy of cancer., Nat Commun, PMID 37857647

PXD045238 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of saliva and salivary gland of Aphis gossypii
Possible reference: Zhao, C. et al. (2025) Identification of candidate host-manipulating effector genes in Aphis gossypii (Hemiptera: Aphididae) using a combination of transcriptome, genome, and differential gene expression data., J Insect Sci, PMID 40435060

PXD045234 Dataset with its publication pending (from PRIDE)
Dataset title: The CASP3 Prodomain Regulates Human Cell Survival and Proliferation
Possible reference: Eskandari, E. et al. (2024) Dependence of human cell survival and proliferation on the CASP3 prodomain., Cell Death Discov, PMID 38321033

PXD045210 Dataset with its publication pending (from jPOST)
Dataset title: Mapping Nanoscale-to-Single Cell Phosphoproteomic Landscape by Chip-DIA
Possible reference: Muneer, G. et al. (2025) Mapping Nanoscale-To-Single-Cell Phosphoproteomic Landscape by Chip-DIA., Adv Sci (Weinh), PMID 39401432

PXD045194 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting metabolic fluxes reverts metastatic transitions in ovarian cancer
Possible reference: Arora, G. et al. (2023) Targeting metabolic fluxes reverts metastatic transitions in ovarian cancer., iScience, PMID 37876796

PXD045192 Dataset with its publication pending (from jPOST)
Dataset title: Hands-free Proteomic Profiling of Urinary Extracellular Vesicles with a High-throughput Automated Workflow
Possible reference: Lee, ZC. et al. (2023) Hands-Free Proteomic Profiling of Urinary Extracellular Vesicles with a High-Throughput Automated Workflow., J Am Soc Mass Spectrom, PMID 37870912

PXD045185 Dataset with its publication pending (from PRIDE)
Dataset title: Structural recognition and stabilization of tyrosine hydroxylase by the J-domain protein DNAJC12
Possible reference: Tai, MDS. et al. (2025) Structural recognition and stabilization of tyrosine hydroxylase by the J-domain protein DNAJC12., Nat Commun, PMID 40113792

PXD045179 Dataset with its publication pending (from PRIDE)
Dataset title: A Non-symmetrical p97 Conformation Favors Ufd1/Npl4 Recruitment
Possible reference: Arie, M. et al. (2024) A non-symmetrical p97 conformation initiates a multistep recruitment of Ufd1/Npl4., iScience, PMID 38947518

PXD045171 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized SWATH Proteomics Workflow
Possible reference: Jin, L. et al. (2023) Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized Sequential Window Acquisition of All THeoretical Mass Spectra (SWATH) Proteomics Workflow., Proteomes, PMID 37873874

PXD045154 Dataset with its publication pending (from PRIDE)
Dataset title: Interferon restores replication fork stability and cell viability in BRCA-defective cells via ISG15
Possible reference: Moro, RN. et al. (2023) Interferon restores replication fork stability and cell viability in BRCA-defective cells via ISG15., Nat Commun, PMID 37783689

PXD045091 Dataset with its publication pending (from iProX)
Dataset title: Proteome analysis of coral Porites lutea holobionts
Possible reference: Tang, X. et al. (2025) Elaborating the molecular characteristics of corals' different tolerance to environmental stress in Sanya Luhuitou based on multi-omics analysis., Front Microbiol, PMID 41568056

PXD045088 Dataset with its publication pending (from PRIDE)
Dataset title: Impaired cAMP Processivity by Phosphodiesterase-Protein Kinase A complexes in Acrodysostosis
Possible reference: Venkatakrishnan, V. et al. (2023) Impaired cAMP processivity by phosphodiesterase-protein kinase A complexes in acrodysostosis., Front Mol Biosci, PMID 37808519

PXD045086 no publication (from MassIVE)
Dataset title: Imidacloprid increases the prevalence of Lotmaria passim in honey bee workers
Possible reference: Erban, T. et al. (2023) Imidacloprid increases the prevalence of the intestinal parasite Lotmaria passim in honey bee workers., Sci Total Environ, PMID 37699488

PXD045058 Dataset with its publication pending (from PRIDE)
Dataset title: Large scale cerebrospinal fluid proteomics reveals biomarkers of Multiple Sclerosis
Possible reference: Bader, JM. et al. (2026) Large-scale proteomics across neurological disorders uncovers biomarker panel and targets in multiple sclerosis., Cell, PMID 41747728

PXD045054 Dataset with its publication pending (from PRIDE)
Dataset title: Conserved immunomodulation and variation in host association by Xanthomonadales commensals in Arabidopsis root microbiota
Possible reference: Ordon, J. et al. (2025) Conserved immunomodulation and variation in host association by Xanthomonadales commensals in Arabidopsis root microbiota., Nat Plants, PMID 39972185

PXD045052 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of eDHFR-tagged proteins with trimethoprim PROTACs
Possible reference: Etersque, JM. et al. (2023) Regulation of eDHFR-tagged proteins with trimethoprim PROTACs., Nat Commun, PMID 37923771

PXD045042 Dataset with its publication pending (from PRIDE)
Dataset title: Adipose triglyceride lipase is a therapeutic target in advanced prostate cancer that promotes metabolic plasticity
Possible reference: Awad, D. et al. (2024) Adipose Triglyceride Lipase Is a Therapeutic Target in Advanced Prostate Cancer That Promotes Metabolic Plasticity., Cancer Res, PMID 38038968

PXD045015 Dataset with its publication pending (from iProX)
Dataset title: FBXO7 Ubiquitinates PRMT1 to Suppress Serine Synthesis and Tumor Growth in Hepatocellular Carcinoma
Possible reference: Luo, L. et al. (2024) FBXO7 ubiquitinates PRMT1 to suppress serine synthesis and tumor growth in hepatocellular carcinoma., Nat Commun, PMID 38839752

PXD045010 Dataset with its publication pending (from PRIDE)
Dataset title: Reduced PRC2 function causes asparaginase resistance in T-ALL by decreasing WNT pathway activity
Possible reference: Lefeivre, T. et al. (2026) Reduced PRC2 function causes asparaginase resistance in T-ALL by decreasing WNT pathway activity., Blood Adv, PMID 41337688

PXD044991 Dataset with its publication pending (from PRIDE)
Dataset title: One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes
Possible reference: Ye, Z. et al. (2024) One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes., Nat Commun, PMID 38503780

PXD044989 Dataset with its publication pending (from iProX)
Dataset title: The resistance mechanism of baohuoside I in Staphylococcus aureus
Possible reference: Wen, Z. et al. (2024) Baohuoside I inhibits virulence of multidrug-resistant Staphylococcus aureus by targeting the transcription Staphylococcus accessory regulator factor SarZ., Phytomedicine, PMID 38810547

PXD044980 Dataset with its publication pending (from PRIDE)
Dataset title: Paternal under and over nutrition modify semen composition and preimplantation embryo developmental kinetics in mice
Possible reference: Morgan, HL. et al. (2024) Paternal undernutrition and overnutrition modify semen composition and preimplantation embryo developmental kinetics in mice., BMC Biol, PMID 39278917

PXD044979 no publication (from MassIVE)
Dataset title: Speg Interactions that Regulate the Stability of Excitation-Contraction Coupling Protein Complexes in Triads and Dyads
Possible reference: Lee, CS. et al. (2023) Speg interactions that regulate the stability of excitation-contraction coupling protein complexes in triads and dyads., Commun Biol, PMID 37709832

PXD044970 Dataset with its publication pending (from PRIDE)
Dataset title: An adaptive biomolecular condensation response is conserved across environmentally divergent species
Possible reference: Kik, SK. et al. (2023) An adaptive biomolecular condensation response is conserved across environmentally divergent species., bioRxiv, PMID 37546789

PXD044965 no publication (from MassIVE)
Dataset title: ALK signalling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition
Possible reference: Boren�s, M. et al. (2024) ALK signaling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition., Proc Natl Acad Sci U S A, PMID 38154064

PXD044950 Dataset with its publication pending (from PRIDE)
Dataset title: Structural basis for the toxicity of Legionella pneumophila effector SidH
Possible reference: Sharma, R. et al. (2023) Structural basis for the toxicity of Legionella pneumophila effector SidH., Nat Commun, PMID 37923743

PXD044925 Dataset with its publication pending (from PRIDE)
Dataset title: Hydrogen Sulfide Coordinates Glucose Metabolism Switch through Destabilizing Tetrameric Pyruvate Kinase M2
Possible reference: Wang, RH. et al. (2024) Hydrogen sulfide coordinates glucose metabolism switch through destabilizing tetrameric pyruvate kinase M2., Nat Commun, PMID 39198443

PXD044917 Dataset with its publication pending (from iProX)
Dataset title: Lymphatic platelet thrombosis inhibits fracture healing by decreased lymphatic transporting DAMPs in mice
Possible reference: Zheng, Y. et al. (2025) Lymphatic platelet thrombosis limits bone repair by precluding lymphatic transporting DAMPs., Nat Commun, PMID 39827193

PXD044915 Dataset with its publication pending (from PRIDE)
Dataset title: Ustilago maydis PR-1-like protein has evolved two distinct domains for dual virulence activities
Possible reference: Lin, YH. et al. (2023) Ustilago maydis PR-1-like protein has evolved two distinct domains for dual virulence activities., Nat Commun, PMID 37716995

PXD044911 Dataset with its publication pending (from PRIDE)
Dataset title: pH-gated nanoparticles selectively regulate lysosomal function of tumour-associated macrophages for cancer immunotherapy
Possible reference: Tang, M. et al. (2023) pH-gated nanoparticles selectively regulate lysosomal function of tumour-associated macrophages for cancer immunotherapy., Nat Commun, PMID 37735462

PXD044898 Dataset with its publication pending (from PRIDE)
Dataset title: DUSP8 dephosphorylates Pur-alpha
Possible reference: Chuang, HC. et al. (2023) DUSP8 induces TGF-β-stimulated IL-9 transcription and Th9-mediated allergic inflammation by promoting nuclear export of Pur-α., J Clin Invest, PMID 37909329

PXD044874 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated widely targeted metabolomics and network pharmacology revealed quality disparities between Guizhou and conventional producing areas of Codonopsis Radix
Possible reference: Zhang, K. et al. (2023) Integrated widely targeted metabolomics and network pharmacology revealed quality disparities between Guizhou and conventional producing areas of Codonopsis Radix., Front Nutr, PMID 37915621

PXD044865 Cruz-Mireles N, Os�s-Ruiz M, Derbyshire P, J�gousse C, Ryder LS, Bautista MJ, Eseola AB, Sklenar J, Tang B, Yan X, Ma W, Findlay KC, Were V, MacLean D, Talbot NJ, Menke FLH. The phosphorylation landscape of infection-related development by the rice blast (from PanoramaPublic)
Dataset title: The phosphorylation landscape of infection-related development by the rice blast fungus
Possible reference: Cruz-Mireles, N. et al. (2024) The phosphorylation landscape of infection-related development by the rice blast fungus., Cell, PMID 38729111

PXD044856 Dataset with its publication pending (from PRIDE)
Dataset title: Germline-specific RNA helicase DDX4 forms cytoplasmic granules in cancer cells and promotes tumor growth
Possible reference: Olotu, O. et al. (2024) Germline-specific RNA helicase DDX4 forms cytoplasmic granules in cancer cells and promotes tumor growth., Cell Rep, PMID 38963760

PXD044850 Dataset with its publication pending (from PRIDE)
Dataset title: Transport properties of canonical PIN proteins and the role of the loop in auxin transport
Possible reference: Janacek, DP. et al. (2024) Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport., Dev Cell, PMID 39413780

PXD044830 Dataset with its publication pending (from PRIDE)
Dataset title: The phosphorylation landscape of infection-related development by the rice blast fungus
Possible reference: Cruz-Mireles, N. et al. (2024) The phosphorylation landscape of infection-related development by the rice blast fungus., Cell, PMID 38729111

PXD044824 Dataset with its publication pending (from PRIDE)
Dataset title: DUSP8 induces TGF-Î²-stimulated IL-9 transcription and Th9-mediated allergic inflammation by promoting nuclear export of Pur-Î±
Possible reference: Chuang, HC. et al. (2023) DUSP8 induces TGF-β-stimulated IL-9 transcription and Th9-mediated allergic inflammation by promoting nuclear export of Pur-α., J Clin Invest, PMID 37909329

PXD044816 no publication (from MassIVE)
Dataset title: PML::RARA and GATA2 proteins interact via DNA templates to induce aberrant self-renewal in hematopoietic cells
Possible reference: Katerndahl, CDS. et al. (2024) PML::RARA and GATA2 proteins interact via DNA templates to induce aberrant self-renewal in mouse and human hematopoietic cells., Proc Natl Acad Sci U S A, PMID 38648485

PXD044812 Dataset with its publication pending (from PRIDE)
Dataset title: Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression
Possible reference: Kramer, NJ. et al. (2023) Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression., Nat Cell Biol, PMID 37770567

PXD044806 Dataset with its publication pending (from jPOST)
Dataset title: HTRA1 prevents and reverses Î±-synuclein aggregation, rendering it non-toxic and seeding incompetent
Possible reference: Chen, S. et al. (2023) HtrA1 prevents and reverses α-synuclein aggregation, rendering it non-toxic and seeding incompetent., Res Sq, PMID 37674720

PXD044800 Dataset with its publication pending (from PRIDE)
Dataset title: A stop-and-go mechanism controls mitochondrial respiration
Possible reference: Moretti-Horten, DN. et al. (2024) Synchronized assembly of the oxidative phosphorylation system controls mitochondrial respiration in yeast., Dev Cell, PMID 38508182

PXD044784 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive proteomic analysis of JC polyomavirus-infected human astrocytes and their extracellular vesicles
Possible reference: Oberholster, L. et al. (2023) Comprehensive proteomic analysis of JC polyomavirus-infected human astrocytes and their extracellular vesicles., Microbiol Spectr, PMID 37815349

PXD044782 Dataset with its publication pending (from PRIDE)
Dataset title: DNA damage stress control is a tLT- and EHMT2-dependent central feature of Merkel Cell Carcinoma
Possible reference: Bachiri, K. et al. (2025) DNA Damage Stress Control Is a Truncated Large T Antigen and Euchromatic Histone Lysine Methyltransferase 2-Dependent Central Feature of Merkel Cell Carcinoma., J Invest Dermatol, PMID 38908781

PXD044749 Dataset with its publication pending (from PRIDE)
Dataset title: A stop-and-go mechanism controls mitochondrial respiration
Possible reference: Moretti-Horten, DN. et al. (2024) Synchronized assembly of the oxidative phosphorylation system controls mitochondrial respiration in yeast., Dev Cell, PMID 38508182

PXD044724 Dataset with its publication pending (from PRIDE)
Dataset title: STPP-UP: A alternative method for drug target identification using protein thermal stability
Possible reference: Zijlmans, DW. et al. (2023) STPP-UP: An alternative method for drug target identification using protein thermal stability., J Biol Chem, PMID 37742922

PXD044714 Dataset with its publication pending (from PRIDE)
Dataset title: Spatial Proteomics of a Human Brain Tumour at 40 µm resolution
Possible reference: Davis, S. et al. (2023) Deep topographic proteomics of a human brain tumour., Nat Commun, PMID 38001067

PXD044710 Dataset with its publication pending (from iProX)
Dataset title: Identification of CBX3 interacting proteins by mass spec
Possible reference: Kulyyassov, A. et al. (2021) Application of Skyline for Analysis of Protein-Protein Interactions In Vivo., Molecules, PMID 34885753

PXD044702 Dataset with its publication pending (from PRIDE)
Dataset title: An adaptive biomolecular condensation response is conserved across environmentally divergent species
Possible reference: Kik, SK. et al. (2023) An adaptive biomolecular condensation response is conserved across environmentally divergent species., bioRxiv, PMID 37546789

PXD044698 Dataset with its publication pending (from PRIDE)
Dataset title: Combined inhibition of MNK signaling and BET proteins reveals TGM2 as a novel vulnerability in melanoma
Possible reference: M�ant, A. et al. (2025) Combined Inhibition of MNK Signaling and BET Proteins Reveals TGM2 as a Novel Vulnerability in Melanoma., J Invest Dermatol, PMID 39357785

PXD044684 Dataset with its publication pending (from PRIDE)
Dataset title: MYL3 protects chondrocytes from senescence by inhibiting clathrin-mediated endocytosis and activating of Notch signaling
Possible reference: Cao, H. et al. (2023) MYL3 protects chondrocytes from senescence by inhibiting clathrin-mediated endocytosis and activating of Notch signaling., Nat Commun, PMID 37794006

PXD044682 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteomic Landscape of Pseudorabies Virus Infection Reveals Multiple Potential Antiviral Targets
Possible reference: Bo, Z. et al. (2024) Phosphoproteomic landscape of pseudorabies virus infection reveals multiple potential antiviral targets., Microbiol Spectr, PMID 37991362

PXD044677 no publication (from MassIVE)
Dataset title: Automated workflow for BioID improves reproducibility and identification of protein-protein interactions
Possible reference: Cirri, E. et al. (2024) Optimized Automated Workflow for BioID Improves Reproducibility and Identification of Protein-Protein Interactions., J Proteome Res, PMID 39231529

PXD044661 no publication (from MassIVE)
Dataset title: CRL4-DCAF15 control of cohesin dynamics sustains 1 cell proliferation
Possible reference: Grothusen, GP. et al. (2024) DCAF15 control of cohesin dynamics sustains acute myeloid leukemia., Nat Commun, PMID 38961054

PXD044642 Dataset with its publication pending (from PRIDE)
Dataset title: Development of pathophysiologically relevant models of sickle cell disease and Î²-thalassemia for therapeutic studies
Possible reference: Gupta, P. et al. (2024) Development of pathophysiologically relevant models of sickle cell disease and β-thalassemia for therapeutic studies., Nat Commun, PMID 38413594

PXD044614 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of Cowpea aphid Aphis craccivora saliva
Possible reference: Pavithran, S. et al. (2024) Identification of salivary proteins of the cowpea aphid Aphis craccivora by transcriptome and LC-MS/MS analyses., Insect Biochem Mol Biol, PMID 38123026

PXD044610 Dataset with its publication pending (from jPOST)
Dataset title: DISTINCT SALIVARY PROTEOMIC PATTERNS AS SIGNATURE FOR MOLAR INCISOR HYPOMINERALIZATION STAGES
Possible reference: Toledo, EDS. et al. (2025) Salivary proteomics as signature for molar incisor hypomineralization stages., Clin Oral Investig, PMID 39890717

PXD044595 Dataset with its publication pending (from PRIDE)
Dataset title: HSF-1 promotes longevity through ubiquilin-1 dependent mitochondrial remodelling
Possible reference: Erinjeri, AP. et al. (2024) HSF-1 promotes longevity through ubiquilin-1-dependent mitochondrial network remodelling., Nat Commun, PMID 39532882

PXD044591 Dataset with its publication pending (from jPOST)
Dataset title: The Alpha-1A Adrenergic Receptor Regulates Fatty Acid-Dependent Oxidative Phosphorylation in the Mouse Heart
Possible reference: Sandroni, PB. et al. (2024) The alpha-1A adrenergic receptor regulates mitochondrial oxidative metabolism in the mouse heart., J Mol Cell Cardiol, PMID 38331556

PXD044576 no publication (from MassIVE)
Dataset title: EndoGenius: Optimized neuropeptide identification from mass spectrometry datasets
Possible reference: Fields, L. et al. (2024) EndoGenius: Optimized Neuropeptide Identification from Mass Spectrometry Datasets., J Proteome Res, PMID 38426863

PXD044569 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics reveals tissue-specific, infection-induced and species-specific neutrophil protein signatures – human blood neutrophils
Possible reference: Sollberger, G. et al. (2024) Quantitative proteomics reveals tissue-specific, infection-induced and species-specific neutrophil protein signatures., Sci Rep, PMID 38472281

PXD044550 Dataset with its publication pending (from PRIDE)
Dataset title: Coordinated miRNA activity mediates the cellular transition into dormancy during embryonic diapause
Possible reference: Iyer, DP. et al. (2024) Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy., Genome Res, PMID 38719471

PXD044535 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of liver of Mus musculus infected by Clonorchis sinensis and the molecular mechanism of the interaction of Clonorchis sinensis with the liver of its host
Possible reference: Wu, Y. et al. (2023) Multilayer omics reveals the molecular mechanism of early infection of Clonorchis sinensis juvenile., Parasit Vectors, PMID 37587524

PXD044528 Dataset with its publication pending (from PRIDE)
Dataset title: Rab30 regulates lipid homeostasis in the hepatocyte during fasting
Possible reference: Régnier, M. et al. (2018) Insights into the role of hepatocyte PPARα activity in response to fasting., Mol Cell Endocrinol, PMID 28774777

PXD044527 no publication (from MassIVE)
Dataset title: Precision-engineered organoids of the human fallopian tube
Possible reference: Crawford, AJ. et al. (2023) Precision-engineered biomimetics: the human fallopian tube., bioRxiv, PMID 37333379

PXD044525 Dataset with its publication pending (from PRIDE)
Dataset title: Eggs of the mosquito Aedes aegypti survive desiccation by rewiring their polyamine and lipid metabolism
Possible reference: Prasad, A. et al. (2023) Eggs of the mosquito Aedes aegypti survive desiccation by rewiring their polyamine and lipid metabolism., PLoS Biol, PMID 37874799

PXD044523 Dataset with its publication pending (from PRIDE)
Dataset title: Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast
Possible reference: Teyssonni�re, E. et al. (2023) Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast., bioRxiv, PMID 37781592

PXD044517 no publication (from MassIVE)
Dataset title: Identification of LMAN1 and SURF4 dependent secretory cargoes
Possible reference: Tang, VT. et al. (2023) Identification of LMAN1 and SURF4 dependent secretory cargoes., bioRxiv, PMID 37066360

PXD044499 Dataset with its publication pending (from iProX)
Dataset title: Irisin reduces Amyloid-Î² by inducing the release of neprilysin from astrocytes following downregulation of ERK-STAT3 signaling
Possible reference: Kim, E. et al. (2023) Irisin reduces amyloid-β by inducing the release of neprilysin from astrocytes following downregulation of ERK-STAT3 signaling., Neuron, PMID 37689059

PXD044498 Dataset with its publication pending (from jPOST)
Dataset title: Integration of shoot-derived polypeptide signals by root TGA transcription factors is essential for survival under fluctuating nitrogen environments
Possible reference: Kobayashi, R. et al. (2024) Integration of shoot-derived polypeptide signals by root TGA transcription factors is essential for survival under fluctuating nitrogen environments., Nat Commun, PMID 39179528

PXD044479 no publication (from MassIVE)
Dataset title: Paleo-proteomic analysis of Iron Age dental calculus provides direct evidence of Scythian reliance on ruminant dairy
Possible reference: Pecnik, J. et al. (2026) Paleo-proteomic analysis of Iron Age dental calculus provides direct evidence of Scythian reliance on ruminant dairy., PLoS One, PMID 41563953

PXD044470 Dataset with its publication pending (from PRIDE)
Dataset title: The selfish yeast plasmid exploits a SWI/SNF-type chromatin remodeling complex for hitchhiking on chromosomes and ensuring high-fidelity propagation
Possible reference: Ma, CH. et al. (2023) The selfish yeast plasmid exploits a SWI/SNF-type chromatin remodeling complex for hitchhiking on chromosomes and ensuring high-fidelity propagation., PLoS Genet, PMID 37812641

PXD044464 Dataset with its publication pending (from jPOST)
Dataset title: Peptide signalling induces rapid stomatal closure under drought stress.
Possible reference: Shimotohno, A. et al. (2025) Local peptide signalling induces stomatal closure under drought stress., Nat Commun, PMID 41444212

PXD044457 Dataset with its publication pending (from PRIDE)
Dataset title: Cytoplasmic sequestering of a fungal stress-activated MAPK in response to a host plant phenolic acid
Possible reference: Zuchman, R. et al. (2025) Cytoplasmic sequestering of a fungal stress-activated MAPK in response to a host plant phenolic acid., PLoS Pathog, PMID 41166398

PXD044456 no publication (from MassIVE)
Dataset title: Tissue-specific proteome profile analysis reveals regulatory and stress responsive networks in passion fruit during storage
Possible reference: Garcia, E. et al. (2024) Tissue-specific proteome profile analysis reveals regulatory and stress responsive networks in passion fruit during storage., Sci Rep, PMID 38346991

PXD044412 Dataset with its publication pending (from PRIDE)
Dataset title: Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation
Possible reference: Sporre, E. et al. (2023) Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation., Commun Biol, PMID 37723200

PXD044410 Dataset with its publication pending (from PRIDE)
Dataset title: UBE2D3 facilitates NHEJ by orchestrating ATM signalling through multi-level control of RNF168
Possible reference: Yal�in, Z. et al. (2024) UBE2D3 facilitates NHEJ by orchestrating ATM signalling through multi-level control of RNF168., Nat Commun, PMID 38866770

PXD044409 Dataset with its publication pending (from PRIDE)
Dataset title: In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation
Possible reference: Llamas, E. et al. (2023) In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation., Nat Aging, PMID 37783816

PXD044408 Dataset with its publication pending (from PRIDE)
Dataset title: In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation.
Possible reference: Llamas, E. et al. (2023) In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation., Nat Aging, PMID 37783816

PXD044405 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of a direct interaction between the Fab domains of IgG antibodies and human FcRn upon IgG-FcRn complex formation
Possible reference: Trabjerg, E. et al. (2025) Identification of a direct interaction between the Fab domains of IgG antibodies and human FcRn upon IgG-FcRn complex formation., Commun Biol, PMID 40506471

PXD044382 Dataset with its publication pending (from PRIDE)
Dataset title: Non-canonical function of histone methyltransferase G9a in the translational regulation of chronic inflammation
Possible reference: Muneer, A. et al. (2023) Non-canonical function of histone methyltransferase G9a in the translational regulation of chronic inflammation., Cell Chem Biol, PMID 37858336

PXD044372 Dataset with its publication pending (from iProX)
Dataset title: Proteomics coupled transcriptomics reveals Slc34a1 and Slc34a3 downregulation as potential features of nephrotoxin-induced acute kidney injury
Possible reference: Zhang, J. et al. (2024) Proteomics coupled transcriptomics reveals Slc34a1 and Slc34a3 downregulation as potential features of nephrotoxin-induced acute kidney injury., J Proteomics, PMID 38782357

PXD044360 Dataset with its publication pending (from PRIDE)
Dataset title: AMPK activator 991 specifically activates SnRK1 and thereby affects seed germination in rice
Possible reference: Hu, Y. et al. (2024) AMPK activator 991 specifically activates SnRK1 and thereby affects seed germination in rice., J Exp Bot, PMID 38465908

PXD044343 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome analysis in the TcMAC21 mouse model of Down syndrome
Possible reference: Kurabayashi, N. et al. (2023) Neocortical neuronal production and maturation defects in the TcMAC21 mouse model of Down syndrome., iScience, PMID 38025769

PXD044341 Dataset with its publication pending (from PRIDE)
Dataset title: Overexpression of protein import machinery subunit ycf1/Tic214 represses photosynthetic complex biogenesis by inhibiting the synthesis of plastid-encoded core subunits in tobacco
Possible reference: Wang, Y. et al. (2025) Overexpression of protein import machinery subunit ycf1/Tic214 represses photosynthetic complex biogenesis by inhibiting the synthesis of plastid-encoded core subunits in tobacco., J Exp Bot, PMID 40720718

PXD044337 Dataset with its publication pending (from PRIDE)
Dataset title: Inducible degradation-coupled phosphoproteomics identifies PP2A-Rts1 as a novel eisosome regulator
Possible reference: DeMarco, AG. et al. (2023) Inducible degradation-coupled phosphoproteomics identifies PP2ARts1 as a novel eisosome regulator., bioRxiv, PMID 37961087

PXD044323 Dataset with its publication pending (from PRIDE)
Dataset title: Autoantigen screening using pull-down and LC-MS
Possible reference: Zhu, L. et al. (2026) DNA Hypermethylation Suppresses Thyroid Peroxidase Expression and May Be a Promising Diagnostic Marker for Thyroid Cancer., Thyroid, PMID 41778292

PXD044313 no publication (from MassIVE)
Dataset title: Quantitative proteomic profiling of HCC1954 cells treated with a CDK12 degrader
Possible reference: Kuchukulla, RR. et al. (2024) Identification of a novel potent CDK inhibitor degrading cyclinK with a superb activity to reverse trastuzumab-resistance in HER2-positive breast cancer in vivo., Eur J Med Chem, PMID 38061230

PXD044293 Dataset with its publication pending (from PRIDE)
Dataset title: In vitro and In vivo Antimicrobial Potential of Lithium Complex against Multi Drug Resistant Acinetobacter baumannii
Possible reference: Zehra, M. et al. (2023) In vitro and in vivo antimicrobial potential of lithium complex against multi-drug resistant Acinetobacter baumannii., Microbiol Spectr, PMID 37861330

PXD044290 Dataset with its publication pending (from jPOST)
Dataset title: LplA modified trastuzumab digested with multiple enzymes
Possible reference: Shikida, N. et al. (2023) Analytical studies on the conjugation site specificity of trastuzumab modified by Escherichia coli lipoate ligase A: multiple-enzyme digestion approach for peptide mapping., Anal Bioanal Chem, PMID 37702772

PXD044287 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting IRE1Î± reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Possible reference: Unal, B. et al. (2024) Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer., Nat Commun, PMID 39406723

PXD044263 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic identification of Rab GTPase interactors in Arabidopsis
Possible reference: Persyn, F. et al. (2024) A Nitrogen-specific Interactome Analysis Sheds Light on the Role of the SnRK1 and TOR Kinases in Plant Nitrogen Signaling., Mol Cell Proteomics, PMID 39307424

PXD044248 Dataset with its publication pending (from iProX)
Dataset title: Interacting proteins of AMPK studied using TurboID proximity labeling technology
Possible reference: Liu, X. et al. (2026) Interacting proteins of AMPK studied using TurboID proximity labeling technology., Exp Ther Med, PMID 42022757

PXD044239 Dataset with its publication pending (from PRIDE)
Dataset title: Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence
Possible reference: Sun, S. et al. (2023) Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence., bioRxiv, PMID 37577636

PXD044211 Dataset with its publication pending (from iProX)
Dataset title: DARTS proteomic response of S. aureus to Baohuoside I
Possible reference: Wen, Z. et al. (2024) Baohuoside I inhibits virulence of multidrug-resistant Staphylococcus aureus by targeting the transcription Staphylococcus accessory regulator factor SarZ., Phytomedicine, PMID 38810547

PXD044207 Dataset with its publication pending (from iProX)
Dataset title: Proteomic response of S. aureus with baohuoside I
Possible reference: Wen, Z. et al. (2024) Baohuoside I inhibits virulence of multidrug-resistant Staphylococcus aureus by targeting the transcription Staphylococcus accessory regulator factor SarZ., Phytomedicine, PMID 38810547

PXD044190 Dataset with its publication pending (from PRIDE)
Dataset title: A phylogenetic approach to explore the Aspergillus fumigatus conidial surfome and its role in pathogenesis
Possible reference: Goldman, G. et al. (2023) A phylogenetic approach to explore the Aspergillus fumigatus conidial surface-associated proteome and its role in pathogenesis., Res Sq, PMID 37790311

PXD044180 Dataset with its publication pending (from PRIDE)
Dataset title: FAM111A regulates replication origin activation and cell fitness
Possible reference: Rios-Szwed, DO. et al. (2023) FAM111A regulates replication origin activation and cell fitness., Life Sci Alliance, PMID 37793778

PXD044179 no publication (from MassIVE)
Dataset title: A promiscuous mechanism to phase separate eukaryotic carbon fixation
Possible reference: Barrett, J. et al. (2024) A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage., Nat Plants, PMID 39384944

PXD044176 Dataset with its publication pending (from PRIDE)
Dataset title: 1 Enhanced assembly of bacteriophage T7 produced in cell-free reactions under simulated microgravity
Possible reference: Lehr, FX. et al. (2024) Enhanced assembly of bacteriophage T7 produced in cell-free reactions under simulated microgravity., NPJ Microgravity, PMID 38491014

PXD044157 Dataset with its publication pending (from PRIDE)
Dataset title: ProteoMixture: A Cell Deconvolution Tool for Bulk Tissue Proteomics Data
Possible reference: Teng, PN. et al. (2024) ProteoMixture: A cell type deconvolution tool for bulk tissue proteomic data., iScience, PMID 38439970

PXD044153 Dataset with its publication pending (from PRIDE)
Dataset title: Biofilm matrix regulation by Candida glabrata Zap1 under acidic conditions: transcriptomic and proteomic analyses
Possible reference: Gon�alves, B. et al. (2024) Biofilm matrix regulation by Candida glabrata Zap1 under acidic conditions: transcriptomic and proteomic analyses., Microbiol Spectr, PMID 39494883

PXD044145 Dataset with its publication pending (from PRIDE)
Dataset title: In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation.
Possible reference: Llamas, E. et al. (2023) In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation., Nat Aging, PMID 37783816

PXD044144 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive proteomic analysis of JC polyomavirus-infected human astrocytes and their extracellular vesicles
Possible reference: Oberholster, L. et al. (2023) Comprehensive proteomic analysis of JC polyomavirus-infected human astrocytes and their extracellular vesicles., Microbiol Spectr, PMID 37815349

PXD044143 Dataset with its publication pending (from jPOST)
Dataset title: Interactome profiling of a lysine deacetylase trapping probe library uncovers crosstalk between HDAC6 and NF-ÎºB signaling
Possible reference: Seidel, J. et al. (2025) Interactome Profiling of a Lysine Deacetylase Trapping Probe Library Uncovers Crosstalk Between HDAC6 and NF-κB Signaling., Angew Chem Int Ed Engl, PMID 40823897

PXD044142 Dataset with its publication pending (from PanoramaPublic)
Dataset title: Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis.
Possible reference: Wiese, C. et al. (2023) Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis., bioRxiv, PMID 37986925

PXD044141 no publication (from MassIVE)
Dataset title: Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation
Possible reference: Nacev, BA. et al. (2024) Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation., Nat Commun, PMID 38886411

PXD044136 Dataset with its publication pending (from PRIDE)
Dataset title: Pteromalus puparum larval saliva
Possible reference: Shi, J. et al. (2022) The larval saliva of an endoparasitic wasp, Pteromalus puparum, suppresses host immunity., J Insect Physiol, PMID 35878702

PXD044126 Dataset with its publication pending (from PRIDE)
Dataset title: Degron mimicry modulates selective substrate recruitment by CTLH E3 supramolecular assembly
Possible reference: Gottemukkala, KV. et al. (2024) Non-canonical substrate recognition by the human WDR26-CTLH E3 ligase regulates prodrug metabolism., Mol Cell, PMID 38759627

PXD044113 no publication (from MassIVE)
Dataset title: The maintenance of oocytes in the mammalian ovary involves extreme protein longevity
Possible reference: Harasimov, K. et al. (2024) The maintenance of oocytes in the mammalian ovary involves extreme protein longevity., Nat Cell Biol, PMID 38902423

PXD044086 Dataset with its publication pending (from PRIDE)
Dataset title: Human lung cancer TMT-labeling LC-MS
Possible reference: Dai, T. et al. (2023) In-depth proteomics reveals the characteristic developmental profiles of early lung adenocarcinoma with epidermal growth factor receptor mutation., Cancer Med, PMID 37004157

PXD044074 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial MOF regulates energy metabolism in heart failure by ATP5B hyperacetylation
Possible reference: Hu, Y. et al. (2024) Mitochondrial MOF regulates energy metabolism in heart failure via ATP5B hyperacetylation., Cell Rep, PMID 39392752

PXD044071 Dataset with its publication pending (from PRIDE)
Dataset title: The divergent ER-mitochondria encounter structures (ERMES) are conserved in parabasalids but lost in several anaerobic lineages with hydrogenosomes.
Possible reference: Kučerová, J. et al. (2023) The divergent ER-mitochondria encounter structures (ERMES) are conserved in parabasalids but lost in several anaerobic lineages with hydrogenosomes., BMC Biol, PMID 37968591

PXD044065 Dataset with its publication pending (from PRIDE)
Dataset title: proteome analysis of Nilaparvata lugens cuticle
Possible reference: Pan, PL. et al. (2018) A comprehensive omics analysis and functional survey of cuticular proteins in the brown planthopper., Proc Natl Acad Sci U S A, PMID 29712872

PXD044019 Dataset with its publication pending (from PRIDE)
Dataset title: The Proteomics landscape of human aorta and mice aorta
Possible reference: Zhou, J. et al. (2019) Combined Single-Cell Profiling of lncRNAs and Functional Screening Reveals that H19 Is Pivotal for Embryonic Hematopoietic Stem Cell Development., Cell Stem Cell, PMID 30639035

PXD044007 Dataset with its publication pending (from iProX)
Dataset title: Identification of proteins interacted with ALKBH1
Possible reference: Nordstrand, LM. et al. (2012) Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes., Nucleic Acids Res, PMID 22965116

PXD044005 Dataset with its publication pending (from PRIDE)
Dataset title: Self-anticoagulant sponges for whole blood auto-transfusion and its mechanism of coagulation factor inactivation
Possible reference: Xu, T. et al. (2023) Self-anticoagulant sponge for whole blood auto-transfusion and its mechanism of coagulation factor inactivation., Nat Commun, PMID 37573353

PXD044004 Dataset with its publication pending (from PRIDE)
Dataset title: Skeletal muscle cell protein dysregulation highlights the pathogenesis mechanism of myopathy-associated p97/VCP R155H mutations
Possible reference: Luzzi, A. et al. (2023) Skeletal muscle cell protein dysregulation highlights the pathogenesis mechanism of myopathy-associated p97/VCP R155H mutations., Front Neurol, PMID 37602234

PXD044001 Dataset with its publication pending (from PRIDE)
Dataset title: A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1
Possible reference: Hai, L. et al. (2024) A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1., Nat Commun, PMID 38320988

PXD043984 Dataset with its publication pending (from PRIDE)
Dataset title: Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling
Possible reference: Bertrand, L. et al. (2025) Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling., Nat Commun, PMID 39966340

PXD043972 Dataset with its publication pending (from iProX)
Dataset title: Proteomics identification of proteins, glycoproteins, and phosphoproteins from sera of healthy controls, RA patients, or RA patients treated with Yunpi Jiedu Tongluo Qushi Granules
Possible reference: Yu, C. et al. (2025) Proteomic and network pharmacology analyses reveal S100A8 as the anti-inflammatory target of Yunpi Jiedu Tongluo Qushi Granule in the treatment of rheumatoid arthritis., J Pharm Biomed Anal, PMID 39442465

PXD043964 Dataset with its publication pending (from PRIDE)
Dataset title: Luminal cerebrovascular proteomic changes during aging
Possible reference: Shi, SM. et al. (2025) Luminal Cerebrovascular Proteomics., Bio Protoc, PMID 40799473

PXD043952 Dataset with its publication pending (from PRIDE)
Dataset title: Iron Drives Anabolic Metabolism Through Active Histone Demethylation and mTORC1
Possible reference: Shapiro, JS. et al. (2023) Iron drives anabolic metabolism through active histone demethylation and mTORC1., Nat Cell Biol, PMID 37749225

PXD043946 Dataset with its publication pending (from PRIDE)
Dataset title: Inceptor facilitates acrosomal vesicle formation in spermatids and is required for male fertility
Possible reference: Bilekova, S. et al. (2023) Inceptor facilitates acrosomal vesicle formation in spermatids and is required for male fertility., Front Cell Dev Biol, PMID 37691832

PXD043931 Dataset with its publication pending (from iProX)
Dataset title: Methylation of KRAS by SETD7 promotes KRAS degradation in non-small cell lung cancer
Possible reference: Chiang, CY. et al. (2023) Methylation of KRAS by SETD7 promotes KRAS degradation in non-small cell lung cancer., Cell Rep, PMID 37682707

PXD043911 Dataset with its publication pending (from PRIDE)
Dataset title: Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts
Possible reference: Deng, M. et al. (2025) Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts., Nat Commun, PMID 41361183

PXD043889 Dataset with its publication pending (from iProX)
Dataset title: LncRNA DGCR5-encoded polypeptide RIP aggravates steroid-induced osteonecrosis of the femoral head by repressing nuclear localization of Î²-catenin in BMSCs
Possible reference: Jiang, W. et al. (2023) LncRNA DGCR5-encoded polypeptide RIP aggravates SONFH by repressing nuclear localization of β-catenin in BMSCs., Cell Rep, PMID 37573506

PXD043878 Dataset with its publication pending (from PRIDE)
Dataset title: Utilization of Stability-based Proteomics for the Investigation of Structured RNA-protein Interactions
Possible reference: Bailey, MA. et al. (2024) Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions., Anal Chem, PMID 38341805

PXD043861 Dataset with its publication pending (from iProX)
Dataset title: Epicardial transplantation of antioxidant polyurethane scaffold based human amniotic epithelial stem cell patch for myocardial infarction treatment
Possible reference: Li, J. et al. (2024) Epicardial transplantation of antioxidant polyurethane scaffold based human amniotic epithelial stem cell patch for myocardial infarction treatment., Nat Commun, PMID 39438477

PXD043844 no publication (from MassIVE)
Dataset title: Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in TimsTOF
Possible reference: Adams, C. et al. (2024) Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF., Nat Commun, PMID 38730277

PXD043837 Dataset with its publication pending (from PRIDE)
Dataset title: The self-association equilibrium of DNAJA2 regulates its interaction with unfolded substrate proteins and with Hsc70
Possible reference: Velasco-Carneros, L. et al. (2023) The self-association equilibrium of DNAJA2 regulates its interaction with unfolded substrate proteins and with Hsc70., Nat Commun, PMID 37670029

PXD043821 Dataset with its publication pending (from iProX)
Dataset title: Proteomic study of colon cancer infected with HIV
Possible reference: Hensley-McBain, T. et al. (2018) Intestinal damage precedes mucosal immune dysfunction in SIV infection., Mucosal Immunol, PMID 29907866

PXD043818 Dataset with its publication pending (from PRIDE)
Dataset title: Defining neutralization and allostery by antibodies against COVID-19 variants
Possible reference: Tulsian, NK. et al. (2023) Defining neutralization and allostery by antibodies against COVID-19 variants., Nat Commun, PMID 37907459

PXD043808 Dataset with its publication pending (from PRIDE)
Dataset title: The transcription factor AP2XI-2 is a key negative regulator of Toxoplasma gondii merogony
Possible reference: Wang, JL. et al. (2024) The transcription factor AP2XI-2 is a key negative regulator of Toxoplasma gondii merogony., Nat Commun, PMID 38278808

PXD043799 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted mass spectrometry analyses of somatic mutations in colorectal cancer specimens using differential ion mobility
Possible reference: Wu, Z. et al. (2024) Targeted Mass Spectrometry Analyses of Somatic Mutations in Colorectal Cancer Specimens Using Differential Ion Mobility., J Proteome Res, PMID 38153093

PXD043793 no publication (from MassIVE)
Dataset title: Outer membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly
Possible reference: Potapova, A. et al. (2024) Outer membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly., mBio, PMID 38206049

PXD043780 Dataset with its publication pending (from iProX)
Dataset title: RH3 enhances antiviral defense by facilitating small RNA loading into Argonaute 2 at endoplasmic reticulum–chloroplast membrane contact sites
Possible reference: Huang, J. et al. (2025) RH3 enhances antiviral defense by facilitating small RNA loading into Argonaute 2 at endoplasmic reticulum-chloroplast membrane contact sites., Nat Commun, PMID 40000658

PXD043770 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping naturally presented T-cell antigens in medulloblastoma based on integrative multi-omics
Possible reference: Velz, J. et al. (2025) Mapping naturally presented T cell antigens in medulloblastoma based on integrative multi-omics., Nat Commun, PMID 39904979

PXD043762 no publication (from MassIVE)
Dataset title: A thylakoid biogenesis BtpA protein is required for the initial step of tetrapyrrole biosynthesis in cyanobacteria
Possible reference: Skotnicov�, P. et al. (2024) A thylakoid biogenesis BtpA protein is required for the initial step of tetrapyrrole biosynthesis in cyanobacteria., New Phytol, PMID 37986097

PXD043759 Dataset with its publication pending (from PRIDE)
Dataset title: A 3D printed plastic frame deeply impacts yeast cell growth
Possible reference: Molina-Menor, E. et al. (2023) A 3D printed plastic frame deeply impacts yeast cell growth., Front Bioeng Biotechnol, PMID 37771573

PXD043752 Dataset with its publication pending (from PRIDE)
Dataset title: Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates ageing in mice
Possible reference: Sirozh, O. et al. (2024) Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates aging in mice., Mol Cell, PMID 38521064

PXD043741 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of larval secreted proteins for Leptopilina boulardi and Leptopilina heterotoma
Possible reference: Heavner, ME. et al. (2017) Novel Organelles with Elements of Bacterial and Eukaryotic Secretion Systems Weaponize Parasites of Drosophila., Curr Biol, PMID 28889977

PXD043740 Dataset with its publication pending (from jPOST)
Dataset title: Personalized serum proteome profiles of COVID-19-associated acute respiratory distress syndrome in response to mesenchymal stem cell therapy
Possible reference: Putri, DU. et al. (2026) Personalized serum proteome profiles of COVID-19-associated acute respiratory distress syndrome in response to mesenchymal stem cell therapy., J Microbiol Immunol Infect, PMID 40685278

PXD043731 Dataset with its publication pending (from PRIDE)
Dataset title: TDP-43 forms amyloid filaments with a distinct fold in type A FTLD-TDP
Possible reference: Arseni, D. et al. (2023) TDP-43 forms amyloid filaments with a distinct fold in type A FTLD-TDP., Nature, PMID 37532939

PXD043725 no publication (from MassIVE)
Dataset title: Distinct states of nucleolar stress induced by anti-cancer drugs
Possible reference: Potapova, TA. et al. (2023) Distinct states of nucleolar stress induced by anticancer drugs., Elife, PMID 38099650

PXD043714 no publication (from MassIVE)
Dataset title: A high-sensitivity low-nanoflow LC-MS configuration for high-throughput sample-limited proteomics
Possible reference: Zheng, R. et al. (2023) A High-Sensitivity Low-Nanoflow LC-MS Configuration for High-Throughput Sample-Limited Proteomics., Anal Chem, PMID 38088903

PXD043691 Dataset with its publication pending (from PRIDE)
Dataset title: Clinical and molecular delineation of classical-like Ehlers–Danlos syndrome through a comprehensive next-generation sequencing-based screening system
Possible reference: Yamaguchi, T. et al. (2023) Clinical and molecular delineation of classical-like Ehlers-Danlos syndrome through a comprehensive next-generation sequencing-based screening system., Front Genet, PMID 37712068

PXD043656 Dataset with its publication pending (from jPOST)
Dataset title: Salivary Metabolomic Identification of Biomarker Candidates for Canine Oral Cancers Using Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry
Possible reference: Ploypetch, S. et al. (2024) Salivary metabolomic identification of biomarker candidates for oral melanoma and oral squamous cell carcinoma in dogs., J Vet Intern Med, PMID 38703129

PXD043645 Dataset with its publication pending (from PRIDE)
Dataset title: PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5�-splice-site selection causing tissue-specific defects
Possible reference: Atkinson, R. et al. (2024) PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5�-splice-site selection causing tissue-specific defects., Nat Commun, PMID 38605034

PXD043639 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial RelA empowers mtDNA G-quadruplex formation for hypoxia adaptation in cancer cells
Possible reference: Tang, GX. et al. (2024) Mitochondrial RelA empowers mtDNA G-quadruplex formation for hypoxia adaptation in cancer cells., Cell Chem Biol, PMID 38821064

PXD043619 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative Multi-Omics Atlas of the Model Chordate Ciona
Possible reference: Frese, AN. et al. (2024) Quantitative proteome dynamics across embryogenesis in a model chordate., iScience, PMID 38510129

PXD043608 Dataset with its publication pending (from PRIDE)
Dataset title: Therapeutic potential of pomegranate juice-derived nanovesicles in nude mouse benign prostatic hyperplasia (BPH) xenograft model
Possible reference: Sreekumar, A. et al. (2023) Therapeutic potential of pomegranate juice-derived nanovesicles in nude mouse benign prostatic hyperplasia (BPH) xenograft model., Sci Rep, PMID 37528206

PXD043607 Dataset with its publication pending (from PRIDE)
Dataset title: Supersulphide airway protection in viral and chronic lung diseases
Possible reference: Matsunaga, T. et al. (2023) Supersulphides provide airway protection in viral and chronic lung diseases., Nat Commun, PMID 37491435

PXD043601 Dataset with its publication pending (from PRIDE)
Dataset title: Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators
Possible reference: K�hnisch, J. et al. (2024) Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators., Cardiovasc Res, PMID 37842925

PXD043600 Dataset with its publication pending (from PRIDE)
Dataset title: HYPK controls stability and catalytic activity of the N-terminal acetyltransferase A in Arabidopsis thaliana
Possible reference: Gong, X. et al. (2024) HYPK controls stability and catalytic activity of the N-terminal acetyltransferase A in Arabidopsis thaliana., Cell Rep, PMID 38363676

PXD043582 no publication (from MassIVE)
Dataset title: PfMORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, P. falciparum.
Possible reference: Chahine, ZM. et al. (2024) PfMORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, Plasmodium falciparum., Elife, PMID 39636094

PXD043576 Dataset with its publication pending (from iProX)
Dataset title: The phosphorylation of the MFSD12
Possible reference: He, L. et al. (2023) Lysosomal cyst(e)ine storage potentiates tolerance to oxidative stress in cancer cells., Mol Cell, PMID 37751742

PXD043574 Dataset with its publication pending (from jPOST)
Dataset title: Multi-omics analysis using antibody-based in situ biotinylation technique reveals the mechanism of Cajal body formation
Possible reference: Noguchi, K. et al. (2024) Multi-omics analysis using antibody-based in situ biotinylation technique suggests the mechanism of Cajal body formation., Cell Rep, PMID 39283744

PXD043573 Dataset with its publication pending (from iProX)
Dataset title: Artemisinin mediates neuroprotection against Parkinson’s disease by targeting Adcy5-Gch1-BH4 axis
Possible reference: Yang, XX. et al. (2025) Artemisinin alleviates Parkinson's disease by targeting Adcy5-Gch1 axis to trigger a cascade generation of BH4 and dopamine in rats., Genome Biol, PMID 40908481

PXD043567 Dataset with its publication pending (from PRIDE)
Dataset title: In-host evolution of Yersinia enterocolitica during a chronic human infection
Possible reference: Savin, C. et al. (2025) In-host evolution of Yersinia enterocolitica during a chronic human infection., Nat Commun, PMID 40595576

PXD043560 Dataset with its publication pending (from PRIDE)
Dataset title: A RIPK1-specific PROTAC degrader achieves potent antitumor activity by enhancing immunogenic cell death
Possible reference: Mannion, J. et al. (2024) A RIPK1-specific PROTAC degrader achieves potent antitumor activity by enhancing immunogenic cell death., Immunity, PMID 38788712

PXD043545 Dataset with its publication pending (from PRIDE)
Dataset title: MULTIMODAL STIMULATION SCREENS REVEAL UNIQUE AND SHARED GENES LIMITING T-CELL FITNESS
Possible reference: Lin, CP. et al. (2024) Multimodal stimulation screens reveal unique and shared genes limiting T�cell fitness., Cancer Cell, PMID 38490212

PXD043539 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteome analysis of TgPP1 depleted Toxoplasma gondii tachyzoites
Possible reference: Khelifa, AS. et al. (2024) PP1 phosphatase controls both daughter cell formation and amylopectin levels in Toxoplasma gondii., PLoS Biol, PMID 39255306

PXD043533 Dataset with its publication pending (from PRIDE)
Dataset title: Human and animal skin identified by palaeoproteomics in Scythian leather objects from Ukraine
Possible reference: Brandt, L�. et al. (2023) Human and animal skin identified by palaeoproteomics in Scythian leather objects from Ukraine., PLoS One, PMID 38091270

PXD043532 Dataset with its publication pending (from PRIDE)
Dataset title: A hierarchical assembly pathway directs the unique subunit arrangement of TRiC/CCT
Possible reference: Betancourt Moreira, K. et al. (2023) A hierarchical assembly pathway directs the unique subunit arrangement of TRiC/CCT., Mol Cell, PMID 37625406

PXD043513 Dataset with its publication pending (from PRIDE)
Dataset title: Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation
Possible reference: Park, KC. et al. (2023) Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation., Nat Cardiovasc Res, PMID 38500966

PXD043485 Dataset with its publication pending (from jPOST)
Dataset title: Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells
Possible reference: Zhao, L. et al. (2024) Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells., Nat Commun, PMID 39333085

PXD043482 Dataset with its publication pending (from PRIDE)
Dataset title: A widespread family of oxidoreductive sulfoquinovosidases at the gateway to sulfoquinovose catabolism
Possible reference: Kaur, A. et al. (2023) Widespread Family of NAD+-Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism., J Am Chem Soc, PMID 38100472

PXD043469 Dataset with its publication pending (from iProX)
Dataset title: Proteomics analysis of CD4+ T-cell-derived-exosomes
Possible reference: Huang, L. et al. (2023) Proteomics profiling of CD4�+�T-cell-derived exosomes from patients with rheumatoid arthritis., Int Immunopharmacol, PMID 37423153

PXD043450 Dataset with its publication pending (from PRIDE)
Dataset title: Time of day effects on post-exercise phosphoproteomic profiling in mouse hippocampus
Possible reference: Qian, P. et al. (2026) Time-of-day effects on post-exercise phosphoproteomic profiling in mouse hippocampus., Front Cell Dev Biol, PMID 41948081

PXD043448 Dataset with its publication pending (from PRIDE)
Dataset title: Reward System Activation Improves Recovery from Acute Myocardial Infarction".
Possible reference: Haykin, H. et al. (2024) Reward system activation improves recovery from acute myocardial infarction., Nat Cardiovasc Res, PMID 39196183

PXD043444 Dataset with its publication pending (from PRIDE)
Dataset title: Therapeutic targeting nudix hydrolase 1 creates a MYC-driven metabolic vulnerability
Possible reference: Ye, M. et al. (2024) Therapeutic targeting nudix hydrolase 1 creates a MYC-driven metabolic vulnerability., Nat Commun, PMID 38493213

PXD043437 no publication (from MassIVE)
Dataset title: The X-Linked Intellectual Disability gene, ZDHHC9, is important for oligodendrocyte maturation and myelin formation
Possible reference: White, RB. et al. (2025) The X-Linked Intellectual Disability Gene, ZDHHC9 , Is Important for Oligodendrocyte Subtype Determination and Myelination., Glia, PMID 40105030

PXD043408 no publication (from MassIVE)
Dataset title: Amyloid fibril proteomics of AD brains reveals modifiers of aggregation and toxicity
Possible reference: Konstantoulea, K. et al. (2022) Heterotypic Amyloid β interactions facilitate amyloid assembly and modify amyloid structure., EMBO J, PMID 34842295

PXD043405 no publication (from MassIVE)
Dataset title: Towards the definition of the molecular hallmarks of Idiopathic Membranous Nephropathy in serum proteome: a DIA-PASEF approach
Possible reference: Previtali, P. et al. (2023) Towards the Definition of the Molecular Hallmarks of Idiopathic Membranous Nephropathy in Serum Proteome: A DIA-PASEF Approach., Int J Mol Sci, PMID 37511514

PXD043389 Dataset with its publication pending (from PRIDE)
Dataset title: A multi-omics dataset of human transcriptome and proteome stable reference
Possible reference: Lu, S. et al. (2023) A multi-omics dataset of human transcriptome and proteome stable reference., Sci Data, PMID 37443183

PXD043370 Dataset with its publication pending (from PRIDE)
Dataset title: �Phos: a scalable and sensitive platform for functional phosphoproteomics
Possible reference: Oliinyk, D. et al. (2024) �Phos: a scalable and sensitive platform for high-dimensional phosphoproteomics., Mol Syst Biol, PMID 38907068

PXD043368 Dataset with its publication pending (from jPOST)
Dataset title: Involvement of the AKT pathway in resistance to erlotinib and cabozantinib in triple negative breast cancer cell lines.
Possible reference: Lefebvre, C. et al. (2023) Involvement of the AKT Pathway in Resistance to Erlotinib and Cabozantinib in Triple-Negative Breast Cancer Cell Lines., Biomedicines, PMID 37760847

PXD043367 Dataset with its publication pending (from PRIDE)
Dataset title: The chromatin associated lncREST interacts with the replication fork to ensure effective replication stress response
Possible reference: Statello, L. et al. (2024) The chromatin-associated lncREST ensures effective replication stress response by promoting the assembly of fork signaling factors., Nat Commun, PMID 38302450

PXD043359 Dataset with its publication pending (from PRIDE)
Dataset title: Bergenin inhibits growth of human cervical cancer cells by decreasing Galectin-3 and MMP-9 expression
Possible reference: Chauhan, R. et al. (2024) Bergenin inhibits growth of human cervical cancer cells by decreasing Galectin-3 and MMP-9 expression., Sci Rep, PMID 38961106

PXD043338 Dataset with its publication pending (from PRIDE)
Dataset title: A Spatiotemporal Proteomic Map of Human Adipogenesis
Possible reference: Klingelhuber, F. et al. (2024) A spatiotemporal proteomic map of human adipogenesis., Nat Metab, PMID 38565923

PXD043337 no publication (from MassIVE)
Dataset title: Proteomic profile of extracellular vesicles from plasma and CSF of multiple sclerosis patients reveals disease activity-associated EAAT2
Possible reference: D'Ambrosio, A. et al. (2024) Proteomic profile of extracellular vesicles from plasma and CSF of multiple sclerosis patients reveals disease activity-associated EAAT2., J Neuroinflammation, PMID 39223661

PXD043331 Dataset with its publication pending (from iProX)
Dataset title: ESCRT regulates the termination of STING activity by mediating its degradation
Possible reference: Suklabaidya, S. et al. (2026) Negative feedback regulation of STING signaling by TAX1BP1-directed Golgiphagy., Nat Commun, PMID 41673009

PXD043325 Dataset with its publication pending (from iProX)
Dataset title: Potential binding proteins of CAV1 obtained from LC-MS/MS
Possible reference: Brunet, S. et al. (2015) Phosphorylation sites in the Hook domain of CaVβ subunits differentially modulate CaV1.2 channel function., J Mol Cell Cardiol, PMID 26271711

PXD043317 Waugh S, Ranasinghe A, Gomez A, Houston S, Lithgow KV, Eshghi A, Fleetwood J, Conway K, Reynolds LA and Cameron CE. Syphilis and the host; multi-omic analysis of host cellular responses to Treponema pallidum provides novel insight into syphilis pathogenes (from MassIVE)
Dataset title: Syphilis and the Host; multi-omic analysis of host cellular responses to Treponema pallidum provides novel insight into syphilis pathogenesis.
Possible reference: Waugh, S. et al. (2023) Syphilis and the host: multi-omic analysis of host cellular responses to Treponema pallidum provides novel insight into syphilis pathogenesis., Front Microbiol, PMID 37795301

PXD043293 Dataset with its publication pending (from PRIDE)
Dataset title: Adipogenic characterization of immortalized CD55+ progenitor cells frAdipogenic characterization of immortalized CD55+ progenitor cells from human white adipose tissueom human white adipose tissue
Possible reference: Couchet, M. et al. (2025) Adipogenic characterization of immortalized CD55+ progenitor cells from human white adipose tissue., Adipocyte, PMID 37982546

PXD043289 Dataset with its publication pending (from PRIDE)
Dataset title: DEAD box RNA helicases are pervasive protein kinase interactors and activators
Possible reference: Hirth, A. et al. (2024) DEAD box RNA helicases are pervasive protein kinase interactors and activators., Genome Res, PMID 38986579

PXD043281 Dataset with its publication pending (from PRIDE)
Dataset title: A CPC-shelterin-BTR axis regulates mitotic telomere deprotection
Possible reference: Romero-Zamora, D. et al. (2025) A CPC-shelterin-BTR axis regulates mitotic telomere deprotection., Nat Commun, PMID 40097392

PXD043280 Dataset with its publication pending (from PRIDE)
Dataset title: Glycoproteomic and Proteomic analysis of Burkholderia cenocepacia reveals glycosylation events within FliF and MotB are dispensable for motility. - DIA
Possible reference: Lewis, JM. et al. (2024) Glycoproteomic and proteomic analysis of Burkholderia cenocepacia reveals glycosylation events within FliF and MotB are dispensable for motility., Microbiol Spectr, PMID 38709084

PXD043279 Dataset with its publication pending (from iProX)
Dataset title: protemomics of wolfberry under root rot stress
Possible reference: Li, R. et al. (2024) Effect of potato glycoside alkaloids on mitochondria energy metabolism of Fusarium solani, the root rot pathogen of Lycium barbarum., Front Microbiol, PMID 39943965

PXD043260 Dataset with its publication pending (from PRIDE)
Dataset title: A conserved membrane curvature-generating protein is crucial for autophagosome formation in fission yeast
Possible reference: Wang, N. et al. (2023) A conserved membrane curvature-generating protein is crucial for autophagosome formation in fission yeast., Nat Commun, PMID 37553386

PXD043221 Dataset with its publication pending (from PRIDE)
Dataset title: Glycoproteomic and Proteomic analysis of Burkholderia cenocepacia reveals glycosylation events within FliF and MotB are dispensable for motility.
Possible reference: Lewis, JM. et al. (2024) Glycoproteomic and proteomic analysis of Burkholderia cenocepacia reveals glycosylation events within FliF and MotB are dispensable for motility., Microbiol Spectr, PMID 38709084

PXD043190 Dataset with its publication pending (from PRIDE)
Dataset title: Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis
Possible reference: Zhou, H. et al. (2024) Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis., Nat Commun, PMID 38879536

PXD043183 no publication (from MassIVE)
Dataset title: High-throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF
Possible reference: Bayne, EF. et al. (2024) High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF., J Proteome Res, PMID 38315831

PXD043160 Dataset with its publication pending (from jPOST)
Dataset title: Aurantiochytrium sp SW1 proteomic profile
Possible reference: Prabhakaran, P. et al. (2023) Uncovering global lipid accumulation routes towards docosahexaenoic acid (DHA) production in Aurantiochytrium sp. SW1 using integrative proteomic analysis., Biochim Biophys Acta Mol Cell Biol Lipids, PMID 37625782

PXD043151 Dataset with its publication pending (from jPOST)
Dataset title: Intestinal Paneth cell differentiation relies on asymmetric regulation of Wnt signaling by Daam1/2
Possible reference: Colozza, G. et al. (2023) Intestinal Paneth cell differentiation relies on asymmetric regulation of Wnt signaling by Daam1/2., Sci Adv, PMID 38000028

PXD043141 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic analysis and verification identify global protein profiling dynamics in pig saliva during the estrus cycle
Possible reference: Xin, H. et al. (2023) Quantitative proteomic analysis and verification identify global protein profiling dynamics in pig during the estrous cycle., Front Vet Sci, PMID 37841454

PXD043135 Dataset with its publication pending (from PRIDE)
Dataset title: STPP-UP: A alternative method for drug target identification using protein thermal stability
Possible reference: Zijlmans, DW. et al. (2023) STPP-UP: An alternative method for drug target identification using protein thermal stability., J Biol Chem, PMID 37742922

PXD043133 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibition of GPX4 enhances CDK4/6 inhibitor activity in breast cancer.
Possible reference: Zhu, X. et al. (2024) Cotargeting CDK4/6 and BRD4 Promotes Senescence and Ferroptosis Sensitivity in Cancer., Cancer Res, PMID 38277141

PXD043128 Dataset with its publication pending (from jPOST)
Dataset title: Development of a contacting transwell co-culture system for the in vitro culture of primary central nervous system lymphomas
Possible reference: Nishi, M. et al. (2023) Development of a contacting transwell co-culture system for the in vitro propagation of primary central nervous system lymphoma., Front Cell Dev Biol, PMID 38089883

PXD043112 no publication (from MassIVE)
Dataset title: Endocytic vesicles act as vehicles for glucose uptake in response to growth factor stimulation
Possible reference: Tsutsumi, R. et al. (2023) Endocytic vesicles act as vehicles for glucose uptake in response to growth factor stimulation., bioRxiv, PMID 37546742

PXD043103 Dataset with its publication pending (from PRIDE)
Dataset title: Immunorecognition of Streptococcus mutans secreted proteins protects against caries by limiting tooth adhesion
Possible reference: Bender, O. et al. (2024) Immunorecognition of Streptococcus mutans secreted proteins protects against caries by limiting tooth adhesion., J Dent, PMID 38101504

PXD043084 Dataset with its publication pending (from PRIDE)
Dataset title: ZNF524 directly interacts with telomeric DNA and supports telomere integrity
Possible reference: Braun, H. et al. (2023) ZNF524 directly interacts with telomeric DNA and supports telomere integrity., Nat Commun, PMID 38086788

PXD043076 Dataset with its publication pending (from PRIDE)
Dataset title: A protein kinase coordinates cycles of autophagy and glutaminolysis in invasive hyphae of the fungus Magnaporthe oryzae within rice cells
Possible reference: Li, G. et al. (2023) A protein kinase coordinates cycles of autophagy and glutaminolysis in invasive hyphae of the fungus Magnaporthe oryzae within rice cells., Nat Commun, PMID 37438395

PXD043058 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular Vesicles in COVID-19 convalescence can regulate T cell metabolism and function
Possible reference: George, MS. et al. (2023) Extracellular vesicles in COVID-19 convalescence can regulate T�cell metabolism and function., iScience, PMID 37520724

PXD043038 Dataset with its publication pending (from iProX)
Dataset title: PIAS3/TGF-Î²/TXNIP axis promotes ferroptosis in HCC
Possible reference: Bao, W. et al. (2023) PIAS3 promotes ferroptosis by regulating TXNIP via TGF-β signaling pathway in hepatocellular carcinoma., Pharmacol Res, PMID 37689128

PXD043033 Dataset with its publication pending (from PRIDE)
Dataset title: Infected erythrocytes and plasma proteomics reveal a specific protein signature of severe malaria
Possible reference: Fraering, J. et al. (2024) Infected erythrocytes and plasma proteomics reveal a specific protein signature of severe malaria., EMBO Mol Med, PMID 38297098

PXD043027 Dataset with its publication pending (from jPOST)
Dataset title: Characterization of Unbranched Ubiquitin Tetramers by Combining Ultraviolet Photodissociation with Proton Transfer Charge Reduction Reactions
Possible reference: Bashyal, A. et al. (2023) Characterization of Unbranched Ubiquitin Tetramers by Combining Ultraviolet Photodissociation with Proton Transfer Charge Reduction Reactions., Anal Chem, PMID 37677053

PXD043024 no publication (from MassIVE)
Dataset title: The twin-arginine translocation system of Achromobacter xylosoxidans
Possible reference: Khademi, SMH. et al. (2024) The twin-arginine translocation system is vital for cell adhesion and uptake of iron in the cystic fibrosis pathogen Achromobacter xylosoxidans., Virulence, PMID 37974335

PXD043023 no publication (from MassIVE)
Dataset title: derailed protein turnover in the aging mammalian brain
Possible reference: Danckwardt, S. et al. (2023) Post-transcriptional control of haemostatic genes: mechanisms and emerging therapeutic concepts in thrombo-inflammatory disorders., Cardiovasc Res, PMID 36943786

PXD043021 Dataset with its publication pending (from PRIDE)
Dataset title: Escherichia coli displays a conserved membrane proteomic response to a range of alcohols
Possible reference: Sen, O. et al. (2023) Escherichia coli displays a conserved membrane proteomic response to a range of alcohols., Biotechnol Biofuels Bioprod, PMID 37789404

PXD043002 Dataset with its publication pending (from PRIDE)
Dataset title: Global phosphoproteome of Leishmania mexicana developmental stages
Possible reference: Porta, EO. et al. (2023) Inhibition of HSP90 distinctively modulates the global phosphoproteome of Leishmania mexicana developmental stages., Microbiol Spectr, PMID 37905935

PXD042994 Dataset with its publication pending (from PRIDE)
Dataset title: Altered GM1 catabolism affects NMDAR-mediated Ca2+ signaling at ER-PM junctions and increases synaptic spine formation
Possible reference: Weesner, JA. et al. (2024) Altered GM1 catabolism affects NMDAR-mediated Ca2+ signaling at ER-PM junctions and increases synaptic spine formation in a GM1-gangliosidosis model., Cell Rep, PMID 38630590

PXD042993 Dataset with its publication pending (from PRIDE)
Dataset title: Nardilysin-Regulated Scission Mechanism Activates Polo-like Kinase 3 to Suppress the Development of Pancreatic Cancer
Possible reference: Fu, J. et al. (2024) Nardilysin-regulated scission mechanism activates polo-like kinase 3 to suppress the development of pancreatic cancer., Nat Commun, PMID 38605037

PXD042976 Dataset with its publication pending (from jPOST)
Dataset title: The Plasmodium falciparum CCCH zinc finger protein MD3 regulates male gametocytogenesis through its interaction with RNA-binding proteins
Possible reference: Farrukh, A. et al. (2024) The Plasmodium falciparum CCCH zinc finger protein MD3 regulates male gametocytogenesis through its interaction with RNA-binding proteins., Mol Microbiol, PMID 38148574

PXD042965 Dataset with its publication pending (from PRIDE)
Dataset title: BAG5, a co-chaperone protein, regulates the assembly of HTCA in sperm
Possible reference: Gan, S. et al. (2024) BAG5 regulates HSPA8-mediated protein folding required for sperm head-tail coupling apparatus assembly., EMBO Rep, PMID 38454159

PXD042963 Dataset with its publication pending (from iProX)
Dataset title: GP73-dependent regulation of exosome biogenesis promotes colorectal cancer liver metastasis
Possible reference: Huang, L. et al. (2025) GP73-dependent regulation of exosome biogenesis promotes colorectal cancer liver metastasis., Mol Cancer, PMID 40414849

PXD042954 Dataset with its publication pending (from PRIDE)
Dataset title: Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge
Possible reference: Can, H. et al. (2023) Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge., Cells, PMID 37566077

PXD042949 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted proteomics quantittation of NRF2 signaling and predictive biomarkers in HNSCC
Possible reference: Wamsley, NT. et al. (2023) Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC., Mol Cell Proteomics, PMID 37716475

PXD042936 Dataset with its publication pending (from PRIDE)
Dataset title: High Efficiency Enrichment by Saturating Nanoliters of Protein Affinity Media
Possible reference: Raval, S. et al. (2023) High-Efficiency Enrichment by Saturating Nanoliters of Protein Affinity Media., Anal Chem, PMID 37851921

PXD042921 Dataset with its publication pending (from PRIDE)
Dataset title: 5xFAD transgenic mouse Abeta proteoforms
Possible reference: Bugrova, AE. et al. (2021) The Dynamics of β-Amyloid Proteoforms Accumulation in the Brain of a 5xFAD Mouse Model of Alzheimer's Disease., Int J Mol Sci, PMID 35008451

PXD042905 Dataset with its publication pending (from PRIDE)
Dataset title: The assembly of the Mitochondrial Complex I Assembly complex uncovers a redox pathway coordination
Possible reference: McGregor, L. et al. (2023) The assembly of the Mitochondrial Complex I Assembly complex uncovers a redox pathway coordination., Nat Commun, PMID 38086790

PXD042903 Dataset with its publication pending (from PRIDE)
Dataset title: Pulse-SILAC and interactomics reveal distinct DDB1-CUL4 associated factors (DCAFs), cellular functions, and protein substrates
Possible reference: Raisch, J. et al. (2023) Pulse-SILAC and Interactomics Reveal Distinct DDB1-CUL4-Associated Factors, Cellular Functions, and Protein Substrates., Mol Cell Proteomics, PMID 37689310

PXD042895 Dataset with its publication pending (from PRIDE)
Dataset title: Epigenome-wide impact of MAT2A sustains the androgen-indifferent state and confers synthetic vulnerability in ERG fusion-positive prostate cancer
Possible reference: Cacciatore, A. et al. (2024) Epigenome-wide impact of MAT2A sustains the androgen-indifferent state and confers synthetic vulnerability in ERG fusion-positive prostate cancer., Nat Commun, PMID 39107274

PXD042878 Dataset with its publication pending (from PRIDE)
Dataset title: Bidirectional substrate shuttling between the 26S proteasome and the Cdc48 ATPase promotes protein degradation
Possible reference: Li, H. et al. (2023) Bidirectional substrate shuttling between the 26S proteasome and the Cdc48 ATPase promotes protein degradation., bioRxiv, PMID 38187576

PXD042871 Dataset with its publication pending (from jPOST)
Dataset title: Validity of the cell-extracted proteome as a substrate pool for exploring phosphorylation motifs of kinases
Possible reference: Niinae, T. et al. (2023) Validity of the cell-extracted proteome as a substrate pool for exploring phosphorylation motifs of kinases., Genes Cells, PMID 37658684

PXD042868 Yixuan Huang, Bhagyashree N. Swarge, Winfried Roseboom, Jurre D. Bleeker, Stanley Brul, Peter Setlow, Gertjan Kramer. Integrative metabolomics and proteomics allow the global intracellular characterization of Bacillus subtilis cells and spores. bioRxiv 20 (from MassIVE)
Dataset title: Integrative metabolomics and proteomics allow the global intracellular characterization of Bacillus subtilis cells and spores.
Possible reference: Huang, Y. et al. (2024) Integrative Metabolomics and Proteomics Allow the Global Intracellular Characterization of Bacillus subtilis Cells and Spores., J Proteome Res, PMID 38190553

PXD042860 Dataset with its publication pending (from PRIDE)
Dataset title: Spatially differential regulation of ATF2 phosphorylation contributes to warning coloration of gregarious locusts
Possible reference: Kang, X. et al. (2023) Spatially differential regulation of ATF2 phosphorylation contributes to warning coloration of gregarious locusts., Sci Adv, PMID 37611100

PXD042855 Dataset with its publication pending (from PRIDE)
Dataset title: The kinesin Kif21b regulates radial migration of cortical projection neurons through a non-canonical function on actin cytoskeleton.
Possible reference: Rivera Alvarez, J. et al. (2023) The kinesin Kif21b regulates radial migration of cortical projection neurons through a non-canonical function on actin cytoskeleton., Cell Rep, PMID 37418324

PXD042852 Dataset with its publication pending (from PRIDE)
Dataset title: Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping
Possible reference: Suhre, K. et al. (2024) Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping., Nat Commun, PMID 38307861

PXD042850 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamics of the blood plasma proteome during hyperacute HIV-1 infection
Possible reference: Nazziwa, J. et al. (2024) Dynamics of the blood plasma proteome during hyperacute HIV-1 infection., Nat Commun, PMID 39632834

PXD042824 no publication (from MassIVE)
Dataset title: Parascedosporium putredinis NO1 tailors its secretome for different lignocellulosic substrates
Possible reference: Scott, CJR. et al. (2024) Parascedosporium putredinis NO1 tailors its secretome for different lignocellulosic substrates., Microbiol Spectr, PMID 38757984

PXD042806 Dataset with its publication pending (from PRIDE)
Dataset title: Cardiomyocyte precursors generated by direct reprogramming and molecular beacon selection attenuate ventricular remodeling after experimental myocardial infarction
Possible reference: Bachamanda Somesh, D. et al. (2023) Cardiomyocyte precursors generated by direct reprogramming and molecular beacon selection attenuate ventricular remodeling after experimental myocardial infarction., Stem Cell Res Ther, PMID 37840130

PXD042803 no publication (from MassIVE)
Dataset title: The Effect of Tamoxifen on Proteome Expression During in vitro Myogenesis in Murine Skeletal Muscle C2C12 Cells
Possible reference: Morris, EA. et al. (2023) Effect of Tamoxifen on Proteome Expression during In Vitro Myogenesis in Murine Skeletal Muscle C2C12 Cells., J Proteome Res, PMID 37552804

PXD042788 no publication (from MassIVE)
Dataset title: Metabolic switch from fatty acid oxidation to glycolysis in knock-in mouse model of Barth Syndrome.
Possible reference: Chowdhury, A. et al. (2023) Metabolic switch from fatty acid oxidation to�glycolysis in knock-in mouse model of Barth�syndrome., EMBO Mol Med, PMID 37533404

PXD042771 no publication (from MassIVE)
Dataset title: Deoxyhypusine synthase (DHPS) mutations alter the post-translational modification of eukaryotic initiation factor 5A (eIF5A) resulting in impaired human and mouse neural homeostasis
Possible reference: Padgett, LR. et al. (2023) Deoxyhypusine synthase mutations alter the post-translational modification of eukaryotic initiation factor 5A resulting in impaired human and mouse neural homeostasis., HGG Adv, PMID 37333770

PXD042770 Dataset with its publication pending (from PRIDE)
Dataset title: A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS
Possible reference: Kusebauch, U. et al. (2023) A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS., Sci Data, PMID 37833331

PXD042761 Dataset with its publication pending (from PRIDE)
Dataset title: LSM14B is essential for oocyte meiotic maturation by regulating maternal mRNA storage and clearance
Possible reference: Wan, Y. et al. (2023) LSM14B is essential for oocyte meiotic maturation by regulating maternal mRNA storage and clearance., Nucleic Acids Res, PMID 37889087

PXD042736 no publication (from MassIVE)
Dataset title: Mus musculus brown adipose tissue histone proteoforms
Possible reference: Taylor, BC. et al. (2024) Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress., bioRxiv, PMID 38328142

PXD042693 Dataset with its publication pending (from PRIDE)
Dataset title: Ubiquitin-specific proximity labeling for the identification of E3 ubiquitin ligase substrates
Possible reference: Huang, HT. et al. (2024) Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates., Nat Chem Biol, PMID 38514884

PXD042687 Dataset with its publication pending (from PRIDE)
Dataset title: Ubiquitin-specific proximity labeling for the identification of E3 ubiquitin ligase substrates
Possible reference: Huang, HT. et al. (2024) Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates., Nat Chem Biol, PMID 38514884

PXD042665 Dataset with its publication pending (from PRIDE)
Dataset title: DNA framework-engineered chimeras platform enables selectively targeted protein degradation
Possible reference: Zhou, L. et al. (2023) DNA framework-engineered chimeras platform enables selectively targeted protein degradation., Nat Commun, PMID 37495569

PXD042661 Dataset with its publication pending (from PRIDE)
Dataset title: The VE-cadherin/AmotL2 mechanosensory pathway suppresses aortic inflammation and the formation of abdominal aortic aneurysms
Possible reference: Zhang, Y. et al. (2023) The VE-cadherin/AmotL2 mechanosensory pathway suppresses aortic inflammation and the formation of abdominal aortic aneurysms., Nat Cardiovasc Res, PMID 39195920

PXD042657 Dataset with its publication pending (from PRIDE)
Dataset title: Ubiquitin-specific proximity labeling for the identification of E3 ubiquitin ligase substrates
Possible reference: Huang, HT. et al. (2024) Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates., Nat Chem Biol, PMID 38514884

PXD042616 Dataset with its publication pending (from PRIDE)
Dataset title: Functional analysis of the Aspergillus fumigatus kinome reveals a DYRK kinase involved in septal plugging is a novel antifungal drug target
Possible reference: van Rhijn, N. et al. (2023) Functional analysis of the Aspergillus fumigatus kinome reveals a DYRK kinase involved in septal plugging is a novel antifungal drug target., Res Sq, PMID 37398159

PXD042586 Dataset with its publication pending (from jPOST)
Dataset title: Sex-specific role of galectin-3 in aortic stenosis
Possible reference: Matilla, L. et al. (2023) Sex-specific role of galectin-3 in aortic stenosis., Biol Sex Differ, PMID 37875993

PXD042579 Dataset with its publication pending (from PRIDE)
Dataset title: O-GlcNAcylation of RIPK1 Rescues Red Blood Cells from Necroptosis
Possible reference: Seo, J. et al. (2023) O-GlcNAcylation of RIPK1 rescues red blood cells from necroptosis., Front Immunol, PMID 37359541

PXD042548 no publication (from MassIVE)
Dataset title: Cysteine Counting via Isotopic Chemical Labeling for Intact Mass Proteoform Identifications in Tissue
Possible reference: Pavek, JG. et al. (2023) Cysteine Counting via Isotopic Chemical Labeling for Intact Mass Proteoform Identifications in Tissue., Anal Chem, PMID 37791746

PXD042541 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-Tiered Chemical Proteomic Maps of Tryptoline Acrylamide-Protein Interactions in Cancer Cells
Possible reference: Njomen, E. et al. (2024) Multi-tiered chemical proteomic maps of tryptoline acrylamide-protein interactions in cancer cells., Nat Chem, PMID 39138346

PXD042523 Dataset with its publication pending (from iProX)
Dataset title: proteome responses of tomato root exposed to cadmium stress
Possible reference: Borges, KLR. et al. (2019) Quantitative proteomic analysis of tomato genotypes with differential cadmium tolerance., Environ Sci Pollut Res Int, PMID 31278641

PXD042513 no publication (from MassIVE)
Dataset title: Combined transcriptomics and proteomics analysis unveiled the impact of vitamin C in modulating specific mitochondrial protein abundance in the mouse liver
Possible reference: Aumailley, L. et al. (2024) Combined transcriptomics and proteomics unveil the impact of vitamin C in modulating specific protein abundance in the mouse liver., Biol Res, PMID 38735981

PXD042503 Dataset with its publication pending (from PRIDE)
Dataset title: Infected erythrocytes and plasma proteomics reveal a specific protein signature of severe malaria.
Possible reference: Fraering, J. et al. (2024) Infected erythrocytes and plasma proteomics reveal a specific protein signature of severe malaria., EMBO Mol Med, PMID 38297098

PXD042495 Dataset with its publication pending (from PRIDE)
Dataset title: LSD1 knockout effects on proteome
Possible reference: Ravasio, R. et al. (2020) Targeting the scaffolding role of LSD1 (KDM1A) poises acute myeloid leukemia cells for retinoic acid-induced differentiation., Sci Adv, PMID 32284990

PXD042487 Dataset with its publication pending (from iProX)
Dataset title: The CprRS two-component system regulates virulence in Pseudomonas aeruginosa
Possible reference: Zhao, NL. et al. (2023) Host-derived peptide signals regulate Pseudomonas aeruginosa virulence stress via the ParRS and CprRS two-component systems., J Hazard Mater, PMID 37703740

PXD042482 no publication (from MassIVE)
Dataset title: Fit for Purpose Approach to Evaluate Detection of Amino Acid Substitutions in Shotgun Proteomics
Possible reference: Lundgren, TJ. et al. (2024) Fit for Purpose Approach To Evaluate Detection of Amino Acid Substitutions in Shotgun Proteomics., J Proteome Res, PMID 38478054

PXD042464 Dataset with its publication pending (from PRIDE)
Dataset title: DipM controls multiple autolysins and mediates a regulatory feedback loop promoting cell constriction in Caulobacter crescentus
Possible reference: Izquierdo-Martinez, A. et al. (2023) DipM controls multiple autolysins and mediates a regulatory feedback loop promoting cell constriction in Caulobacter crescentus., Nat Commun, PMID 37433794

PXD042451 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanisms of hepatic steatosis in chickens: integrated analysis of the host genome, molecular phenomes and gut microbiome
Possible reference: Sun, C. et al. (2024) Mechanisms of hepatic steatosis in chickens: integrated analysis of the host genome, molecular phenomics and gut microbiome., Gigascience, PMID 38837944

PXD042444 Dataset with its publication pending (from PRIDE)
Dataset title: Global Protein-Turnover Quantification in Escherichia Coli Reveals Cytoplasmic Recycling under Nitrogen Limitation
Possible reference: Gupta, M. et al. (2024) Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation., Nat Commun, PMID 39003262

PXD042427 Dataset with its publication pending (from PRIDE)
Dataset title: Obatoclax rescues FUS-ALS phenotypes in iPSC-derived neurons by inducing autophagy
Possible reference: Castillo Bautista, CM. et al. (2023) Obatoclax Rescues FUS-ALS Phenotypes in iPSC-Derived Neurons by Inducing Autophagy., Cells, PMID 37759469

PXD042416 Dataset with its publication pending (from PRIDE)
Dataset title: Peptide collision cross section of 22 post-translational modifications
Possible reference: Will, A. et al. (2023) Peptide collision cross sections of 22 post-translational modifications., Anal Bioanal Chem, PMID 37758903

PXD042413 Dataset with its publication pending (from jPOST)
Dataset title: Absolute quantification of mTOR related signaling molecules
Possible reference: Reddy, BR. et al. (2021) Proteome profile of telencephalon associates attenuated neurogenesis with chronic stress induced mood disorder phenotypes in zebrafish model., Pharmacol Biochem Behav, PMID 33684455

PXD042382 Dataset with its publication pending (from PRIDE)
Dataset title: A transient protein folding response targets aggregation in the early phase of TDP-43-mediated disease
Possible reference: San Gil, R. et al. (2024) A transient protein folding response targets aggregation in the early phase of TDP-43-mediated neurodegeneration., Nat Commun, PMID 38374041

PXD042381 Dataset with its publication pending (from PRIDE)
Dataset title: An integrated multi-omics analysis of identiﬁes distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa
Possible reference: Yang, Y. et al. (2023) An integrated multi-omics analysis of identifies distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa., PLoS Pathog, PMID 37643174

PXD042380 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of Triple Negative Breast Cancer Cells Treated with SU056
Possible reference: Dheeraj, A. et al. (2024) Inhibition of protein translational machinery in triple-negative breast cancer as a promising therapeutic strategy., Cell Rep Med, PMID 38729158

PXD042369 Dataset with its publication pending (from PRIDE)
Dataset title: Membrane proteomics of Caldalkalibacillus thermarum TA2.A1
Possible reference: de Jong, SI. et al. (2023) Membrane proteome of the thermoalkaliphile Caldalkalibacillus thermarum TA2.A1., Front Microbiol, PMID 37577439

PXD042367 Dataset with its publication pending (from PRIDE)
Dataset title: A framework for ultra-low input spatial tissue proteomics
Possible reference: Makhmut, A. et al. (2023) A framework for ultra-low-input spatial tissue proteomics., Cell Syst, PMID 37909047

PXD042358 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of membrane proteins regulated by ADAM15 by SUSPECS proteomics
Possible reference: Calligaris, M. et al. (2023) Identification of membrane proteins regulated by ADAM15 by SUSPECS proteomics., Front Mol Biosci, PMID 37388246

PXD042334 no publication (from MassIVE)
Dataset title: SoDA-PAL Protein Profiling Proteomics of Sorgoleone Catabolizing Microbial Isolate Acinetobacter pittii SO1
Possible reference: Van Fossen, EM. et al. (2024) Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in Acinetobacter pittii., Appl Environ Microbiol, PMID 39248464

PXD042327 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic and functional characterisation of Extracellular Vesicles from collagen VI deficient human fibroblasts reveals a role in cell motility.
Possible reference: Badosa, C. et al. (2023) Proteomic and functional characterisation of extracellular vesicles from collagen VI deficient human fibroblasts reveals a role in cell motility., Sci Rep, PMID 37670049

PXD042309 no publication (from PanoramaPublic)
Dataset title: S-Adenosylmethionine Negatively Regulates the Mitochondrial Respiratory Chain Repressor MCJ in the Liver
Possible reference: Barbier-Torres, L. et al. (2024) S-Adenosylmethionine Negatively Regulates the Mitochondrial Respiratory Chain Repressor MCJ in the Liver., Int J Biol Sci, PMID 38385082

PXD042307 Dataset with its publication pending (from PRIDE)
Dataset title: Direct mapping of ligandable tyrosines and lysines in cells with chiral sulfonyl fluoride probes
Possible reference: Chen, Y. et al. (2023) Direct mapping of ligandable tyrosines and lysines in cells with chiral sulfonyl fluoride probes., Nat Chem, PMID 37460812

PXD042301 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process.
Possible reference: Gerlach, GF. et al. (2023) Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process., Front Cell Dev Biol, PMID 37325559

PXD042266 Dataset with its publication pending (from PRIDE)
Dataset title: Direct mass spectrometry-based detection and antibody sequencing of Monoclonal Gammopathy of Undetermined Significance from patient serum
Possible reference: Peng, W. et al. (2023) Direct Mass Spectrometry-Based Detection and Antibody Sequencing of Monoclonal Gammopathy of Undetermined Significance from Patient Serum: A Case Study., J Proteome Res, PMID 37499263

PXD042262 no publication (from MassIVE)
Dataset title: Systems level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation
Possible reference: Rodina, A. et al. (2023) Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation., Nat Commun, PMID 37353488

PXD042243 Dataset with its publication pending (from PRIDE)
Dataset title: Design of a mucin-selective protease for targeted degradation of cancer-associated mucins
Possible reference: Pedram, K. et al. (2024) Design of a mucin-selective protease for targeted degradation of cancer-associated mucins., Nat Biotechnol, PMID 37537499

PXD042234 Dataset with its publication pending (from PRIDE)
Dataset title: Mesothelin secretion by pancreatic cancer cells co-opts macrophages and promotes metastasis
Possible reference: Luckett, T. et al. (2024) Mesothelin Secretion by Pancreatic Cancer Cells Co-opts Macrophages and Promotes Metastasis., Cancer Res, PMID 38356443

PXD042200 Dataset with its publication pending (from PRIDE)
Dataset title: Deep Proteome of the Developing Chick Midbrain
Possible reference: Stepler, KE. et al. (2023) Deep Proteome of the Developing Chick Midbrain., J Proteome Res, PMID 37616547

PXD042179 Dataset with its publication pending (from PRIDE)
Dataset title: Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes
Possible reference: Dereli, I. et al. (2023) Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes., bioRxiv, PMID 38077023

PXD042130 Dataset with its publication pending (from jPOST)
Dataset title: Disruption of the Productive Encounter Complex Results in Dysregulation of DIAPH1 Activity
Possible reference: Theophall, GG. et al. (2023) Disruption of the productive encounter complex results in dysregulation of DIAPH1 activity., J Biol Chem, PMID 37832872

PXD042127 no publication (from MassIVE)
Dataset title: Stable isotope informed metaproteogenomics of an anaerobic syntrophic acetate oxidizing consortium
Possible reference: McDaniel, EA. et al. (2023) Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium., ISME J, PMID 37880541

PXD042124 Dataset with its publication pending (from jPOST)
Dataset title: Helicobacter pylori cagA+ induces cancer-associated fibroblasts proliferation and migration in vitro
Possible reference: Gonciarz, W. et al. (2019) The effect of Helicobacter pylori infection and different H. pylori components on the proliferation and apoptosis of gastric epithelial cells and fibroblasts., PLoS One, PMID 31390383

PXD042103 Dataset with its publication pending (from PRIDE)
Dataset title: HDL functionality is dependent on hepatocyte stress defense factors NRF1 and NRF2
Possible reference: Trites, MJ. et al. (2023) HDL functionality is dependent on hepatocyte stress defense factors Nrf1 and Nrf2., Front Physiol, PMID 37501930

PXD042090 Dataset with its publication pending (from PRIDE)
Dataset title: Cas1-Cas2 and DnaK physically and functionally interact to modulate CRISPR Adaptation
Possible reference: Killelea, T. et al. (2023) Cas1-Cas2 physically and functionally interacts�with DnaK to modulate CRISPR Adaptation., Nucleic Acids Res, PMID 37264902

PXD042079 Dataset with its publication pending (from PRIDE)
Dataset title: The V-ATPase complex component RNAseK is required for lysosomal hydrolase delivery and autophagosome degradation
Possible reference: Makar, AN. et al. (2024) The V-ATPase complex component RNAseK is required for lysosomal hydrolase delivery and autophagosome degradation., Nat Commun, PMID 39231962

PXD042077 Dataset with its publication pending (from PRIDE)
Dataset title: Versatile human cardiac tissues engineered with perfusable heart extracellular microenvironment for biomedical applications
Possible reference: Min, S. et al. (2024) Versatile human cardiac tissues engineered with perfusable heart extracellular microenvironment for biomedical applications., Nat Commun, PMID 38519491

PXD042030 Dataset with its publication pending (from iProX)
Dataset title: Quantitative proteomics profiling during the development of fungal fluconazole resistance
Possible reference: Gutierrez-Gongora, D. et al. (2024) Natural compounds from freshwater mussels disrupt fungal virulence determinants and influence fluconazole susceptibility in the presence of macrophages in Cryptococcus neoformans., Microbiol Spectr, PMID 38329361

PXD042024 Dataset with its publication pending (from PRIDE)
Dataset title: Vitamin D binding protein induces skeletal muscle atrophy and contributes to cancer-associated muscle wasting
Possible reference: Raiteri, T. et al. (2026) Vitamin D binding protein induces skeletal muscle atrophy and contributes to cancer-associated muscle wasting independently of vitamin D status in preclinical models., Nat Commun, PMID 41963327

PXD041990 Dataset with its publication pending (from PRIDE)
Dataset title: Carnitine palmitoyltransferase 1A promotes mitochondrial fission by enhancing MFF succinylation in ovarian cancer
Possible reference: Zhu, Y. et al. (2023) Carnitine palmitoyltransferase 1A promotes mitochondrial fission by enhancing MFF succinylation in ovarian cancer., Commun Biol, PMID 37291333

PXD041978 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach
Possible reference: Noszka, M. et al. (2023) Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach., Nat Commun, PMID 37872172

PXD041973 Dataset with its publication pending (from PRIDE)
Dataset title: Removal of senescent cells reduces the viral load and attenuates pulmonary and systemic inflammation in SARS-CoV-2-infected, aged hamsters
Possible reference: Delval, L. et al. (2023) Removal of senescent cells reduces the viral load and attenuates pulmonary and systemic inflammation in SARS-CoV-2-infected, aged hamsters., Nat Aging, PMID 37414987

PXD041970 no publication (from MassIVE)
Dataset title: A phase-separated CO2-fixing pyrenoid proteome determined by TurboID in Chlamydomonas reinhardtii
Possible reference: Lau, CS. et al. (2023) A phase-separated CO2-fixing pyrenoid proteome determined by TurboID in Chlamydomonas reinhardtii., Plant Cell, PMID 37195994

PXD041951 Dataset with its publication pending (from PRIDE)
Dataset title: Flavodoxin Landscape in Clostridioides�difficile
Possible reference: Deshpande, A. et al. (2020) Chromosomal Resistance to Metronidazole in Clostridioides difficile Can Be Mediated by Epistasis between Iron Homeostasis and Oxidoreductases., Antimicrob Agents Chemother, PMID 32457109

PXD041938 Dataset with its publication pending (from PRIDE)
Dataset title: Multiomics analysis of naturally efficacious LNP coronas reveals high-density lipoprotein is necessary for LNP function. Individual corona
Possible reference: Liu, K. et al. (2023) Multiomics analysis of naturally efficacious lipid nanoparticle coronas reveals high-density lipoprotein is necessary for their function., Nat Commun, PMID 37414857

PXD041928 no publication (from MassIVE)
Dataset title: A region-resolved proteomic map of the human brain enabled by high-throughput proteomics
Possible reference: T�shaus, J. et al. (2023) A region-resolved proteomic map of the human brain enabled by high-throughput proteomics., EMBO J, PMID 37916885

PXD041925 Dataset with its publication pending (from PRIDE)
Dataset title: Multiomics analysis of naturally efficacious LNP coronas reveals high-density lipoprotein is necessary for LNP function. Rat Plasma
Possible reference: Liu, K. et al. (2023) Multiomics analysis of naturally efficacious lipid nanoparticle coronas reveals high-density lipoprotein is necessary for their function., Nat Commun, PMID 37414857

PXD041924 Dataset with its publication pending (from PRIDE)
Dataset title: Taxanes trigger cancer cell killing in vivo by inducing non-canonical T cell cytotoxicity
Possible reference: Vennin, C. et al. (2023) Taxanes trigger cancer cell killing in�vivo by inducing non-canonical T�cell cytotoxicity., Cancer Cell, PMID 37311414

PXD041910 no publication (from MassIVE)
Dataset title: Comparative proteomic analysis of tail regeneration in the green anole lizard Anolis carolinensis
Possible reference: Xu, C. et al. (2024) Comparative proteomic analysis of tail regeneration in the green anole lizard, Anolis carolinensis., Nat Sci (Weinh), PMID 38505006

PXD041907 Dataset with its publication pending (from PRIDE)
Dataset title: The Toxoplasma protein phosphatase 6 catalytic subunit (TgPP6C) is essential for cell cycle progression and virulence
Possible reference: Liang, QL. et al. (2023) The Toxoplasma protein phosphatase 6 catalytic subunit (TgPP6C) is essential for cell cycle progression and virulence., PLoS Pathog, PMID 38091362

PXD041899 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome and Phosphoproteome of Circulating Extracellular Vesicles in Type 1 Diabetes and Controls
Possible reference: Casu, A. et al. (2023) The proteome and phosphoproteome of circulating extracellular vesicle-enriched preparations are associated with characteristic clinical features in type 1 diabetes., Front Endocrinol (Lausanne), PMID 37576973

PXD041898 Dataset with its publication pending (from PRIDE)
Dataset title: XCP1 cleaves Pathogenesis-related protein 1 into CAPE9 for systemic immunity in Arabidopsis
Possible reference: Chen, YL. et al. (2023) XCP1 cleaves Pathogenesis-related protein 1 into CAPE9 for systemic immunity in Arabidopsis., Nat Commun, PMID 37542077

PXD041888 no publication (from MassIVE)
Dataset title: Brain cell type specific proteomics approach to discover pathological mechanisms in the childhood CNS disorder mucolipidosis type IV
Possible reference: Sangster, M. et al. (2023) Brain cell type specific proteomics approach to discover pathological mechanisms in the childhood CNS disorder mucolipidosis type IV., Front Mol Neurosci, PMID 37609073

PXD041883 no publication (from MassIVE)
Dataset title: mARC1 knockdown protects liver from diet-induced NASH in mouse
Possible reference: Guo, Y. et al. (2024) Liver-specific mitochondrial amidoxime-reducing component 1 (Mtarc1) knockdown protects the liver from diet-induced MASH in multiple mouse models., Hepatol Commun, PMID 38696369

PXD041862 Dataset with its publication pending (from PRIDE)
Dataset title: Integrative analysis reveals a conserved role for the amyloid precursor protein in proteostasis during aging
Possible reference: Nithianandam, V. et al. (2023) Integrative analysis reveals a conserved role for the amyloid precursor protein in proteostasis during aging., Nat Commun, PMID 37923712

PXD041858 no publication (from MassIVE)
Dataset title: Light Activated BioID (LAB): an optically activated proximity labeling system to study protein-protein interactions
Possible reference: Shafraz, O. et al. (2023) Light-activated BioID - an optically activated proximity labeling system to study protein-protein interactions., J Cell Sci, PMID 37756605

PXD041852 no publication (from MassIVE)
Dataset title: Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes
Possible reference: Younis, S. et al. (2023) Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes., Proc Natl Acad Sci U S A, PMID 37252988

PXD041850 Dataset with its publication pending (from PRIDE)
Dataset title: Astrocyte-Oligodendrocyte interaction regulates central nervous system regeneration
Possible reference: Molina-Gonzalez, I. et al. (2023) Astrocyte-oligodendrocyte interaction regulates central nervous system regeneration., Nat Commun, PMID 37291151

PXD041848 no publication (from MassIVE)
Dataset title: Complexome Profiling of the chloroplast proteome from Arabidopsis thaliana
Possible reference: R�hricht, H. et al. (2021) Complexome profiling reveals novel insights into the composition and assembly of the mitochondrial ATP synthase of Arabidopsis thaliana., Biochim Biophys Acta Bioenerg, PMID 33785316

PXD041844 Dataset with its publication pending (from PRIDE)
Dataset title: Longitudinal Effects of Elexacaftor/Tezacaftor/Ivacaftor on Sputum Viscoelastic Properties, Airway Infection and Inflammation in Patients with Cystic Fibrosis
Possible reference: Schaupp, L. et al. (2023) Longitudinal effects of elexacaftor/tezacaftor/ivacaftor on sputum viscoelastic properties, airway infection and inflammation in patients with cystic fibrosis., Eur Respir J, PMID 37414422

PXD041837 Dataset with its publication pending (from PRIDE)
Dataset title: Involvement of extracellular vesicles in the progression, diagnosis, treatment, and prevention of whole-body ionizing radiation-induced immune dysfunction.
Possible reference: Seim, RF. et al. (2023) Involvement of extracellular vesicles in the progression, diagnosis, treatment, and prevention of whole-body ionizing radiation-induced immune dysfunction., Front Immunol, PMID 37404812

PXD041824 Dataset with its publication pending (from PRIDE)
Dataset title: ALK signalling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition
Possible reference: Boren�s, M. et al. (2024) ALK signaling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition., Proc Natl Acad Sci U S A, PMID 38154064

PXD041804 Dataset with its publication pending (from PRIDE)
Dataset title: Immunoprecipitation methods impact the peptide repertoire in immunopeptidomics
Possible reference: Kuznetsov, A. et al. (2020) Critical Review of Existing MHC I Immunopeptidome Isolation Methods., Molecules, PMID 33228004

PXD041801 no publication (from MassIVE)
Dataset title: Integrated post-genomic cell wall analysis reveals floating biofilm formation associated with high expression of flocculins in the pathogen Candida krusei.
Possible reference: Alvarado, M. et al. (2023) Integrated post-genomic cell wall analysis reveals floating biofilm formation associated with high expression of flocculins in the pathogen Pichia kudriavzevii., PLoS Pathog, PMID 37196016

PXD041796 Dataset with its publication pending (from jPOST)
Dataset title: PP2A mediates phosphorylation events during shade avoidance response in Arabidopsis
Possible reference: Li, F. et al. (2025) Dephosphorylation of bZIP59 by PP2A ensures appropriate shade avoidance response in Arabidopsis., Dev Cell, PMID 39536759

PXD041794 Dataset with its publication pending (from PRIDE)
Dataset title: A Bioconductor workflow for processing, evaluating and interpreting expression proteomics data: Case data
Possible reference: Hutchings, C. et al. (2023) A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data., F1000Res, PMID 38021401

PXD041784 Dataset with its publication pending (from jPOST)
Dataset title: HtrA1 prevents and reverses Î±-synuclein aggregation, rendering it non-toxic and seeding incompetent
Possible reference: Chen, S. et al. (2023) HtrA1 prevents and reverses α-synuclein aggregation, rendering it non-toxic and seeding incompetent., Res Sq, PMID 37674720

PXD041783 Dataset with its publication pending (from PRIDE)
Dataset title: Defective mitochondrial translation due to loss of COX14 function triggers ROS-induced inflammation in liver
Possible reference: Aich, A. et al. (2024) Defective mitochondrial COX1 translation due to loss of COX14 function triggers ROS-induced inflammation in mouse liver., Nat Commun, PMID 39134548

PXD041781 Dataset with its publication pending (from PRIDE)
Dataset title: Plasma Instead of Serum Avoids Critical Confounding of Clinical Metabolomics Studies by Platelets – serum and plasma
Possible reference: Hagn, G. et al. (2024) Plasma Instead of Serum Avoids Critical Confounding of Clinical Metabolomics Studies by Platelets., J Proteome Res, PMID 38520676

PXD041726 no publication (from MassIVE)
Dataset title: Determining Site Specific Glycan Profiles of Recombinant SARS CoV 2 Spike Proteins from Multiple Sources
Possible reference: Burke, MC. et al. (2023) Determining Site-Specific Glycan Profiles of Recombinant SARS-CoV-2 Spike Proteins from Multiple Sources., J Proteome Res, PMID 37647588

PXD041712 no publication (from MassIVE)
Dataset title: The TDG interactome connects active DNA demethylation with chromatin and RNA biology
Possible reference: Richina, F. et al. (2025) The TDG protein environment connects active DNA demethylation with chromatin and RNA biology., Cell Mol Life Sci, PMID 41291101

PXD041707 Dataset with its publication pending (from PRIDE)
Dataset title: A bacterial effector manipulates host lysosomal protease activity-dependent plasticity in cell death modalities to facilitate infection
Possible reference: Lu, Z. et al. (2025) A bacterial effector manipulates host lysosomal protease activity-dependent plasticity in cell death modalities to facilitate infection., Proc Natl Acad Sci U S A, PMID 39964716

PXD041696 Dataset with its publication pending (from PRIDE)
Dataset title: mTORC2-NDRG1-Cdc42 axis couples fasting to mitochondrial fission
Possible reference: Martinez-Lopez, N. et al. (2023) mTORC2-NDRG1-CDC42 axis couples fasting to mitochondrial fission., Nat Cell Biol, PMID 37386153

PXD041689 Dataset with its publication pending (from PRIDE)
Dataset title: Fibrotic Response to anti-CSF-1R Treatment Potentiates Glioblastoma Recurrence
Possible reference: Watson, SS. et al. (2024) Fibrotic response to anti-CSF-1R therapy potentiates glioblastoma recurrence., Cancer Cell, PMID 39255775

PXD041686 Dataset with its publication pending (from PRIDE)
Dataset title: Transcriptome and proteome analysis reveals the anti-cancer properties of Hypnea musciformis macroalgae extract in liver and intestinal cancer cells
Possible reference: Begolli, R. et al. (2023) Transcriptome and proteome analysis reveals the anti-cancer properties of Hypnea musciformis marine macroalga extract in liver and intestinal cancer cells., Hum Genomics, PMID 37525271

PXD041680 Dataset with its publication pending (from jPOST)
Dataset title: Proteomics in striatal EVs from WT and R6/1 mice
Possible reference: Solana-Balaguer, J. et al. (2024) Motor skill learning modulates striatal extracellular vesicles' content in a mouse model of Huntington's disease., Cell Commun Signal, PMID 38863004

PXD041679 Dataset with its publication pending (from PRIDE)
Dataset title: Transcription-coupled DNA-Protein Crosslink repair by CSB and CRL4(CSA)-mediated degradation
Possible reference: van Sluis, M. et al. (2024) Transcription-coupled DNA-protein crosslink repair by CSB and CRL4CSA-mediated degradation., Nat Cell Biol, PMID 38600236

PXD041625 Dataset with its publication pending (from PRIDE)
Dataset title: Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumor deposits in colorectal cancer
Possible reference: Brouwer, NP. et al. (2023) Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumour deposits in colorectal cancer., J Pathol, PMID 37792663

PXD041613 Dataset with its publication pending (from jPOST)
Dataset title: gastric adenocarcinoma HER2 mass spectrometry-based quantification
Possible reference: Xu, B. et al. (2023) A comparative study of gastric adenocarcinoma HER2 IHC phenotype and mass spectrometry-based quantification., Front Oncol, PMID 37350943

PXD041612 Dataset with its publication pending (from iProX)
Dataset title: MS Data of CO-IP in LBR-GFP-expressing Mitotic Cell
Possible reference: Chen, S. et al. (2024) USP44 regulates HEXIM1 stability to inhibit tumorigenesis and metastasis of oral squamous cell carcinoma., Biol Direct, PMID 39722007

PXD041600 Dataset with its publication pending (from iProX)
Dataset title: Dynamic phosphoproteomics profiling captured early signaling events of cold acclimation in larval zebrafish
Possible reference: Yan, J. et al. (2026) Dynamic Phosphoproteomic Profiling Captured Early Signaling Events for Cold Acclimation in Larval Zebrafish., Proteomics, PMID 41906457

PXD041589 no publication (from MassIVE)
Dataset title: High efficiency preparation of monodisperse plasma membrane derived extracellular vesicles for therapeutic applications
Possible reference: Alter, CL. et al. (2023) High efficiency preparation of monodisperse plasma membrane derived extracellular vesicles for therapeutic applications., Commun Biol, PMID 37137966

PXD041562 Dataset with its publication pending (from PRIDE)
Dataset title: Transmembrane nuclease NUMEN/ENDOD1 regulates DNA repair pathway choice at the nuclear periphery
Possible reference: Chen, B. et al. (2023) Transmembrane nuclease NUMEN/ENDOD1 regulates DNA repair pathway choice at the nuclear periphery., Nat Cell Biol, PMID 37322289

PXD041551 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of two novel proteins involved in mitochondrial DNA anchoring in Trypanosoma brucei
Possible reference: Amodeo, S. et al. (2023) Characterization of two novel proteins involved in mitochondrial DNA anchoring in Trypanosoma brucei., PLoS Pathog, PMID 37459364

PXD041538 Dataset with its publication pending (from iProX)
Dataset title: Multi-omics analysis explores the effect of chronic exercise on liver metabolic reprogramming in mice
Possible reference: Lu, Z. et al. (2023) Multi-omics analysis explores the effect of chronic exercise on liver metabolic reprogramming in mice., Front Cell Dev Biol, PMID 37408533

PXD041493 Dataset with its publication pending (from jPOST)
Dataset title: Top-Down Analysis of Supercharged Proteins Using Collision-, Electron-, and Photon-Based Activation Methods
Possible reference: Juetten, KJ. et al. (2023) Top-Down Analysis of Supercharged Proteins Using Collision-, Electron-, and Photon-Based Activation Methods., J Am Soc Mass Spectrom, PMID 37358018

PXD041485 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic characterization of aging-driven changes in the mouse brain by co-expression network analysis
Possible reference: Tsumagari, K. et al. (2023) Proteomic characterization of aging-driven changes in the mouse brain by co-expression network analysis., Sci Rep, PMID 37875604

PXD041452 Dataset with its publication pending (from PRIDE)
Dataset title: Human - plasma extracellular vesicles from pSS patients, SLE patients and HD
Possible reference: Ferrant, J. et al. (2023) Phenotypic and proteomic analysis of plasma extracellular vesicles highlights them as potential biomarkers of primary Sj�gren syndrome., Front Immunol, PMID 37529039

PXD041418 Dataset with its publication pending (from PRIDE)
Dataset title: A genetic deficiency screen in vivo reveals rescue mechanisms of mitochondrial dysfunction
Possible reference: Russi, M. et al. (2020) A Drosophila model of Friedreich ataxia with CRISPR/Cas9 insertion of GAA repeats in the frataxin gene reveals in vivo protection by N-acetyl cysteine., Hum Mol Genet, PMID 32744307

PXD041412 Dataset with its publication pending (from PRIDE)
Dataset title: Filter-aided expansion proteomics
Possible reference: Dong, Z. et al. (2024) Spatial proteomics of single cells and organelles on tissue slides using filter-aided expansion proteomics., Nat Commun, PMID 39477916

PXD041411 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of fatty liver induced by starvation of medaka fish larvae
Possible reference: Ikeda, T. et al. (2023) Proteomic analysis of fatty liver induced by starvation of medaka fish larvae., Cell Struct Funct, PMID 37380437

PXD041362 Dataset with its publication pending (from iProX)
Dataset title: Human Pancreatic cancer sh-RUFY1 MIAPaCa-2 cell label-free quantification proteomics analysis
Possible reference: Miao, X. et al. (2024) Systems Pharmacodynamic Model of Combined Gemcitabine and Trabectedin in Pancreatic Cancer Cells. Part I: Effects on Signal Transduction Pathways Related to Tumor Growth., J Pharm Sci, PMID 38498417

PXD041359 Dataset with its publication pending (from PRIDE)
Dataset title: Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein
Possible reference: Russell Lewis, B. et al. (2023) Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein., Nat Commun, PMID 37463890

PXD041355 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of an outer membrane protease of Rickettsia rickettsii responsible for maturation of surface exposed autotransporters
Possible reference: Nock, AM. et al. (2023) Identification of an autotransporter peptidase of Rickettsia rickettsii responsible for maturation of surface exposed autotransporters., PLoS Pathog, PMID 37523399

PXD041351 Dataset with its publication pending (from PRIDE)
Dataset title: Adipocyte p53 coordinates the adipose tissue immune cell landscape upon intermittent fasting
Possible reference: Reinisch, I. et al. (2024) Adipocyte p53 coordinates the response to intermittent fasting by regulating adipose tissue immune cell landscape., Nat Commun, PMID 38360943

PXD041346 Dataset with its publication pending (from PRIDE)
Dataset title: Cellular Validation of Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2
Possible reference: Gan, J. et al. (2023) Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2., ACS Chem Biol, PMID 37642399

PXD041345 Dataset with its publication pending (from jPOST)
Dataset title: Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells
Possible reference: Wang, H. et al. (2023) Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells., J Integr Plant Biol, PMID 37226855

PXD041343 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins Regulated by H3K36me3
Possible reference: Yin, J. et al. (2023) Targeted Profiling of Epitranscriptomic Reader, Writer, and Eraser Proteins Regulated by H3K36me3., Anal Chem, PMID 37296074

PXD041314 Dataset with its publication pending (from PRIDE)
Dataset title: Assigning functionality to cysteines by base editing of cancer dependency genes
Possible reference: Li, H. et al. (2023) Assigning functionality to cysteines by base editing of cancer dependency genes., Nat Chem Biol, PMID 37783940

PXD041308 Dataset with its publication pending (from PRIDE)
Dataset title: Plasma proteomic profiling of bacterial cold-water disease-resistant and -susceptible rainbow trout lines and biomarker discovery
Possible reference: Wiens, GD. et al. (2023) Plasma proteomic profiling of bacterial cold water disease-resistant and -susceptible rainbow trout lines and biomarker discovery., Front Immunol, PMID 37928534

PXD041301 Dataset with its publication pending (from PRIDE)
Dataset title: The proteome of bacterial membrane vesicles in Escherichia coli - a time course comparison study in two different media
Possible reference: Yu, MSC. et al. (2024) The proteome of bacterial membrane vesicles in Escherichia coli-a time course comparison study in two different media., Front Microbiol, PMID 38510998

PXD041296 Dataset with its publication pending (from PRIDE)
Dataset title: Functional viromic screens uncover regulatory RNA elements
Possible reference: Seo, JJ. et al. (2023) Functional viromic screens uncover regulatory RNA elements., Cell, PMID 37413987

PXD041295 Dataset with its publication pending (from jPOST)
Dataset title: Rapid and Highly-Efficient Purification of Extracellular Vesicles Enabled by TiO2 hybridized Spongy-like Polymer
Possible reference: Kanao, E. et al. (2023) Rapid and Highly Efficient Purification of Extracellular Vesicles Enabled by a TiO2 Hybridized Spongy-like Polymer., Anal Chem, PMID 37703188

PXD041280 Dataset with its publication pending (from PRIDE)
Dataset title: A conserved tryptophan in the acylated segment controls Î²2- integrin-independent cell penetration of RTX toxins
Possible reference: Osickova, A. et al. (2023) A conserved tryptophan in the acylated segment of RTX toxins controls their β2 integrin-independent cell penetration., J Biol Chem, PMID 37390987

PXD041229 Dataset with its publication pending (from PRIDE)
Dataset title: The genetic and dietary landscape of the muscle insulin signalling network
Possible reference: van Gerwen, J. et al. (2024) The genetic and dietary landscape of the muscle insulin signalling network., Elife, PMID 38329473

PXD041215 Dataset with its publication pending (from PRIDE)
Dataset title: Changes in Protein Turn-over Rates Regulate Tryptophan and Glucosinolate Biosynthesis, IAA Transport and Photosynthesis in Arabidopsis Growth and Defense Transitions
Possible reference: Abukhalaf, M. et al. (2023) Changing turn-over rates regulate abundance of tryptophan, GS biosynthesis, IAA transport and photosynthesis proteins in Arabidopsis growth defense transitions., BMC Biol, PMID 37940940

PXD041197 Dataset with its publication pending (from PRIDE)
Dataset title: Mtfp1 ablation enhances respiration and protects against hepatic steatosis
Possible reference: Patitucci, C. et al. (2023) Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis., Nat Commun, PMID 38123539

PXD041186 Dataset with its publication pending (from PRIDE)
Dataset title: SAA1-dependent reprogramming of adipocytes by tumor cells is associated with triple negative breast cancer aggressiveness
Possible reference: Rybinska, I. et al. (2024) SAA1-dependent reprogramming of adipocytes by tumor cells is associated with triple negative breast cancer aggressiveness., Int J Cancer, PMID 38289016

PXD041163 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted proteomic quantitation of NRF2 signaling and predictive biomarkers in HNSCC
Possible reference: Wamsley, NT. et al. (2023) Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC., Mol Cell Proteomics, PMID 37716475

PXD041162 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted proteomic quantitation of NRF2 signaling and predictive biomarkers in HNSCC
Possible reference: Wamsley, NT. et al. (2023) Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC., Mol Cell Proteomics, PMID 37716475

PXD041151 Dataset with its publication pending (from PRIDE)
Dataset title: Detection of Nâglycoprotein associated with IgA nephropathy in urine as a potential diagnostic biomarker using glycosylated proteomic analysis
Possible reference: Liu, J. et al. (2023) Detection of N‑glycoprotein associated with IgA nephropathy in urine as a potential diagnostic biomarker using glycosylated proteomic analysis., Exp Ther Med, PMID 37753295

PXD041149 Dataset with its publication pending (from iProX)
Dataset title: Venom proteome of two egg parasitic wasps
Possible reference: Nguyen, TT. et al. (2013) Early presence of an enolase in the oviposition injecta of the aphid parasitoid Aphidius ervi analyzed with chitosan beads as artificial hosts., J Insect Physiol, PMID 23201274

PXD041130 no publication (from MassIVE)
Dataset title: The intracellular helical bundle of human glucose transporter GLUT4 is of importance for complex formation with ASPL
Possible reference: Huang, P. et al. (2023) The intracellular helical bundle of human glucose transporter GLUT4 is important for complex formation with ASPL., FEBS Open Bio, PMID 37731227

PXD041118 Dataset with its publication pending (from jPOST)
Dataset title: A One-pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles
Possible reference: Liu, YK. et al. (2023) One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles., J Proteome Res, PMID 37702715

PXD041110 Dataset with its publication pending (from PRIDE)
Dataset title: Yolk-deprived Caenorhabditis elegans secure brood size at the expense of competitive fitness
Possible reference: Geens, E. et al. (2023) Yolk-deprived Caenorhabditis elegans secure brood size at the expense of competitive fitness., Life Sci Alliance, PMID 37059473

PXD041093 Dataset with its publication pending (from PRIDE)
Dataset title: Cerebrospinal fluid proteomics in recent-onset Narcolepsy type 1 reveals activation of the complement system
Possible reference: Ayoub, I. et al. (2023) Cerebrospinal fluid proteomics in recent-onset Narcolepsy type 1 reveals activation of the complement system., Front Immunol, PMID 37122721

PXD041085 Dataset with its publication pending (from jPOST)
Dataset title: Mapping adipocyte interactome networks by HaloTag-enrichment–mass spectrometry
Possible reference: Yazaki, J. et al. (2024) Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry., Biol Methods Protoc, PMID 38884001

PXD041069 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Landscape of Endoplasmic Reticulum Remodeling During Neurogenesis via Combinatorial Selective ER-phagy
Possible reference: Hoyer, MJ. et al. (2023) Combinatorial selective ER-phagy remodels the ER during neurogenesis., bioRxiv, PMID 37425907

PXD041046 Dataset with its publication pending (from PRIDE)
Dataset title: SAPrIm, A Semi-Automated Protocol for mid-throughput Immunopeptidomics
Possible reference: Lim Kam Sian, TCC. et al. (2023) SAPrIm, a semi-automated protocol for mid-throughput immunopeptidomics., Front Immunol, PMID 37334365

PXD041040 Dataset with its publication pending (from PRIDE)
Dataset title: A Treg specific long non-coding RNA maintains immune-metabolic homeostasis in ageing liver
Possible reference: Ding, C. et al. (2023) A Treg-specific long noncoding RNA maintains immune-metabolic homeostasis in aging liver., Nat Aging, PMID 37277640

PXD041035 Dataset with its publication pending (from PRIDE)
Dataset title: Identification and characterization of CC-AMP1-like and CC-AMP2-like peptides in Capsicum spp.
Possible reference: Culver, KD. et al. (2024) Identification and Characterization of CC-AMP1-like and CC-AMP2-like Peptides in Capsicum spp., J Proteome Res, PMID 38367000

PXD041022 Dataset with its publication pending (from jPOST)
Dataset title: Ustilago maydis PR-1-like protein has evolved two distinct domains for dual virulence activities
Possible reference: Lin, YH. et al. (2023) Ustilago maydis PR-1-like protein has evolved two distinct domains for dual virulence activities., Nat Commun, PMID 37716995

PXD041013 no publication (from MassIVE)
Dataset title: Comprehensive Characterization of Endogenous Phospholamban Proteoforms Enabled by Photocleavable Surfactant and Top-down Proteomics
Possible reference: Rogers, HT. et al. (2023) Comprehensive Characterization of Endogenous Phospholamban Proteoforms Enabled by Photocleavable Surfactant and Top-down Proteomics., bioRxiv, PMID 37090578

PXD041009 Dataset with its publication pending (from jPOST)
Dataset title: Computational ranking-assisted identification of Plexin-B2 in homotypic and heterotypic clustering of circulating tumor cells in breast cancer
Possible reference: Schuster, E. et al. (2023) Computational ranking-assisted identification of Plexin-B2 in homotypic and heterotypic clustering of circulating tumor cells in breast cancer metastasis., bioRxiv, PMID 37090580

PXD041005 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic-based computational stratification of intermediate-risk prostate cancer patients.
Possible reference: Zhong, Q. et al. (2024) Proteomic-based stratification of intermediate-risk prostate cancer patients., Life Sci Alliance, PMID 38052461

PXD041000 Dataset with its publication pending (from jPOST)
Dataset title: Application of peptide barcoding to obtain high-affinity anti-PD-1 nanobodies
Possible reference: Miyazaki, T. et al. (2023) Application of peptide barcoding to obtain high-affinity anti-PD-1 nanobodies., J Biosci Bioeng, PMID 37487915

PXD040995 no publication (from MassIVE)
Dataset title: Arginine reprograms metabolism in liver cancer via RBM39
Possible reference: Mossmann, D. et al. (2023) Arginine reprograms metabolism in liver cancer via RBM39., Cell, PMID 37804830

PXD040985 no publication (from MassIVE)
Dataset title: Beta-hydroxybutyrate is a metabolic regulator of proteostasis in aging and Alzheimer disease
Possible reference: Madhavan, SS. et al. (2023) β-hydroxybutyrate is a metabolic regulator of proteostasis in the aged and Alzheimer disease brain., bioRxiv, PMID 37461525

PXD040953 Dataset with its publication pending (from PRIDE)
Dataset title: UBR5 Forms Ligand-Dependent Complexes on Chromatin to Regulate Nuclear Hormone Receptor Stability
Possible reference: Tsai, JM. et al. (2023) UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability., Mol Cell, PMID 37478846

PXD040948 Dataset with its publication pending (from PRIDE)
Dataset title: The heme-responsive PrrH sRNA regulates Pseudomonas aeruginosa pyochelin gene expression
Possible reference: Hoang, TM. et al. (2023) The heme-responsive PrrH sRNA regulates Pseudomonas aeruginosa pyochelin gene expression., bioRxiv, PMID 36712080

PXD040947 Dataset with its publication pending (from PRIDE)
Dataset title: Expanding the Characterization of Microbial Ecosystems using DIA-PASEF Metaproteomics
Possible reference: G�mez-Varela, D. et al. (2023) Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics., Front Microbiol, PMID 37908546

PXD040941 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery of a Highly Potent and Selective HDAC3 and HDAC8 PROTAC Dual Degrader
Possible reference: Xiao, Y. et al. (2024) Discovery of a Highly Potent and Selective HDAC8 Degrader: Advancing the Functional Understanding and Therapeutic Potential of HDAC8., J Med Chem, PMID 38949959

PXD040935 Dataset with its publication pending (from PRIDE)
Dataset title: Distinct microRNA and protein profiles of extracellular vesicles secreted from myotubes from morbidly obese donors with type 2 diabetes in response to electrical pulse stimulation
Possible reference: Aas, V. et al. (2023) Distinct microRNA and protein profiles of extracellular vesicles secreted from myotubes from morbidly obese donors with type 2 diabetes in response to electrical pulse stimulation., Front Physiol, PMID 37064893

PXD040919 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analyses of venom of Pepsis decorata
Possible reference: Nolasco, M. et al. (2023) Proteomic analyses of venom from a Spider Hawk, Pepsis decorata., J Venom Anim Toxins Incl Trop Dis, PMID 37965483

PXD040918 Dataset with its publication pending (from PRIDE)
Dataset title: Human limbal epithelial cell-derived exosomes cargo profile and their regulatory roles in limbal stromal cells in diabetic and non-diabetic cornea
Possible reference: Verma, N. et al. (2023) MicroRNA and Protein Cargos of Human Limbal Epithelial Cell-Derived Exosomes and Their Regulatory Roles in Limbal Stromal Cells of Diabetic and Non-Diabetic Corneas., Cells, PMID 37947602

PXD040915 Dataset with its publication pending (from PRIDE)
Dataset title: Cytochrome c Lysine Acetylation Regulates Cellular Respiration and Cell Death in Ischemic Skeletal Muscle
Possible reference: Morse, PT. et al. (2023) Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle., Nat Commun, PMID 37443314

PXD040897 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative, TMT-based proteomics and phosphoproteomics analysis of SARS-COV-2 infected cells.
Possible reference: Dos Santos, FM. et al. (2025) Dynamic Cellular Proteome Remodeling during SARS-CoV-2 Infection. Identification of Plasma Protein Readouts., J Proteome Res, PMID 39593238

PXD040868 Dataset with its publication pending (from PRIDE)
Dataset title: Resolving the temporal and spatial splenic proteome during fungal infection for putative dual perspective biomarker discovery
Possible reference: Muselius, B. et al. (2023) Resolving the Temporal Splenic Proteome during Fungal Infection for Discovery of Putative Dual Perspective Biomarker Signatures., J Am Soc Mass Spectrom, PMID 37222660

PXD040866 Dataset with its publication pending (from PRIDE)
Dataset title: "Dissection of paracrine/autocrine interplay in lung tumor microenvironment mimicking cancer cell-monocyte co-culture models reveals proteins that promote inflammation and metastasis"
Possible reference: Amin, A. et al. (2023) Dissection of paracrine/autocrine interplay in lung tumor microenvironment mimicking cancer cell-monocyte co-culture models reveals proteins that promote inflammation and metastasis., BMC Cancer, PMID 37784035

PXD040858 Dataset with its publication pending (from PRIDE)
Dataset title: A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics
Possible reference: Li, X. et al. (2023) A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics., Cell Rep Methods, PMID 37426762

PXD040852 Dataset with its publication pending (from PRIDE)
Dataset title: Bacterial Secretion Systems Contribute to Rapid Tissue Decay in Button Mushroom Soft Rot Disease
Possible reference: Wein, P. et al. (2023) Bacterial secretion systems contribute to rapid tissue decay in button mushroom soft rot disease., mBio, PMID 37486262

PXD040847 Dataset with its publication pending (from PRIDE)
Dataset title: Altered profile of glycosylated proteins in serum samples obtained from patients with Hashimoto′s thyroiditis following depletion of highly abundant proteins
Possible reference: Xu, Y. et al. (2023) Altered profile of glycosylated proteins in serum samples obtained from patients with Hashimoto's thyroiditis following depletion of highly abundant proteins., Front Immunol, PMID 37457741

PXD040825 Dataset with its publication pending (from PRIDE)
Dataset title: Generation of zero-valent sulfur from dissimilatory sulfate reduction in sulfate-reducing microorganisms
Possible reference: Fang, W. et al. (2020) Generation of zero valent sulfur from dissimilatory sulfate reduction under methanogenic conditions., J Hazard Mater, PMID 31541951

PXD040824 Dataset with its publication pending (from PRIDE)
Dataset title: Subcellular proteomics for determining iron limited remodeling of plastids in the model diatom Thalassiosira pseudonana
Possible reference: Gomes, KM. et al. (2023) Subcellular proteomics for determining iron-limited remodeling of plastids in the model diatom Thalassiosira pseudonana (Bacillariophyta)., J Phycol, PMID 37615442

PXD040822 no publication (from MassIVE)
Dataset title: Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin
Possible reference: Wydorski, PM. et al. (2023) Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin., bioRxiv, PMID 35547846

PXD040819 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative analysis of proteomic adaptations in Enterococcus faecalis and Enterococcus faecium after long term bile acid exposure
Possible reference: Dreyer, A. et al. (2024) Comparative analysis of proteomic adaptations in Enterococcus faecalis and Enterococcus faecium after long term bile acid exposure., BMC Microbiol, PMID 38570789

PXD040818 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic mapping reveals dysregulated angiogenesis in the cerebral arteries of rats with early-onset hypertension
Possible reference: Bastrup, JA. et al. (2023) Proteomic mapping reveals dysregulated angiogenesis in the cerebral arteries of rats with early-onset hypertension., J Biol Chem, PMID 37660920

PXD040807 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profile in the diagnostics of portal hypertension in patients with compensated advanced liver disease
Possible reference: Pastrovic, F. et al. (2024) Serum proteomic profiling of patients with compensated advanced chronic liver disease with and without clinically significant portal hypertension., PLoS One, PMID 38603681

PXD040787 Dataset with its publication pending (from PRIDE)
Dataset title: comparative phosphoproteomics uncover proteins from the mechanobiome in Entamoeba histolytica
Possible reference: Jhingan, GD. et al. (2023) Live Cells Imaging and Comparative Phosphoproteomics Uncover Proteins from the Mechanobiome in Entamoeba histolytica., Int J Mol Sci, PMID 37240072

PXD040783 Dataset with its publication pending (from PRIDE)
Dataset title: The RBPome of influenza A virus mRNA reveals a role for TDP-43 in viral replication
Possible reference: Dupont, M. et al. (2024) The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication., Nucleic Acids Res, PMID 38686810

PXD040769 Dataset with its publication pending (from PRIDE)
Dataset title: Functional genomics identifies extension of complex N-glycans as a mechanism to evade lysis by natural killer cells
Possible reference: Zhuang, X. et al. (2024) Functional genomics identifies N-acetyllactosamine extension of complex N-glycans as a mechanism to evade lysis by natural killer cells., Cell Rep, PMID 38619967

PXD040767 Dataset with its publication pending (from jPOST)
Dataset title: Proteome analysis to understand the promotive effects of safranal on soybean growth under salt stress
Possible reference: Kausar, R. et al. (2024) Proteomic and molecular analyses to understand the promotive effect of safranal on soybean growth under salt stress., J Proteomics, PMID 38218428

PXD040759 Dataset with its publication pending (from jPOST)
Dataset title: Detection of bacteria neutral ceramidase in diabetic foot ulcers with optimized substrate and chemoenzymatic probes
Possible reference: Zou, JX. et al. (2023) Detection of Bacterial Neutral Ceramidase in Diabetic Foot Ulcers with an Optimized Substrate and Chemoenzymatic Probes., Angew Chem Int Ed Engl, PMID 37340712

PXD040758 Dataset with its publication pending (from PRIDE)
Dataset title: Inceptor binds and directs insulin to lysosomal degradation in ï¢-cells
Possible reference: Siehler, J. et al. (2024) Inceptor binds to and directs insulin towards lysosomal degradation in β cells., Nat Metab, PMID 39587340

PXD040756 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic Discovery and Array-Based Validation of Biomarkers from Urinary Exosome by Supramolecular Probe
Possible reference: Feng, X. et al. (2023) Proteomic Discovery and Array-Based Validation of Biomarkers from Urinary Exosome by Supramolecular Probe., J Proteome Res, PMID 37126797

PXD040754 Dataset with its publication pending (from PRIDE)
Dataset title: Intact Transition Epitope Mapping – Serological Inspection by Epitope EXtraction (ITEM – SIX)
Possible reference: Zammataro, A. et al. (2023) Intact Transition Epitope Mapping-Serological Inspection by Epitope EXtraction (ITEM-SIX)., Molecules, PMID 37049857

PXD040737 Dataset with its publication pending (from PRIDE)
Dataset title: A solid-phase compatible silane-based cleavable linker enables custom isobaric quantitative chemoproteomics
Possible reference: Burton, NR. et al. (2023) Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics., J Am Chem Soc, PMID 37738129

PXD040721 Dataset with its publication pending (from PRIDE)
Dataset title: Merging full-spectrum and fragment ion intensity predictions from deep learning for high quality spectral libraries
Possible reference: Chan, CMJ. et al. (2023) Merging Full-Spectrum and Fragment Ion Intensity Predictions from Deep Learning for High-Quality Spectral Libraries., J Proteome Res, PMID 37910637

PXD040718 Dataset with its publication pending (from PRIDE)
Dataset title: N-linked glycosylation of the M-protein variable region: Glycoproteogenomics reveals a new layer of personalized complexity in multiple myeloma.
Possible reference: Langerhorst, P. et al. (2024) N-linked glycosylation of the M-protein variable region: glycoproteogenomics reveals a new layer of personalized complexity in multiple myeloma., Clin Chem Lab Med, PMID 38332688

PXD040716 Dataset with its publication pending (from PRIDE)
Dataset title: The GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform
Possible reference: Armony, G. et al. (2023) The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform., Int J Mol Sci, PMID 37175577

PXD040715 Dataset with its publication pending (from PRIDE)
Dataset title: Repertoire and abundance of secreted virulence factors shape the pathogenic capacity of Pseudomonas syringae pv. aptata
Possible reference: Nikolić, I. et al. (2023) Repertoire and abundance of secreted virulence factors shape the pathogenic capacity of Pseudomonas syringae pv. aptata., Front Microbiol, PMID 37383635

PXD040703 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of circulating immune cells identifies novel cellular phenotypes associated with COVID-19 severity
Possible reference: Yang, Z. et al. (2022) Genetic Landscape of the ACE2 Coronavirus Receptor., Circulation, PMID 35387486

PXD040696 Dataset with its publication pending (from PRIDE)
Dataset title: A solid-phase compatible silane-based cleavable linker enables custom isobaric quantitative chemoproteomics
Possible reference: Burton, NR. et al. (2023) Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics., J Am Chem Soc, PMID 37738129

PXD040693 no publication (from MassIVE)
Dataset title: An N-acetyltransferase required for N-terminal protein acetylation and virulence in Mycobacterium marinum
Possible reference: Collars, OA. et al. (2023) An N-acetyltransferase required for EsxA N-terminal protein acetylation and virulence in Mycobacterium marinum., bioRxiv, PMID 36993388

PXD040676 Dataset with its publication pending (from PRIDE)
Dataset title: PDHE1Î±, PARylation, Acetyl-CoA, Acetylation, Histones, DNA damage repair
Possible reference: Zhang, J. et al. (2023) PARylated PDHE1α generates acetyl-CoA for local chromatin acetylation and DNA damage repair., Nat Struct Mol Biol, PMID 37735618

PXD040670 no publication (from MassIVE)
Dataset title: Arabidopsis thaliana responses to LCO and Th17 under drought stress
Possible reference: Subramanian, S. et al. (2023) Lipo-chitooligosaccharide and thuricin 17 act as plant growth promoters and alleviate drought stress in Arabidopsis thaliana., Front Microbiol, PMID 37601342

PXD040668 Dataset with its publication pending (from PRIDE)
Dataset title: ITK Degradation to Block T-cell Receptor Signaling and Overcome Therapeutic Resistance in T-Cell Lymphomas
Possible reference: Jiang, B. et al. (2023) ITK degradation to block T�cell receptor signaling and overcome therapeutic resistance in T�cell lymphomas., Cell Chem Biol, PMID 37015223

PXD040666 Dataset with its publication pending (from PRIDE)
Dataset title: The effect of cannabinoid receptor agonists on triple-negative breast cancer cell line (MDA-MB-231)
Possible reference: Younes, M. et al. (2024) The molecular anti-metastatic potential of CBD and THC from Lebanese Cannabis via apoptosis induction and alterations in autophagy., Sci Rep, PMID 39463375

PXD040658 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling of the Cellular Proteome and Phosphoproteome of Klebsiella pneumoniae under Iron Limited and Iron Replete Conditions
Possible reference: Reitzel, C. et al. (2023) Profiling of the Klebsiella pneumoniae Phosphoproteome under Iron-Limited and Iron-Replete Conditions., Microbiol Resour Announc, PMID 37358437

PXD040652 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Analysis of Neural Stem Cell to Oligodendrocyte Precursor Cell Differentiation Reveals Phosphorylation-Dependent Dclk1 Processing
Possible reference: Hardt, R. et al. (2023) Proteomic investigation of neural stem cell to oligodendrocyte precursor cell differentiation reveals phosphorylation-dependent Dclk1 processing., Cell Mol Life Sci, PMID 37594553

PXD040651 Dataset with its publication pending (from PRIDE)
Dataset title: PRAME and CTCFL-reactive TCRs for the treatment of ovarian cancer
Possible reference: van Amerongen, RA. et al. (2023) PRAME and CTCFL-reactive TCRs for the treatment of ovarian cancer., Front Immunol, PMID 37026005

PXD040624 no publication (from MassIVE)
Dataset title: Integrative systems biology characterizes immune-mediated neurodevelopmental changes in murine Zika Virus microcephaly
Possible reference: Fujimura, K. et al. (2023) Integrative systems biology characterizes immune-mediated neurodevelopmental changes in murine Zika virus microcephaly., iScience, PMID 37332674

PXD040606 Dataset with its publication pending (from iProX)
Dataset title: A peptide encoded by LINC00944 suppresses the growth of melanoma cells by diminishing EP400-MYC interaction
Possible reference: Ren, Z. et al. (2025) A peptide encoded by LINC00944 suppresses the growth of melanoma cells by diminishing EP400-MYC interaction., Biochem Pharmacol, PMID 39586403

PXD040585 no publication (from MassIVE)
Dataset title: DiLeu isobaric labeling coupled with limited proteolysis mass spectrometry for high-throughput profiling of protein structural changes in Alzheimers disease
Possible reference: Lu, H. et al. (2023) DiLeu Isobaric Labeling Coupled with Limited Proteolysis Mass Spectrometry for High-Throughput Profiling of Protein Structural Changes in Alzheimer's Disease., Anal Chem, PMID 37307028

PXD040584 Dataset with its publication pending (from PRIDE)
Dataset title: Boundary of Life and Death: changes in mitochondrial and cytosolic proteomes of Arabidopsis thaliana suspension cells associated with programmed cell death
Possible reference: Schwarze, J. et al. (2023) The boundary of life and death: changes in mitochondrial and cytosolic proteomes associated with programmed cell death of Arabidopsis thaliana suspension culture cells., Front Plant Sci, PMID 37593044

PXD040579 Dataset with its publication pending (from PRIDE)
Dataset title: Evidence of a role for CutRS and actinorhodin in the secretion stress response in Streptomyces coelicolor M145
Possible reference: McLean, TC. et al. (2023) Evidence of a role for CutRS and actinorhodin in the secretion stress response in Streptomyces coelicolor M145., Microbiology (Reading), PMID 37418299

PXD040555 no publication (from MassIVE)
Dataset title: Proteomes Reveal Robust Metabolic Capabilities of Yarrowia lipolytica for Biological Upcycling of Polyethylene into High-Value Chemicals
Possible reference: Walker, C. et al. (2023) Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals., mSystems, PMID 37882587

PXD040535 no publication (from MassIVE)
Dataset title: The HLA class-I immunopeptidomes of AAV capsid proteins
Possible reference: Brito-Sierra, CA. et al. (2023) The HLA class I immunopeptidomes of AAV capsid proteins., Front Immunol, PMID 37662941

PXD040534 no publication (from MassIVE)
Dataset title: Global analysis of post-translational sidechain arginylation using pan-arginylation antibodies
Possible reference: MacTaggart, B. et al. (2023) Global Analysis of Post-Translational Side-Chain Arginylation Using Pan-Arginylation Antibodies., Mol Cell Proteomics, PMID 37832787

PXD040524 Dataset with its publication pending (from PRIDE)
Dataset title: Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial-Mesenchymal Transition
Possible reference: Fang, L. et al. (2024) Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial-Mesenchymal Transition., Cancer Res, PMID 38190710

PXD040521 Dataset with its publication pending (from PRIDE)
Dataset title: Succinylation in pseudorabies virus infection
Possible reference: Chen, X. et al. (2023) Role of Succinylation in Pseudorabies Virus Infection., J Virol, PMID 36975827

PXD040513 Dataset with its publication pending (from iProX)
Dataset title: Analysis of proteins interacting with LSM14B
Possible reference: Li, H. et al. (2023) LSM14B is an Oocyte-Specific RNA-Binding Protein Indispensable for Maternal mRNA Metabolism and Oocyte Development in Mice., Adv Sci (Weinh), PMID 37083226

PXD040509 Dataset with its publication pending (from iProX)
Dataset title: Proteomics data of Fusobacterium nucleatum outer membrane vesicles
Possible reference: Liu, J. et al. (2019) Proteomic characterization of outer membrane vesicles from gut mucosa-derived fusobacterium nucleatum., J Proteomics, PMID 30634002

PXD040506 Dataset with its publication pending (from PRIDE)
Dataset title: Salicylic acid treatment and its effect on seed yield and seed molecular composition of Pisum sativum under abiotic stress
Possible reference: Berkov�, V. et al. (2023) Salicylic Acid Treatment and Its Effect on Seed Yield and Seed Molecular Composition of Pisum sativum under Abiotic Stress., Int J Mol Sci, PMID 36982529

PXD040502 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial mechanotransduction through MIEF1 coordinates the nuclear response to forces
Possible reference: Romani, P. et al. (2024) Mitochondrial mechanotransduction through MIEF1 coordinates the nuclear response to forces., Nat Cell Biol, PMID 39433949

PXD040476 Dataset with its publication pending (from jPOST)
Dataset title: ATR phosphoproteomics - substrate validation
Possible reference: Reichlmeir, M. et al. (2024) The ataxia-telangiectasia disease protein ATM controls vesicular protein secretion via CHGA and microtubule dynamics via CRMP5., Neurobiol Dis, PMID 39615799

PXD040469 Dataset with its publication pending (from jPOST)
Dataset title: ATR phosphoproteomics screening using berzosertib and gartisertib
Possible reference: Jadav, R. et al. (2024) Chemo-Phosphoproteomic Profiling with ATR Inhibitors Berzosertib and Gartisertib Uncovers New Biomarkers and DNA Damage Response Regulators., Mol Cell Proteomics, PMID 38880245

PXD040459 Dataset with its publication pending (from PRIDE)
Dataset title: Development of multifunctional synthetic nucleosomes
Possible reference: Liu, Z. et al. (2023) Development of multifunctional synthetic nucleosomes to interrogate chromatin-mediated protein interactions., Sci Adv, PMID 37134166

PXD040456 Dataset with its publication pending (from PRIDE)
Dataset title: mRNA 3â€™UTR lengthening by alternative polyadenylation attenuates inflammatory responses and correlates with virulence of Influenza A virus
Possible reference: Bergant, V. et al. (2023) mRNA 3'UTR lengthening by alternative polyadenylation attenuates inflammatory responses and correlates with virulence of Influenza A virus., Nat Commun, PMID 37582777

PXD040436 Dataset with its publication pending (from PRIDE)
Dataset title: TIMP1 mediates astrocyte-dependent local immunosuppression in brain metastasis acting on infiltrating CD8+ T cells.
Possible reference: Priego, N. et al. (2025) TIMP1 Mediates Astrocyte-Dependent Local Immunosuppression in Brain Metastasis Acting on Infiltrating CD8+ T Cells., Cancer Discov, PMID 39354883

PXD040435 Dataset with its publication pending (from PRIDE)
Dataset title: The Plant Unique ESCRT Component FREE1 Regulates Autophagosome Closure
Possible reference: Zeng, Y. et al. (2023) The plant unique ESCRT component FREE1 regulates autophagosome closure., Nat Commun, PMID 36997511

PXD040434 Dataset with its publication pending (from PRIDE)
Dataset title: Human adipose tissue proteomics reveal adaptations to exercise and type 2 diabetes
Possible reference: Schering, L. et al. (2015) Identification of novel putative adipomyokines by a cross-species annotation of secretomes and expression profiles., Arch Physiol Biochem, PMID 26599229

PXD040428 Dataset with its publication pending (from PRIDE)
Dataset title: UNC-45 assisted myosin folding depends on a conserved FX3HY motif implicated in Freeman Sheldon Syndrome
Possible reference: Vogel, A. et al. (2024) UNC-45 assisted myosin folding depends on a conserved FX3HY motif implicated in Freeman Sheldon Syndrome., Nat Commun, PMID 39054317

PXD040416 Dataset with its publication pending (from jPOST)
Dataset title: Deregulated transcription and proteostasis in adult mapt knockout mice
Possible reference: Andr�s-Benito, P. et al. (2023) Deregulated Transcription and Proteostasis in Adult mapt Knockout Mouse., Int J Mol Sci, PMID 37047532

PXD040412 Dataset with its publication pending (from PRIDE)
Dataset title: Drosophila brain O-GlcNAc proteome
Possible reference: Yu, H. et al. (2024) Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in Drosophila mushroom body contributing to olfactory learning., Elife, PMID 38619103

PXD040409 Dataset with its publication pending (from iProX)
Dataset title: BmATAD3A mediates mitochondrial ribosomal protein expression to maintain the mitochondrial energy metabolism of the silkworm Bombyx mori
Possible reference: Dong, Z. et al. (2025) BmATAD3A mediates mitochondrial ribosomal protein expression to maintain the mitochondrial energy metabolism of the silkworm, Bombyx mori., Insect Sci, PMID 38616538

PXD040398 Dataset with its publication pending (from PRIDE)
Dataset title: Towards unravelling biological mechanisms behind radiation-induced oral mucositis via mass spectrometry-based proteomics
Possible reference: Subedi, P. et al. (2023) Towards unravelling biological mechanisms behind radiation-induced oral mucositis via mass spectrometry-based proteomics., Front Oncol, PMID 37384298

PXD040397 no publication (from MassIVE)
Dataset title: Integrated Multi-Omic Analysis of Epithelial and Stromal Changes during Progression of Barrett s Esophagus to Adenocarcinoma
Possible reference: Strasser, MK. et al. (2023) Concerted epithelial and stromal changes during progression of Barrett's Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis., bioRxiv, PMID 37333362

PXD040350 Dataset with its publication pending (from PRIDE)
Dataset title: Sts2, a transcriptional activator effector of Ustilago maydis, regulates hyperplasia in maize during pathogen-induced tumor formation
Possible reference: Zuo, W. et al. (2023) A transcriptional activator effector of Ustilago maydis regulates hyperplasia in maize during pathogen-induced tumor formation., Nat Commun, PMID 37872143

PXD040338 Dataset with its publication pending (from PRIDE)
Dataset title: A farnesyl-dependent structural role for CENP-E in expansion of the fibrous corona
Possible reference: Wu, J. et al. (2024) A farnesyl-dependent structural role for CENP-E in expansion of the fibrous corona., J Cell Biol, PMID 37934467

PXD040329 Dataset with its publication pending (from PRIDE)
Dataset title: The mode of action of antimicrobial agents albofungins in eradicating penicillins and cephalosporins-resistant Vibrio parahaemolyticus biofilm
Possible reference: She, W. et al. (2023) Mode of action of antimicrobial agents albofungins in eradicating penicillin- and cephalosporin-resistant Vibrio parahaemolyticus biofilm., Microbiol Spectr, PMID 37610246

PXD040325 Dataset with its publication pending (from jPOST)
Dataset title: Proteome analysis of Nicotiana tabacum cells following isonitrosoacetophenone treatment reveals defence-related responses associated with priming
Possible reference: da Camara, N. et al. (2023) Proteome Analysis of Nicotiana tabacum Cells following Isonitrosoacetophenone Treatment Reveals Defence-Related Responses Associated with Priming., Plants (Basel), PMID 36903995

PXD040314 Dataset with its publication pending (from jPOST)
Dataset title: Destabilization of atherosclerotic plaque by bilirubin deficiency
Possible reference: Chen, W. et al. (2023) Destabilization of Atherosclerotic Plaque by Bilirubin Deficiency., Circ Res, PMID 36876485

PXD040312 no publication (from MassIVE)
Dataset title: Acute ACAT1/SOAT1 blockade increases MAM cholesterol and strengthens ER-mitochondria connectivity
Possible reference: Harned, TC. et al. (2023) Acute ACAT1/SOAT1 Blockade Increases MAM Cholesterol and Strengthens ER-Mitochondria Connectivity., Int J Mol Sci, PMID 36982602

PXD040302 Dataset with its publication pending (from PRIDE)
Dataset title: Control of TurboID-dependent biotinylation intensity in proximity ligation screens
Possible reference: Garloff, V. et al. (2023) Control of TurboID-dependent biotinylation intensity in proximity ligation screens., J Proteomics, PMID 36966971

PXD040299 Dataset with its publication pending (from iProX)
Dataset title: Proteomics and metabolomics analysis of nasal lavage fluid in chronic rhinosinusitis with nasal polyps
Possible reference: Yang, Y. et al. (2023) Proteomics and metabolomics analysis of nasal lavage fluid in chronic rhinosinusitis with nasal polyps., Int Forum Allergy Rhinol, PMID 36898695

PXD040288 Dataset with its publication pending (from PRIDE)
Dataset title: Insulin reverses impaired alveolar fluid clearance in ARDS by inhibiting LPS-induced autophagy and inflammatory
Possible reference: Wen, XP. et al. (2023) Insulin reverses impaired alveolar fluid clearance in ARDS by inhibiting LPS-induced autophagy and inflammatory., Front Immunol, PMID 37654494

PXD040275 Dataset with its publication pending (from PRIDE)
Dataset title: Therapeutic TNF Inhibitors Exhibit Differential Levels of Efficacy in Accelerating Cutaneous Wound Healing
Possible reference: Cao, Y. et al. (2024) Therapeutic TNF Inhibitors Exhibit Differential Levels of Efficacy in Accelerating Cutaneous Wound Healing., JID Innov, PMID 38226320

PXD040269 Dataset with its publication pending (from PRIDE)
Dataset title: Host innate immune responses and microbiome profile of neonatal calves challenged with Cryptosporidium parvum and the effect of bovine colostrum supplementation
Possible reference: Gamsj�ger, L. et al. (2023) Host innate immune responses and microbiome profile of neonatal calves challenged with Cryptosporidium parvum and the effect of bovine colostrum supplementation., Front Cell Infect Microbiol, PMID 37207189

PXD040262 Dataset with its publication pending (from PRIDE)
Dataset title: A Spatiotemporal Map of Co-Receptor Signaling Networks Underlying B Cell Activation
Possible reference: Susa, KJ. et al. (2023) A Spatiotemporal Map of Co-Receptor Signaling Networks Underlying B Cell Activation., bioRxiv, PMID 36993395

PXD040260 Dataset with its publication pending (from iProX)
Dataset title: Two C4 variants are translated during virus infection
Possible reference: Hipp, K. et al. (2016) Translation, modification and cellular distribution of two AC4 variants of African cassava mosaic virus in yeast and their pathogenic potential in plants., Virology, PMID 27584591

PXD040256 Dataset with its publication pending (from iProX)
Dataset title: Identification of maize xylem sap
Possible reference: Constantino, NN. et al. (2013) Root-expressed maize lipoxygenase 3 negatively regulates induced systemic resistance to Colletotrichum graminicola in shoots., Front Plant Sci, PMID 24391653

PXD040229 Dataset with its publication pending (from PRIDE)
Dataset title: MiRNA 3’ ends shorten during adolescent brain maturation
Possible reference: Thomas, KT. et al. (2023) MicroRNA 3' ends shorten during adolescent brain maturation., Front Mol Neurosci, PMID 37122627

PXD040227 Dataset with its publication pending (from PRIDE)
Dataset title: Membranes prime the RapGEF EPAC1 to transduce cAMP signaling
Possible reference: Sartre, C. et al. (2023) Membranes prime the RapGEF EPAC1 to transduce cAMP signaling., Nat Commun, PMID 37438343

PXD040220 Dataset with its publication pending (from PRIDE)
Dataset title: HA-GABARAPL1 immunoprecipitation with siRNA-mediated NPM1 depletion
Possible reference: Song, J. et al. (2021) Nucleolar Phosphoprotein NPM1 Interacts With Porcine Circovirus Type 3 Cap Protein and Facilitates Viral Replication., Front Microbiol, PMID 34113334

PXD040217 Dataset with its publication pending (from jPOST)
Dataset title: phosphopeptides from primary microglia
Possible reference: Viengkhou, B. et al. (2021) A novel phosphoproteomic landscape evoked in response to type I interferon in the brain and in glial cells., J Neuroinflammation, PMID 34656141

PXD040213 Dataset with its publication pending (from PRIDE)
Dataset title: Geometric morphometrics and paleoproteomics enlighten the paleodiversity of Pongo
Possible reference: Kubat, J. et al. (2023) Geometric morphometrics and paleoproteomics enlighten the paleodiversity of Pongo., PLoS One, PMID 38100471

PXD040212 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping the Binding Interactions Between human Gasdermin D and human Caspase-1 Using Carbene Footprinting
Possible reference: Lloyd, JR. et al. (2023) Mapping the Binding Interactions between Human Gasdermin D and Human Caspase-1 Using Carbene Footprinting., JACS Au, PMID 37502151

PXD040207 Dataset with its publication pending (from PRIDE)
Dataset title: Cell type-specific control of secondary cell wall formation by Musashi-type translational regulators in Arabidopsis
Possible reference: Kairouani, A. et al. (2023) Cell-type-specific control of secondary cell wall formation by Musashi-type translational regulators in Arabidopsis., Elife, PMID 37773033

PXD040202 Dataset with its publication pending (from PRIDE)
Dataset title: Norbergenin prevents LPS-induced inflammatory responses in macrophages through inhibiting NFÎºB, MAPK and STAT3 activation, and blocking metabolic reprogramming
Possible reference: Li, W. et al. (2023) Norbergenin prevents LPS-induced inflammatory responses in macrophages through inhibiting NFκB, MAPK and STAT3 activation and blocking metabolic reprogramming., Front Immunol, PMID 37251401

PXD040191 Dataset with its publication pending (from PRIDE)
Dataset title: A Lysosome membrane regeneration pathway depends on TBC1D15 and autophagic lysosomal reformation proteins
Possible reference: Bhattacharya, A. et al. (2023) A lysosome membrane regeneration pathway depends on TBC1D15 and autophagic lysosomal reformation proteins., Nat Cell Biol, PMID 37024685

PXD040166 Dataset with its publication pending (from PRIDE)
Dataset title: STAT5b is a key effector of NRG-1/ERBB4-mediated cardiomyocyte growth
Possible reference: Vaparanta, K. et al. (2023) STAT5b is a key effector of NRG-1/ERBB4-mediated myocardial growth., EMBO Rep, PMID 37009825

PXD040155 Dataset with its publication pending (from PRIDE)
Dataset title: A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance
Possible reference: van der Krift, F. et al. (2023) A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance., Life Sci Alliance, PMID 37591722

PXD040141 Dataset with its publication pending (from PRIDE)
Dataset title: Dopamine transporter and synaptic vesicle sorting defects underlie auxilin-associated Parkinson’s disease
Possible reference: Vidyadhara, DJ. et al. (2023) Dopamine transporter and synaptic vesicle sorting defects underlie auxilin-associated Parkinson's disease., Cell Rep, PMID 36920906

PXD040128 no publication (from MassIVE)
Dataset title: A contractile injection system is required for developmentally regulated cell death in Streptomyces coelicolor
Possible reference: Vladimirov, M. et al. (2023) A contractile injection system is required for developmentally regulated cell death in Streptomyces coelicolor., Nat Commun, PMID 36927736

PXD040126 no publication (from MassIVE)
Dataset title: FTD-tau S320F mutation stabilizes local structure and allosterically promotes amyloid motif-dependent aggregation
Possible reference: Chen, D. et al. (2023) FTD-tau S320F mutation stabilizes local structure and allosterically promotes amyloid motif-dependent aggregation., Nat Commun, PMID 36959205

PXD040115 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics coupled with AhR-reporter gene bioassay for human and environmental safety assessment of sewage sludge and hydrochar
Possible reference: Landi, C. et al. (2023) Proteomics coupled with AhR-reporter gene bioassay for human and environmental safety assessment of sewage sludge and hydrochar., Sci Total Environ, PMID 37277040

PXD040114 no publication (from MassIVE)
Dataset title: Endothelial FAT1 inhibits angiogenesis by controlling YAP/TAZ protein degradation via E3 ligase MIB2
Possible reference: Li, R. et al. (2023) Endothelial FAT1 inhibits angiogenesis by controlling YAP/TAZ protein degradation via E3 ligase MIB2., Nat Commun, PMID 37031213

PXD040079 Dataset with its publication pending (from iProX)
Dataset title: sRNA SNC137 regulation in Sphingomonas melonis TY
Possible reference: Wang, X. et al. (2024) sRNA molecules participate in hyperosmotic stress response regulation in Sphingomonas melonis TY., Appl Environ Microbiol, PMID 38289134

PXD040040 Dataset with its publication pending (from PRIDE)
Dataset title: SWATH proteomics analysis of pig liver microsomes
Possible reference: Popescu, RG. et al. (2023) Natural Antioxidant By-Product Mixture Counteracts the Effects of Aflatoxin B1 and Ochratoxin A Exposure of Piglets after Weaning: A Proteomic Survey on Liver Microsomal Fraction., Toxins (Basel), PMID 37104237

PXD040008 no publication (from MassIVE)
Dataset title: Overexpression of the citrate transporters SLC13A5 and SLC25A1 in the mouse elicit different metabolic responses and phenotypes
Possible reference: Fernandez-Fuente, G. et al. (2023) The citrate transporters SLC13A5 and SLC25A1 elicit different metabolic responses and phenotypes in the mouse., Commun Biol, PMID 37689798

PXD039995 Dataset with its publication pending (from PRIDE)
Dataset title: A combinatorial approach to uncover an additional Integrator subunit
Possible reference: Offley, SR. et al. (2023) A combinatorial approach to uncover an additional Integrator subunit., Cell Rep, PMID 36920904

PXD039993 Dataset with its publication pending (from PRIDE)
Dataset title: Charge site manipulation to enhance top-down fragmentation efficiency
Possible reference: Habeck, T. et al. (2024) Charge site manipulation to enhance top-down fragmentation efficiency., Proteomics, PMID 37043727

PXD039991 Dataset with its publication pending (from PRIDE)
Dataset title: The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation.
Possible reference: Li, Z. et al. (2023) The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation., bioRxiv, PMID 36711532

PXD039969 no publication (from MassIVE)
Dataset title: Proteome-Wide Identification of RNA-Dependent Proteins: An Emerging Role of RNAs in Plasmodium falciparum Protein Complexes
Possible reference: Hollin, T. et al. (2024) Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes., Nat Commun, PMID 38355719

PXD039955 Dataset with its publication pending (from PRIDE)
Dataset title: CD99-mediated immunological synapse formation potentiates CAR-T cell function
Possible reference: Nam, G. et al. (2025) CD99-mediated immunological synapse formation potentiates CAR-T cell function., Nat Commun, PMID 40866332

PXD039950 no publication (from MassIVE)
Dataset title: Osteopontin depletion in macrophages perturbs proteostasis via regulation of UCHL1-UPS pathway and activation of mitochondria-mediated apoptosis
Possible reference: Rentsendorj, A. et al. (2023) Osteopontin depletion in macrophages perturbs proteostasis via regulating UCHL1-UPS axis and mitochondria-mediated apoptosis., Front Immunol, PMID 37325640

PXD039932 no publication (from MassIVE)
Dataset title: Vibrio natriegens genome-scale metabolic modelling (GSMM) reveals insights into halophilic adaptations and resource allocation
Possible reference: Coppens, L. et al. (2023) Vibrio natriegens genome-scale modeling reveals insights into halophilic adaptations and resource allocation., Mol Syst Biol, PMID 36847213

PXD039931 Dataset with its publication pending (from PRIDE)
Dataset title: Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows
Possible reference: Faucher, FF. et al. (2023) Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows., bioRxiv, PMID 36824748

PXD039928 Dataset with its publication pending (from PRIDE)
Dataset title: Short-term UVB irradiation leads to persistent DNA damage in limbal epithelial stem cells, partially reversed by DNA repairing enzymes
Possible reference: Volatier, T. et al. (2023) Short-Term UVB Irradiation Leads to Persistent DNA Damage in Limbal Epithelial Stem Cells, Partially Reversed by DNA Repairing Enzymes., Biology (Basel), PMID 36829542

PXD039927 Dataset with its publication pending (from PRIDE)
Dataset title: Composition of the mitoribosome of Diplonema papillatum
Possible reference: Valach, M. et al. (2023) Miniature RNAs are embedded in an exceptionally protein-rich mitoribosome via an elaborate assembly pathway., Nucleic Acids Res, PMID 37207340

PXD039924 Dataset with its publication pending (from PRIDE)
Dataset title: Chemoproteomics-Enabled Discovery of a Covalent Molecular Glue Degrader
Possible reference: King, EA. et al. (2023) Chemoproteomics-enabled discovery of a covalent molecular glue degrader targeting NF-κB., Cell Chem Biol, PMID 36898369

PXD039923 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic comparison of human milk, cow's milk and infant formula extracellular vesicles
Possible reference: Turner, NP. et al. (2023) Omics Analysis of Extracellular Vesicles Recovered from Infant Formula Products and Milk: Towards Personalized Infant Nutrition., Mol Nutr Food Res, PMID 37562982

PXD039915 Dataset with its publication pending (from PRIDE)
Dataset title: The direct effect of mycophenolate mofetil on podocytes in nephrotoxic serum nephritis
Possible reference: Hackl, A. et al. (2023) The effect of mycophenolate mofetil on podocytes in nephrotoxic serum nephritis., Sci Rep, PMID 37644089

PXD039913 Dataset with its publication pending (from jPOST)
Dataset title: Serum proteome of dogs with precursor-targeted immune-mediated anemia before and after splenectomy
Possible reference: Sugawara-Suda, M. et al. (2023) Transcriptome and proteome analysis of dogs with precursor targeted immune-mediated anemia treated with splenectomy., PLoS One, PMID 37146011

PXD039910 Dataset with its publication pending (from iProX)
Dataset title: Hepatic Glucuronyl C5-epimerase combats obesity via stabilizing GDF15
Possible reference: He, F. et al. (2023) Hepatic glucuronyl C5-epimerase combats obesity by stabilising GDF15., J Hepatol, PMID 37217020

PXD039908 Dataset with its publication pending (from iProX)
Dataset title: Nucleophilic covalent ligand discovery for the cysteine redoxome
Possible reference: Gupta, V. et al. (2017) Diverse Redoxome Reactivity Profiles of Carbon Nucleophiles., J Am Chem Soc, PMID 28355876

PXD039903 no publication (from MassIVE)
Dataset title: Distinctive Interactomes of RNA polymerase II phosphorylation during different stages of transcription
Possible reference: Nemec, CM. et al. (2017) Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner., Proc Natl Acad Sci U S A, PMID 28465432

PXD039891 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of SMIM26 interacting proteins
Possible reference: Heizler, K. et al. (2026) The microprotein SMIM26 connects metabolite transporters of the outer and inner mitochondrial membranes and is essential for respiratory chain function., Genes Dev, PMID 41991342

PXD039890 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of SMIM26 RNA-binding proteins
Possible reference: Heizler, K. et al. (2026) The microprotein SMIM26 connects metabolite transporters of the outer and inner mitochondrial membranes and is essential for respiratory chain function., Genes Dev, PMID 41991342

PXD039882 Dataset with its publication pending (from PRIDE)
Dataset title: Composition of the mitoribosome of Diplonema papillatum
Possible reference: Valach, M. et al. (2023) Miniature RNAs are embedded in an exceptionally protein-rich mitoribosome via an elaborate assembly pathway., Nucleic Acids Res, PMID 37207340

PXD039881 Dataset with its publication pending (from PRIDE)
Dataset title: Iron limitation restores autophagy and increases lifespan in the yeast model of Niemann-Pick type C1
Possible reference: Martins, TS. et al. (2023) Iron Limitation Restores Autophagy and Increases Lifespan in the Yeast Model of Niemann-Pick Type C1., Int J Mol Sci, PMID 37047194

PXD039870 Dataset with its publication pending (from iProX)
Dataset title: Comparative proteomic analysis reveals the response mechanism of freshwater leech (Whitmania pigra Whitman) under heat-stress challenge
Possible reference: Wang, S. et al. (2025) Comparative proteomic analysis reveals the response mechanism of freshwater leech (Whitmania pigra) under heat-stress challenge., Comp Biochem Physiol Part D Genomics Proteomics, PMID 39729945

PXD039865 Dataset with its publication pending (from PRIDE)
Dataset title: EPLIN-Beta is a novel substrate of ornithine decarboxylase antizyme 1, mediating cellular migration
Possible reference: Li, D. et al. (2023) EPLIN-β is a novel substrate of ornithine decarboxylase antizyme 1 and mediates cellular migration., J Cell Sci, PMID 37325974

PXD039859 no publication (from MassIVE)
Dataset title: Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis
Possible reference: Rosenberger, G. et al. (2023) Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis., bioRxiv, PMID 36824919

PXD039858 Dataset with its publication pending (from jPOST)
Dataset title: Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells
Possible reference: Wang, H. et al. (2023) Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells., J Integr Plant Biol, PMID 37226855

PXD039857 Dataset with its publication pending (from jPOST)
Dataset title: Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells
Possible reference: Wang, H. et al. (2023) Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells., J Integr Plant Biol, PMID 37226855

PXD039856 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of Asian elephant (Elephas maximus) seminal plasma using liquid chromatography tandem-mass spectrometry (LC- MS/MS)
Possible reference: Wattananit, P. et al. (2023) Non-targeted proteomic analysis of Asian elephant (Elephas maximus) seminal plasma using an in-solution digestion technique and liquid chromatography tandem-mass spectrometry., Front Vet Sci, PMID 37799407

PXD039855 no publication (from MassIVE)
Dataset title: Real-time spectral library matching for sample multiplexed quantitative proteomics
Possible reference: McGann, CD. et al. (2023) Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics., J Proteome Res, PMID 37557900

PXD039830 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics and RNA-sequencing of mouse liver endothelial cells identify novel regulators of BMP6 by iron
Possible reference: Fisher, AL. et al. (2023) Quantitative proteomics and RNA-sequencing of mouse liver endothelial cells identify novel regulators of BMP6 by iron., iScience, PMID 38125029

PXD039810 Dataset with its publication pending (from PRIDE)
Dataset title: Translatome analyses by bio-orthogonal non-canonical amino acid labeling reveal that MR1-activated MAIT cells induce an M1 phenotype and antiviral programming in antigen-presenting monocytes_bicellular 3
Possible reference: Jakob, J. et al. (2023) Translatome analyses by bio-orthogonal non-canonical amino acid labeling reveal that MR1-activated MAIT cells induce an M1 phenotype and antiviral programming in antigen-presenting monocytes., Front Immunol, PMID 36875139

PXD039809 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of metronidazole resistance in the human facultative pathogen Bacteroides fragilis
Possible reference: Paunkov, A. et al. (2023) Proteomic analysis of metronidazole resistance in the human facultative pathogen Bacteroides fragilis., Front Microbiol, PMID 37065137

PXD039806 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation of the African swine fever virus-induced host shutoff using dynamic stable isotope labeling with amino acids in cell culture (SILAC)
Possible reference: W�hnke, E. et al. (2023) Mass-Spectrometric Evaluation of the African Swine Fever Virus-Induced Host Shutoff Using Dynamic Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)., Viruses, PMID 37376583

PXD039805 Dataset with its publication pending (from PRIDE)
Dataset title: Brain Endothelial Cells Exposure to Malaria Parasites Links Type I Interferon Signalling to Antigen Presentation, Immunoproteasome Activation Endothelium Disruption, and Cellular Metabolism
Possible reference: Shafi, AM. et al. (2023) Brain endothelial cells exposure to malaria parasites links type I interferon signalling to antigen presentation, immunoproteasome activation, endothelium disruption, and cellular metabolism., Front Immunol, PMID 36993973

PXD039804 Dataset with its publication pending (from PRIDE)
Dataset title: Translatome analyses by bio-orthogonal non-canonical amino acid labeling reveal that MR1-activated MAIT cells induce an M1 phenotype and antiviral programming in antigen-presenting monocytes_bicellular2
Possible reference: Jakob, J. et al. (2023) Translatome analyses by bio-orthogonal non-canonical amino acid labeling reveal that MR1-activated MAIT cells induce an M1 phenotype and antiviral programming in antigen-presenting monocytes., Front Immunol, PMID 36875139

PXD039787 Dataset with its publication pending (from PRIDE)
Dataset title: Antibody N-linked glycosylation profiling with PEAKS GlycanFinder
Possible reference: Sun, W. et al. (2023) Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics., Nat Commun, PMID 37422459

PXD039785 Dataset with its publication pending (from PRIDE)
Dataset title: Translatome analyses by bio-orthogonal non-canonical amino acid labeling reveal that MR1-activated MAIT cells induce an M1 phenotype and antiviral programming in antigen-presenting monocytes_bicellular1
Possible reference: Jakob, J. et al. (2023) Translatome analyses by bio-orthogonal non-canonical amino acid labeling reveal that MR1-activated MAIT cells induce an M1 phenotype and antiviral programming in antigen-presenting monocytes., Front Immunol, PMID 36875139

PXD039784 Dataset with its publication pending (from PRIDE)
Dataset title: Detection of structure-specific protein–protein interactions of alpha-synuclein
Possible reference: Holfeld, A. et al. (2024) Systematic identification of structure-specific protein-protein interactions., Mol Syst Biol, PMID 38702390

PXD039764 Dataset with its publication pending (from PRIDE)
Dataset title: The Extracellular Vesicles Proteome of Endometrial Cells Simulating the Receptive Menstrual Phase Differs from That of Endometrial Cells Simulating the Non-Receptive Menstrual Phase
Possible reference: Hart, AR. et al. (2023) The Extracellular Vesicles Proteome of Endometrial Cells Simulating the Receptive Menstrual Phase Differs from That of Endometrial Cells Simulating the Non-Receptive Menstrual Phase., Biomolecules, PMID 36830648

PXD039752 Dataset with its publication pending (from jPOST)
Dataset title: Development of cytosol-facing organelle outer membrane proximity labeling systems in Arabidopsis
Possible reference: Bao, X. et al. (2024) Mapping of cytosol-facing organelle outer membrane proximity proteome by proximity-dependent biotinylation in living Arabidopsis cells., Plant J, PMID 38261530

PXD039729 no publication (from MassIVE)
Dataset title: Proteogenomic Identification and Validation of Key Differentially Expressed Molecular Targets for Keloid Disease
Possible reference: Kidzeru, EB. et al. (2025) Subcellular Fractionation and Metaproteogenomic Identification and Validation of Key Differentially Expressed Molecular Targets for Keloid Disease., J Invest Dermatol, PMID 39122141

PXD039725 Dataset with its publication pending (from iProX)
Dataset title: A draft map of the human sputum proteome
Possible reference: Long, F. et al. (2026) Sputum proteomics and phosphoproteomics for improving chronic obstructive pulmonary disease knowledge., J Proteomics, PMID 41565155

PXD039691 no publication (from MassIVE)
Dataset title: Lectin receptor-like kinase signaling during engineered ectomycorrhiza colonization
Possible reference: Shrestha, H. et al. (2023) Lectin Receptor-like Kinase Signaling during Engineered Ectomycorrhiza Colonization., Cells, PMID 37048154

PXD039686 no publication (from MassIVE)
Dataset title: Robust and easy-to-use one pot workflow for label free single cell proteomics
Possible reference: Matzinger, M. et al. (2023) Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics., Anal Chem, PMID 36802514

PXD039681 Dataset with its publication pending (from PRIDE)
Dataset title: Peptide and MUC5B hydrolysis by the Mucin Degrading Protease (MdpL) from Limosilactobacillus fermentum
Possible reference: Leo, F. et al. (2023) Characterization of a highly conserved MUC5B-degrading protease, MdpL, from Limosilactobacillus fermentum., Front Microbiol, PMID 36925480

PXD039666 Cucina, A., Schmidt, A.L., Di Gianvincenzo, F. et al. Paleoproteomic identification of the species used in fourteenth century gut-skin garments from the archaeological site of Nuulliit, Greenland. Scientific Reports 2024 14(13431). doi: 10.1038/s41598-024 (from MassIVE)
Dataset title: Paleoproteomic identification of the species used in fourteenth century gut-skin garments from the archaeological site of Nuulliit, Greenland
Possible reference: Cucina, A. et al. (2024) Paleoproteomic identification of the species used in fourteenth century gut-skin garments from the archaeological site of Nuulliit, Greenland., Sci Rep, PMID 38862633

PXD039664 Dataset with its publication pending (from PRIDE)
Dataset title: Tetraspanin 4 stabilizes membrane swellings and facilitates their maturation into migrasomes
Possible reference: Dharan, R. et al. (2023) Tetraspanin 4 stabilizes membrane swellings and facilitates their maturation into migrasomes., Nat Commun, PMID 36823145

PXD039645 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic analysis of human serum using tandem mass tags to predict cardiovascular risks in patients with psoriasis
Possible reference: Kim, NY. et al. (2023) Quantitative proteomic analysis of human serum using tandem mass tags to predict cardiovascular risks in patients with psoriasis., Sci Rep, PMID 36804462

PXD039597 no publication (from MassIVE)
Dataset title: Proteomics, metabolomics and single cell metabolomics of cells treated with KRASG12D inhibitor MRTX1133
Possible reference: Orsburn, BC. et al. (2023) Metabolomic, Proteomic, and Single-Cell Proteomic Analysis of Cancer Cells Treated with the KRASG12D Inhibitor MRTX1133., J Proteome Res, PMID 37983312

PXD039569 Dataset with its publication pending (from PRIDE)
Dataset title: Herpes simplex virus type 1 modifies the protein composition of extracellular vesicles to promote neurite outgrowth and facilitate neuroinfection
Possible reference: Sun, G. et al. (2024) Herpes simplex virus type 1 modifies the protein composition of extracellular vesicles to promote neurite outgrowth and neuroinfection., mBio, PMID 38275838

PXD039568 Dataset with its publication pending (from PRIDE)
Dataset title: The effect of obesity on uterine receptivity is mediated by endometrial extracellular vesicles that control human endometrial stromal cell decidualization and trophoblast invasion
Possible reference: Galio, L. et al. (2023) The effect of obesity on uterine receptivity is mediated by endometrial extracellular vesicles that control human endometrial stromal cell decidualization and trophoblast invasion., J Extracell Biol, PMID 38939074

PXD039554 Dataset with its publication pending (from PRIDE)
Dataset title: Cytokine signaling converging on IL11 signalling in ILD fibroblasts induces aberrant epithelial differentiation signatures
Possible reference: Kastlmeier, MT. et al. (2023) Cytokine signaling converging on IL11 in ILD fibroblasts provokes aberrant epithelial differentiation signatures., Front Immunol, PMID 37266432

PXD039547 Dataset with its publication pending (from PRIDE)
Dataset title: Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1
Possible reference: Bhandari, SK. et al. (2023) Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1., Sci Rep, PMID 36928068

PXD039530 no publication (from MassIVE)
Dataset title: Autophagy controls the protein composition of hair shafts
Possible reference: Sukseree, S. et al. (2024) Autophagy Controls the Protein Composition of Hair Shafts., J Invest Dermatol, PMID 37517514

PXD039527 Dataset with its publication pending (from iProX)
Dataset title: PekUSZ_Development of Lysine Crotonyl-mimic Probe to Covalently Identify H3K27Cr Interacting Proteins
Possible reference: Guo, X. et al. (2023) Development of Lysine Crotonyl-Mimic Probe to Covalently Identify H3K27Cr Interacting Proteins., Chemistry, PMID 37587551

PXD039523 Dataset with its publication pending (from PRIDE)
Dataset title: Deep proteome profiling of white adipose tissue reveals marked conservation and distinct features between different anatomical depots
Possible reference: Madsen, S. et al. (2023) Deep Proteome Profiling of White Adipose Tissue Reveals Marked Conservation and Distinct Features Between Different Anatomical Depots., Mol Cell Proteomics, PMID 36787876

PXD039508 Dataset with its publication pending (from PRIDE)
Dataset title: Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung
Possible reference: Martins, LR. et al. (2024) Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung., Nat Commun, PMID 38472236

PXD039504 no publication (from MassIVE)
Dataset title: Data-independent acquisition phosphoproteomics of urinary extracellular vesicles enables renal cell carcinoma grade differentiation
Possible reference: Hadisurya, M. et al. (2023) Data-Independent Acquisition Phosphoproteomics of Urinary Extracellular Vesicles Enables Renal Cell Carcinoma Grade Differentiation., Mol Cell Proteomics, PMID 36997065

PXD039498 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome draft of Tremella fuciformis
Possible reference: Li, Y. et al. (2023) A chromosome-scale genome and proteome draft of Tremella fuciformis., Int J Biol Macromol, PMID 37429350

PXD039492 Dataset with its publication pending (from PRIDE)
Dataset title: Proximity labelling reveals intracristal quality control in mitochondria
Possible reference: Kang, MG. et al. (2025) Intracristal space proteome mapping using super-resolution proximity labeling with isotope-coded probes., Nat Commun, PMID 40835710

PXD039474 Dataset with its publication pending (from PRIDE)
Dataset title: Dual IKZF2 and CK1Î± degrader targets acute myeloid leukemia cells
Possible reference: Park, SM. et al. (2023) Dual IKZF2 and CK1α degrader targets acute myeloid leukemia cells., Cancer Cell, PMID 36898380

PXD039472 Dataset with its publication pending (from PRIDE)
Dataset title: Ninety-six–hour starved peripheral blood mononuclear cell supernatant inhibited LA7 breast cancer stem cells induced tumor
Possible reference: Mehri, M. et al. (2022) Ninety-six-hour starved peripheral blood mononuclear cell supernatant inhibited LA7 breast cancer stem cells induced tumor via reduction in angiogenesis and alternations in Gch1 and Spr expressions., Front Immunol, PMID 36908807

PXD039462 Dataset with its publication pending (from jPOST)
Dataset title: LC-MS/MS-PRM Quantification of IgG glycoforms using stable isotope labeled IgG1 Fc glycopeptide standard
Possible reference: Sanda, M. et al. (2022) LC-MS/MS-PRM Quantification of IgG glycoforms using stable isotope labeled IgG1 Fc glycopeptide standard., bioRxiv, PMID 35982648

PXD039441 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of Arginine Methylation in Cancer Cell using LC-MS/MS
Possible reference: Park, JH. et al. (2015) Protein arginine methyltransferase 5 is a key regulator of the MYCN oncoprotein in neuroblastoma cells., Mol Oncol, PMID 25475372

PXD039429 no publication (from MassIVE)
Dataset title: Circadian rhythm disruption is associated with skeletal muscle dysfunction within the blind Mexican Cavefish
Possible reference: Olsen, L. et al. (2023) Circadian rhythm disruption is associated with skeletal muscle dysfunction within the blind Mexican Cavefish., bioRxiv, PMID 36747688

PXD039419 Dataset with its publication pending (from PRIDE)
Dataset title: Development of resistance to type II JAK2 inhibition in MPN depends on AXL kinase and is targetable
Possible reference: Codilupi, T. et al. (2024) Development of Resistance to Type II JAK2 Inhibitors in MPN Depends on AXL Kinase and Is Targetable., Clin Cancer Res, PMID 37992313

PXD039416 Dataset with its publication pending (from PRIDE)
Dataset title: Ex vivo proteomics of Mycobacterium marinum
Possible reference: Hammar�n, MM. et al. (2023) In vitro and ex vivo proteomics of Mycobacterium marinum biofilms and the development of biofilm-binding synthetic nanobodies., mSystems, PMID 37184670

PXD039409 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of spatial heterogeneity in metastasized colorectal cancer by MALDI imaging
Possible reference: Turtoi, A. et al. (2014) Organized proteomic heterogeneity in colorectal cancer liver metastases and implications for therapies., Hepatology, PMID 23832580

PXD039369 no publication (from MassIVE)
Dataset title: Reduced binding of apoE4 to complement factor H promotes amyloid-beta oligomerization and neuroinflammation
Possible reference: Chernyaeva, L. et al. (2023) Reduced binding of apoE4 to complement factor H promotes amyloid-β oligomerization and neuroinflammation., EMBO Rep, PMID 37155564

PXD039364 no publication (from MassIVE)
Dataset title: Mocetinostat activates Kruppel-like factor 4 and protects against tissue destruction and inflammation in osteoarthritis
Possible reference: Kawata, M. et al. (2023) Mocetinostat activates Kr�ppel-like factor 4 and protects against tissue destruction and inflammation in osteoarthritis., JCI Insight, PMID 37681413

PXD039363 no publication (from MassIVE)
Dataset title: Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics
Possible reference: Lee, CY. et al. (2024) Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics., Mol Syst Biol, PMID 38177929

PXD039355 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of circadian rhythms in mouse skeletal muscle tissue during time-restricted feeding
Possible reference: Chen, J. et al. (2025) Dietary timing enhances exercise by modulating fat-muscle crosstalk via adipocyte AMPKα2 signaling., Cell Metab, PMID 40088888

PXD039351 no publication (from MassIVE)
Dataset title: DOCK8 is a Novel Regulator of Lysosome Mediated Pancreatic Cancer Invasion
Possible reference: Gutierrez-Ruiz, OL. et al. (2023) Ectopic expression of DOCK8 regulates lysosome-mediated pancreatic tumor cell invasion., Cell Rep, PMID 37651233

PXD039345 Dataset with its publication pending (from jPOST)
Dataset title: On-capillary Alkylation Micro-reactor: A facile strategy for proteo-metabolome profiling in the same single mouse oocytes
Possible reference: He, Y. et al. (2023) On-capillary alkylation micro-reactor: a facile strategy for proteo-metabolome profiling in the same single cells., Chem Sci, PMID 38033888

PXD039339 Dataset with its publication pending (from PRIDE)
Dataset title: Tissue expression of N-terminal proteoforms.
Possible reference: Bamberger, C. et al. (2021) The Host Interactome of Spike Expands the Tropism of SARS-CoV-2., bioRxiv, PMID 33619478

PXD039319 Dataset with its publication pending (from PRIDE)
Dataset title: Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level
Possible reference: Godbole, S. et al. (2024) Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level., Nat Commun, PMID 39043693

PXD039291 no publication (from MassIVE)
Dataset title: Persistence of targetable lesions, predicted therapy sensitivity and proteomes through disease evolution in pediatric acute lymphoblastic leukemia
Possible reference: Lorentzian, AC. et al. (2023) Targetable lesions and proteomes predict therapy sensitivity through disease evolution in pediatric acute lymphoblastic leukemia., Nat Commun, PMID 37989729

PXD039288 Dataset with its publication pending (from PRIDE)
Dataset title: Oxygen-sensing through ERFVII action and modulation in Arabidopsis thaliana
Possible reference: Zubrycka, A. et al. (2023) ERFVII action and modulation through oxygen-sensing in Arabidopsis thaliana., Nat Commun, PMID 37537157

PXD039284 no publication (from MassIVE)
Dataset title: Cardiomyocyte external mechanical unloading activates modifications of alpha-actinin differently from sarcomere-originated unloading
Possible reference: Solís, C. et al. (2023) Cardiomyocyte external mechanical unloading activates modifications of α-actinin differently from sarcomere-originated unloading., FEBS J, PMID 37551968

PXD039270 Dataset with its publication pending (from PRIDE)
Dataset title: USING DESIGN OF EXPERIMENTS (DoE) TO OPTIMIZE PERFORMANCE AND STABILITY OF BIOMIMETIC CELL MEMBRANE-COATED NANOSTRUCTURES FOR CANCER THERAPY
Possible reference: Ferreira, NN. et al. (2023) Using design of experiments (DoE) to optimize performance and stability of biomimetic cell membrane-coated nanostructures for cancer therapy., Front Bioeng Biotechnol, PMID 36815878

PXD039268 Dataset with its publication pending (from PRIDE)
Dataset title: Alkaline-SDS cell lysis with acetone protein precipitation for proteomic sample preparation of microbes in 96-well plate format
Possible reference: Chen, Y. et al. (2023) Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format., PLoS One, PMID 37418444

PXD039255 Dataset with its publication pending (from PRIDE)
Dataset title: The mode of action of antifouling compound albofungin in inhibiting barnacle settlement
Possible reference: She, W. et al. (2023) Mode of action of antifouling compound albofungin in inhibiting barnacle larval settlement., iScience, PMID 37534162

PXD039254 Dataset with its publication pending (from PRIDE)
Dataset title: Development and characterization of selective FAK inhibitors and PROTACs with in vivo activity
Possible reference: Koide, E. et al. (2023) Development and Characterization of Selective FAK Inhibitors and PROTACs with In Vivo Activity., Chembiochem, PMID 37088717

PXD039249 Dataset with its publication pending (from PRIDE)
Dataset title: Temporal Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins during Osteogenic Differentiation of Human Embryonic Stem Cells
Possible reference: Yin, J. et al. (2023) Temporal Profiling of Epitranscriptomic Modulators during Osteogenic Differentiation of Human Embryonic Stem Cells., J Proteome Res, PMID 37348120

PXD039241 Dataset with its publication pending (from PRIDE)
Dataset title: TRIM16 overexpression in HEK293T cells results in cell line-specific antiviral activity
Possible reference: Nigos, LR. et al. (2023) TRIM16 Overexpression in HEK293T Cells Results in Cell Line-Specific Antiviral Activity., Pathogens, PMID 37375542

PXD039233 Dataset with its publication pending (from iProX)
Dataset title: Regulation of Cellular Metabolism by Protein Crotonylation Coordinates Pancreatic Cancer Progression
Possible reference: Hou, JY. et al. (2024) PTBP1 crotonylation promotes colorectal cancer progression through alternative splicing-mediated upregulation of the PKM2 gene., J Transl Med, PMID 39497094

PXD039215 Dataset with its publication pending (from PRIDE)
Dataset title: Development and characterization of selective FAK inhibitors and PROTACs with in vivo activity
Possible reference: Koide, E. et al. (2023) Development and Characterization of Selective FAK Inhibitors and PROTACs with In Vivo Activity., Chembiochem, PMID 37088717

PXD039214 Dataset with its publication pending (from PRIDE)
Dataset title: Patient-derived podocyte spheroids reveals new insights into the etiopathogenesis of Alport Syndrome
Possible reference: Romero-Guevara, R. et al. (2023) Patient-derived podocyte spheroids reveal new insights into the etiopathogenesis of Alport syndrome., Front Cell Dev Biol, PMID 36936689

PXD039209 Dataset with its publication pending (from PRIDE)
Dataset title: Breast cancer identity is determined by glucocorticoid receptor activity status
Possible reference: Prekovic, S. et al. (2023) Luminal breast cancer identity is determined by loss of glucocorticoid receptor activity., EMBO Mol Med, PMID 37902007

PXD039183 Dataset with its publication pending (from PRIDE)
Dataset title: The autophagy receptor NBR1 directs the clearance of photodamaged chloroplasts
Possible reference: Lee, HN. et al. (2023) The autophagy receptor NBR1 directs the clearance of photodamaged chloroplasts., Elife, PMID 37070813

PXD039182 Dataset with its publication pending (from PRIDE)
Dataset title: Proteogenomic characterization of pancreatic solid pseudopapillary neoplasm
Possible reference: Tanaka, A. et al. (2025) Deep proteogenomic characterization of pancreatic solid pseudopapillary neoplasm reveals unique features distinct from other pancreatic tumors., Biomark Res, PMID 41310888

PXD039165 Dataset with its publication pending (from PRIDE)
Dataset title: A Dataset for Developing Proteomic Tools in Pathogen Detection via Differential Cell Lysis from Whole�Blood�Samples
Possible reference: de Oliveira Veloso Rezende, J. et al. (2024) A dataset for developing proteomic tools for pathogen detection via differential cell lysis of whole blood samples., Sci Data, PMID 39384817

PXD039155 Dataset with its publication pending (from PRIDE)
Dataset title: A novel role for Teneurin C-terminal Associated Peptide (TCAP) in the regulation of cardiac activity in the Sydney rock oyster, Saccostrea glomerata
Possible reference: Abramov, T. et al. (2023) A novel role for Teneurin C-terminal Associated Peptide (TCAP) in the regulation of cardiac activity in the Sydney rock oyster, Saccostrea glomerata., Front Endocrinol (Lausanne), PMID 36814576

PXD039152 Dataset with its publication pending (from PRIDE)
Dataset title: Mass spectrometry analysis of Extracellular vesicles derived from naive HUVEc cells or ZIKV-infected HUVEc cells
Possible reference: Pan, T. et al. (2018) Nonsteroidal Anti-inflammatory Drugs Potently Inhibit the Replication of Zika Viruses by Inducing the Degradation of AXL., J Virol, PMID 30068645

PXD039148 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of Toxoplasma growth and development by AMPK
Possible reference: Yang, J. et al. (2022) The beta subunit of AMP-activated protein kinase is critical for cell cycle progression and parasite development in Toxoplasma gondii., Cell Mol Life Sci, PMID 36205781

PXD039141 Dataset with its publication pending (from iProX)
Dataset title: Glycosylation changes associated with anti-PD-1/PD-L1 Treatment
Possible reference: Cao, X. et al. (2024) Glyco-signatures in patients with advanced lung cancer during anti-PD-1/PD-L1 immunotherapy., Acta Biochim Biophys Sin (Shanghai), PMID 38952341

PXD039138 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles of probiotic microorganism Streptococcus salivarius
Possible reference: Kulig, K. et al. (2024) Isolation and Characteristics of Extracellular Vesicles Produced by Probiotics: Yeast Saccharomyces boulardii CNCM I-745 and Bacterium Streptococcus salivarius K12., Probiotics Antimicrob Proteins, PMID 37209320

PXD039137 Dataset with its publication pending (from PRIDE)
Dataset title: Characteristic of extracellular vesicles of probiotic yeasts Saccharomyces boulardii
Possible reference: Kulig, K. et al. (2024) Isolation and Characteristics of Extracellular Vesicles Produced by Probiotics: Yeast Saccharomyces boulardii CNCM I-745 and Bacterium Streptococcus salivarius K12., Probiotics Antimicrob Proteins, PMID 37209320

PXD039123 Dataset with its publication pending (from PRIDE)
Dataset title: Verticillium dahliae Vta3 promotes ELV1 virulence factor gene expression in xylem sap, but tames Mtf1-mediated late stages of fungus-plant interactions and microsclerotia formation
Possible reference: Maurus, I. et al. (2023) Verticillium dahliae Vta3 promotes ELV1 virulence factor gene expression in xylem sap, but tames Mtf1-mediated late stages of fungus-plant interactions and microsclerotia formation., PLoS Pathog, PMID 36716333

PXD039122 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic profiling of urinary extracellular vesicles differentiates breast cancer patients from healthy women
Possible reference: Jeanmard, N. et al. (2023) Proteomic profiling of urinary extracellular vesicles differentiates breast cancer patients from healthy women., PLoS One, PMID 37922300

PXD039121 Dataset with its publication pending (from jPOST)
Dataset title: L-lactate induced proteomic changes in rat hippocampus
Possible reference: Zhao, L. et al. (2018) Metabolomic Analysis Identifies Lactate as an Important Pathogenic Factor in Diabetes-associated Cognitive Decline Rats., Mol Cell Proteomics, PMID 30171160

PXD039090 no publication (from MassIVE)
Dataset title: Cellular population dynamics shape the route to human pluripotency.
Possible reference: Panariello, F. et al. (2023) Cellular population dynamics shape the route to human pluripotency., Nat Commun, PMID 37198156

PXD039083 Dataset with its publication pending (from PRIDE)
Dataset title: Macrophage DCLK1 promotes atherosclerosis via binding to IKKÎ² and inducing inflammatory responses
Possible reference: Huang, Z. et al. (2023) Macrophage DCLK1 promotes atherosclerosis via binding to IKKβ and inducing inflammatory responses., EMBO Mol Med, PMID 36896602

PXD039054 Dataset with its publication pending (from PRIDE)
Dataset title: Time-resolved profiling of mRNA-protein interaction through mRNA life cycle
Possible reference: Choi, Y. et al. (2024) Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle., Mol Cell, PMID 38593806

PXD039050 Dataset with its publication pending (from PRIDE)
Dataset title: Benefit of circadian clocks in adaptive immunity and vaccination responses
Possible reference: Wyse, CA. et al. (2024) Circadian Variation in the Response to Vaccination: A Systematic Review and Evidence Appraisal., J Biol Rhythms, PMID 38459699

PXD039047 Dataset with its publication pending (from jPOST)
Dataset title: Serum Proteomic Profile of Wild Stump-tailed Macaques (Macaca arctoides) Infected with Malaria Parasites in Thailand
Possible reference: Ruengket, P. et al. (2023) Serum proteomic profile of wild stump-tailed macaques (Macaca arctoides) infected with malaria parasites in Thailand., PLoS One, PMID 37910477

PXD039044 Dataset with its publication pending (from iProX)
Dataset title: Large-scale proteomic analysis of T. spiralis muscle-stage ESPs identifies a novel motif for prediction of secreted products
Possible reference: Nash, B. et al. (2023) Large-scale proteomic analysis of T. spiralis muscle-stage ESPs identifies a novel upstream motif for in silico prediction of secreted products., Front Parasitol, PMID 39816813

PXD039041 no publication (from MassIVE)
Dataset title: Ovol2 sustains postnatal thymic epithelial cell identity
Possible reference: Zhong, X. et al. (2023) OVOL2 sustains postnatal thymic epithelial cell identity., Nat Commun, PMID 38012144

PXD039032 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome changes of fibroblasts and endothelial cells upon incubation with human cytomegalovirus dense bodies
Possible reference: Penner, I. et al. (2023) Proteome changes of fibroblasts and endothelial cells upon incubation with human cytomegalovirus subviral Dense Bodies., Sci Data, PMID 37542058

PXD039021 Dataset with its publication pending (from PRIDE)
Dataset title: Pupylation-independent substrate recruitment to proteasomal degradation in mycobacteria
Possible reference: Imkamp, F. et al. (2015) Pupylation-dependent and -independent proteasomal degradation in mycobacteria., Biomol Concepts, PMID 26352358

PXD039014 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of proteins bound to chromatin of male meiotic cells.
Possible reference: Pal, D. et al. (2022) Identification of PAX6 and NFAT4 as the Transcriptional Regulators of the Long Noncoding RNA Mrhl in Neuronal Progenitors., Mol Cell Biol, PMID 36317923

PXD039012 Dataset with its publication pending (from PRIDE)
Dataset title: Kinase Impaired BTK Mutations Are Susceptible to Clinical Stage BTK and IKZF1/3 Degrader NX-2127
Possible reference: Montoya, S. et al. (2024) Kinase-impaired BTK mutations are susceptible to clinical-stage BTK and IKZF1/3 degrader NX-2127., Science, PMID 38301010

PXD039010 Dataset with its publication pending (from PRIDE)
Dataset title: A Spatiotemporal Notch Interaction Map from Membrane to Nucleus
Possible reference: Martin, AP. et al. (2023) A spatiotemporal Notch interaction map from plasma membrane to nucleus., Sci Signal, PMID 37527352

PXD039008 Dataset with its publication pending (from PRIDE)
Dataset title: A Spatiotemporal Notch Interaction Map from Membrane to Nucleus
Possible reference: Martin, AP. et al. (2023) A spatiotemporal Notch interaction map from plasma membrane to nucleus., Sci Signal, PMID 37527352

PXD038987 Dataset with its publication pending (from PRIDE)
Dataset title: Differentiated protein extracts from freshwater and terrestrial mollusks inhibit virulence factor production in Cryptococcus neoformans
Possible reference: Gutierrez-Gongora, D. et al. (2023) Differentiated extracts from freshwater and terrestrial mollusks inhibit virulence factor production in Cryptococcus neoformans., Sci Rep, PMID 36967422

PXD038966 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics analysis on SETD2 loss induced ccRCC formation
Possible reference: Liu, J. et al. (2019) Loss of SETD2 Induces a Metabolic Switch in Renal Cell Carcinoma Cell Lines toward Enhanced Oxidative Phosphorylation., J Proteome Res, PMID 30406665

PXD038964 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative phyloproteomics identifies conserved plasmodesmal proteins
Possible reference: Johnston, MG. et al. (2023) Comparative phyloproteomics identifies conserved plasmodesmal proteins., J Exp Bot, PMID 36639877

PXD038956 no publication (from MassIVE)
Dataset title: Tracking chromatin state changes using nanoscale photo proximity labeling
Possible reference: Seath, CP. et al. (2023) Tracking chromatin state changes using nanoscale photo-proximity labelling., Nature, PMID 37020029

PXD038929 Dataset with its publication pending (from PRIDE)
Dataset title: Systems-level temporal immune-metabolic profile in Crimean-Congo hemorrhagic fever virus infection
Possible reference: Ambikan, AT. et al. (2023) Systems-level temporal immune-metabolic profile in Crimean-Congo hemorrhagic fever virus infection., Proc Natl Acad Sci U S A, PMID 37669378

PXD038906 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device
Possible reference: Shalon, D. et al. (2023) Profiling the human intestinal environment under physiological conditions., Nature, PMID 37165188

PXD038889 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative comparison of manuka and clover honey proteomes with royal jelly
Possible reference: Paget, BW. et al. (2023) Quantitative comparison of manuka and clover honey proteomes with royal jelly., PLoS One, PMID 36763642

PXD038879 Dataset with its publication pending (from jPOST)
Dataset title: Composition of minor ampullate silk makes its properties different from those of major ampullate silk
Possible reference: Nakamura, H. et al. (2023) Composition of Minor Ampullate Silk Makes Its Properties Different from Those of Major Ampullate Silk., Biomacromolecules, PMID 37002945

PXD038856 Dataset with its publication pending (from PRIDE)
Dataset title: Functional nanovesicles from human trophectodermal cells for embryo implantation
Possible reference: Poh, QH. et al. (2024) Rapid generation of functional nanovesicles from human trophectodermal cells for embryo attachment and outgrowth., Proteomics, PMID 37698557

PXD038848 Dataset with its publication pending (from PRIDE)
Dataset title: An apicomplexan bromodomain, TgBDP1 associates with diverse epigenetic factors to regulate essential transcriptional processes in Toxoplasma gondii.
Possible reference: Fleck, K. et al. (2023) An apicomplexan bromodomain protein, TgBDP1, associates with diverse epigenetic factors to regulate essential transcriptional processes in Toxoplasma gondii., mBio, PMID 37350586

PXD038826 Dataset with its publication pending (from PRIDE)
Dataset title: Growth of complete ammonia oxidizers on guanidine
Possible reference: Palatinszky, M. et al. (2024) Growth of complete ammonia oxidizers on guanidine., Nature, PMID 39143220

PXD038824 Dataset with its publication pending (from PRIDE)
Dataset title: A simple non-invasive method to collect soft tick saliva reveals differences in Ornithodoros moubata saliva composition between ticks infected and uninfected with Borrelia duttonii spirochetes
Possible reference: Filatov, S. et al. (2023) A simple non-invasive method to collect soft tick saliva reveals differences in Ornithodoros moubata saliva composition between ticks infected and uninfected with Borrelia duttonii spirochetes., Front Cell Infect Microbiol, PMID 36743301

PXD038822 Dataset with its publication pending (from PRIDE)
Dataset title: Combinatorial treatment with PARP and MAPK inhibitors to overcome phenotype switch-driven drug resistance in advanced melanoma
Possible reference: Ferretti, LP. et al. (2023) Combinatorial Treatment with PARP and MAPK Inhibitors Overcomes Phenotype Switch-Driven Drug Resistance in Advanced Melanoma., Cancer Res, PMID 37729428

PXD038816 Dataset with its publication pending (from PRIDE)
Dataset title: HDAC6 interacting proteins under different stresses
Possible reference: Ryu, HW. et al. (2017) HDAC6 regulates sensitivity to cell death in response to stress and post-stress recovery., Cell Stress Chaperones, PMID 28116619

PXD038804 Dataset with its publication pending (from iProX)
Dataset title: The proteome and phosphoproteome of Saccharomyces cerevisiae during glucose starvation
Possible reference: Caligaris, M. et al. (2023) Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation., Elife, PMID 36749016

PXD038800 no publication (from MassIVE)
Dataset title: Size-exclusion chromatography combined with DIA-MS enables deep proteome profiling of extracellular vesicles from melanoma plasma and serum
Possible reference: Lattmann, E. et al. (2024) Size-exclusion chromatography combined with DIA-MS enables deep proteome profiling of extracellular vesicles from melanoma plasma and serum., Cell Mol Life Sci, PMID 38353833

PXD038792 Dataset with its publication pending (from PRIDE)
Dataset title: Amino acid availability acts as a metabolic rheostat to determine the magnitude of ILC2 responses - WT ILC2
Possible reference: Hodge, SH. et al. (2023) Amino acid availability acts as a metabolic rheostat to determine the magnitude of ILC2 responses., J Exp Med, PMID 36571761

PXD038790 Dataset with its publication pending (from PRIDE)
Dataset title: Mislocalization of pathogenic RBM20 variants in dilated cardiomyopathy is caused by loss-of-interaction with Transportin-3
Possible reference: Kornienko, J. et al. (2023) Mislocalization of pathogenic RBM20 variants in dilated cardiomyopathy is caused by loss-of-interaction with Transportin-3., Nat Commun, PMID 37463913

PXD038783 Dataset with its publication pending (from PRIDE)
Dataset title: A Universal GlycoDesign for Lysosomal Replacement Enzymes to Improve Circulation Time and Biodistribution
Possible reference: Chen, YH. et al. (2023) A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution., Front Bioeng Biotechnol, PMID 36911201

PXD038782 Dataset with its publication pending (from PRIDE)
Dataset title: TOFIMS mass spectrometry-based immunopeptidomics refines tumor antigen identification
Possible reference: Hoenisch Gravel, N. et al. (2023) TOFIMS mass spectrometry-based immunopeptidomics refines tumor antigen identification., Nat Commun, PMID 37978195

PXD038704 Dataset with its publication pending (from PRIDE)
Dataset title: A unique photoprotection mechanism in Chlorella species
Possible reference: Levin, G. et al. (2023) A desert Chlorella sp. that thrives at extreme high-light intensities using a unique photoinhibition protection mechanism., Plant J, PMID 37036169

PXD038701 Dataset with its publication pending (from PRIDE)
Dataset title: SUMOylation of Protein Phosphatase 5 Regulates Phosphatase Activity and Substrate Release
Possible reference: Sager, RA. et al. (2024) SUMOylation of protein phosphatase 5 regulates phosphatase activity and substrate release., EMBO Rep, PMID 39304777

PXD038699 Dataset with its publication pending (from PRIDE)
Dataset title: Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome
Possible reference: Ben-Moshe, S. et al. (2019) Spatial sorting enables comprehensive characterization of liver zonation., Nat Metab, PMID 31535084

PXD038688 Dataset with its publication pending (from PRIDE)
Dataset title: B4 Raf-like MAPKKK RAF24 regulates Arabidopsis thaliana flowering time
Possible reference: Li, Q. et al. (2025) B4 Raf-like MAPKKK RAF24 regulates Arabidopsis thaliana flowering time through HISTONE MONO-UBIQUITINATION 2., New Phytol, PMID 40394941

PXD038679 no publication (from MassIVE)
Dataset title: Proteomics of egg yolk nanovesicles
Possible reference: Saadeldin, IM. et al. (2023) Isolation, characterization, proteome, miRNAome, and the embryotrophic effects of chicken egg yolk nanovesicles (vitellovesicles)., Sci Rep, PMID 36918605

PXD038675 Dataset with its publication pending (from PRIDE)
Dataset title: Asparagine uptake: a cellular strategy of Methylocystis to combat severe salt stress
Possible reference: Guo, K. et al. (2023) Asparagine Uptake: a Cellular Strategy of Methylocystis to Combat Severe Salt Stress., Appl Environ Microbiol, PMID 37184406

PXD038670 Dataset with its publication pending (from PRIDE)
Dataset title: A proteome level study in the early stages of clubroot infection in Brassica napus canola.
Possible reference: Adhikary, D. et al. (2024) Proteome- and metabolome-level changes during early stages of clubroot infection in Brassica napus canola., Mol Omics, PMID 38334713

PXD038667 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects
Possible reference: Mandelbaum, N. et al. (2023) Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects., NPJ Biofilms Microbiomes, PMID 37270554

PXD038658 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted cross-linker delivery for in situ mapping of protein conformations and interactions in mitochondria
Possible reference: Chen, Y. et al. (2023) Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria., Nat Commun, PMID 37391416

PXD038655 Dataset with its publication pending (from PRIDE)
Dataset title: K6-Linked Ubiquitylation Marks Formaldehyde-Induced RNA–Protein Crosslinks for Resolution
Possible reference: Suryo Rahmanto, A. et al. (2023) K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution., Mol Cell, PMID 37951215

PXD038649 Dataset with its publication pending (from PRIDE)
Dataset title: Leucine-973 is a Crucial Residue Differentiating Insulin and IGF-1 Receptor Signaling
Possible reference: Nagao, H. et al. (2023) Leucine-973 is a crucial residue differentiating insulin and IGF-1 receptor signaling., J Clin Invest, PMID 36548088

PXD038646 Dataset with its publication pending (from PRIDE)
Dataset title: Oil body proteome reveals dynamic changes of oil body protein during embryonic development of Carya cathayensis nuts
Possible reference: Chen, A. et al. (2023) Lipid droplets proteome reveals dynamic changes of lipid droplets protein during embryonic development of Carya cathayensis nuts., Plant Sci, PMID 37268111

PXD038639 Dataset with its publication pending (from PRIDE)
Dataset title: Conservation of the PBL-RBOH immune module in land plants
Possible reference: Chu, J. et al. (2023) Conservation of the PBL-RBOH immune module in land plants., Curr Biol, PMID 36796360

PXD038631 Dataset with its publication pending (from PRIDE)
Dataset title: Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET
Possible reference: Dutka, P. et al. (2023) Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET., Structure, PMID 37040766

PXD038623 Dataset with its publication pending (from PRIDE)
Dataset title: The role of DENND10 in neuronal development
Possible reference: Li, A. et al. (2025) Endosomal protein DENND10 promotes developmental competence of neurite extension., iScience, PMID 40330880

PXD038601 Dataset with its publication pending (from PRIDE)
Dataset title: Diagnosis of T-cell-mediated kidney rejection by biopsy-based proteomic biomarkers and machine learning
Possible reference: Fang, F. et al. (2023) Diagnosis of T-cell-mediated kidney rejection by biopsy-based proteomic biomarkers and machine learning., Front Immunol, PMID 36814924

PXD038582 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of Fasciola gigantica excretory and secretory products (FgESPs) co-immunoprecipitated using a time course of infected buffalo sera
Possible reference: Zheng, M. et al. (2022) Proteomic analysis of Fasciola gigantica excretory and secretory products (FgESPs) co-immunoprecipitated using a time course of infected buffalo sera., Front Microbiol, PMID 36620027

PXD038557 Dataset with its publication pending (from PRIDE)
Dataset title: Brain heterotopia formation by ciliopathic breakdown of neuroepithelial and blood-cerebrospinal fluid barriers
Possible reference: Jung, HJ. et al. (2023) Brain heterotopia formation by ciliopathic breakdown of neuroepithelial and blood-cerebrospinal fluid barriers., Brain Pathol, PMID 36623505

PXD038468 Dataset with its publication pending (from iProX)
Dataset title: Data-independent acquisition (DIA) mass spectrometry for Moyamoya disease
Possible reference: He, S. et al. (2025) Serum amyloid A2-induced phenotypic switching of vascular smooth muscle cells in moyamoya disease., J Neurosurg, PMID 40215623

PXD038456 no publication (from MassIVE)
Dataset title: Structure of an endogenous mycobacterial MCE lipid transporter
Possible reference: Chen, J. et al. (2023) Structure of an endogenous mycobacterial MCE lipid transporter., Res Sq, PMID 36711512

PXD038450 Dataset with its publication pending (from PRIDE)
Dataset title: Redifferentiated cardiomyocytes retain residual dedifferentiation signatures and are protected against ischaemic injury
Possible reference: Shakked, A. et al. (2023) Redifferentiated cardiomyocytes retain residual dedifferentiation signatures and are protected against ischemic injury., Nat Cardiovasc Res, PMID 37974970

PXD038436 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics profiling reveals regulation of immune response to Salmonella enterica serovar Typhimurium infection in mice
Possible reference: Huang, H. et al. (2023) Proteomics Profiling Reveals Regulation of Immune Response to Salmonella enterica Serovar Typhimurium Infection in Mice., Infect Immun, PMID 36511704

PXD038423 Dataset with its publication pending (from PRIDE)
Dataset title: The submandibular and sublingual glands maintain oral microbial homeostasis through multiple antimicrobial proteins
Possible reference: Li, Y. et al. (2022) The submandibular and sublingual glands maintain oral microbial homeostasis through multiple antimicrobial proteins., Front Cell Infect Microbiol, PMID 36704102

PXD038422 Dataset with its publication pending (from PRIDE)
Dataset title: Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer
Possible reference: Ortiz-Barahona, V. et al. (2023) Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer., Mol Cancer, PMID 37173708

PXD038416 Dataset with its publication pending (from PRIDE)
Dataset title: Ventral hippocampal CA1 modulates pain behaviors in mice with peripheral inflammation
Possible reference: Shao, S. et al. (2023) Ventral hippocampal CA1 modulates pain behaviors in mice with peripheral inflammation., Cell Rep, PMID 36662622

PXD038407 Dataset with its publication pending (from PRIDE)
Dataset title: Improving SWATH-MS analysis by Deep-learning
Possible reference: Cadow, J. et al. (2021) On the feasibility of deep learning applications using raw mass spectrometry data., Bioinformatics, PMID 34252933

PXD038391 Dataset with its publication pending (from PRIDE)
Dataset title: Ribonucleotide synthesis by NME6 fuels mitochondrial gene expression
Possible reference: Grotehans, N. et al. (2023) Ribonucleotide synthesis by NME6 fuels mitochondrial gene expression., EMBO J, PMID 37439264

PXD038365 Dataset with its publication pending (from PRIDE)
Dataset title: Intact Transition Epitope Mapping - Force differences between Original and Unusual Residues (ITEM-FOUR)
Possible reference: R�wer, C. et al. (2023) Intact Transition Epitope Mapping-Force Differences between Original and Unusual Residues (ITEM-FOUR)., Biomolecules, PMID 36671572

PXD038364 Dataset with its publication pending (from PRIDE)
Dataset title: Monitoring Î±-synuclein ubiquitination dynamics reveals key endosomal effectors mediating its trafficking and degradation
Possible reference: Zenko, D. et al. (2023) Monitoring α-synuclein ubiquitination dynamics reveals key endosomal effectors mediating its trafficking and degradation., Sci Adv, PMID 37315142

PXD038355 no publication (from MassIVE)
Dataset title: EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling
Possible reference: Schr�der, CM. et al. (2025) EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling., Dev Cell, PMID 39662466

PXD038340 no publication (from MassIVE)
Dataset title: An E3 ligase network engages GCN1 to promote degradation of translation factors on stalled ribosomes
Possible reference: Oltion, K. et al. (2023) An E3 ligase network engages GCN1 to promote the degradation of translation factors on stalled ribosomes., Cell, PMID 36638793

PXD038283 Dataset with its publication pending (from PRIDE)
Dataset title: Robust high throughput proteomics identification and deami-dation quantitation of extinct species up to Pleistocene with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry
Possible reference: Bray, F. et al. (2023) Robust High-Throughput Proteomics Identification and Deamidation Quantitation of Extinct Species up to Pleistocene with Ultrahigh-Resolution MALDI-FTICR Mass Spectrometry., Anal Chem, PMID 37130053

PXD038264 Dataset with its publication pending (from PRIDE)
Dataset title: The role of endosomal protein DENND10/FAM45A in extracellular vesicle release and cancer cell migration
Possible reference: Sun, S. et al. (2024) Endosomal protein DENND10/FAM45A integrates extracellular vesicle release with cancer cell migration., BMC Biol, PMID 38987765

PXD038258 Dataset with its publication pending (from iProX)
Dataset title: LC-MS-based urine metabolomics analysis of chronic subdural hematoma for biomarker discovery
Possible reference: Sun, J. et al. (2024) LC-MS-based urine metabolomics analysis of chronic subdural hematoma for biomarker discovery., Proteomics Clin Appl, PMID 37697649

PXD038239 Dataset with its publication pending (from PRIDE)
Dataset title: Assigning functionality to cysteines by base editing of cancer dependency genes
Possible reference: Li, H. et al. (2023) Assigning functionality to cysteines by base editing of cancer dependency genes., Nat Chem Biol, PMID 37783940

PXD038238 Dataset with its publication pending (from PRIDE)
Dataset title: Bacteria Commonly Associated with Central Nervous System Catheter Infections Elicit Distinct CSF Proteome Signatures
Possible reference: Beaver, M. et al. (2023) Bacteria commonly associated with central nervous system catheter infections elicit distinct CSF proteome signatures., Front Neurol, PMID 36864917

PXD038235 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis defines the interactome of telomerase in the protozoan parasite, Trypanosoma brucei
Possible reference: Davis, JA. et al. (2023) Proteomic analysis defines the interactome of telomerase in the protozoan parasite, Trypanosoma brucei., Front Cell Dev Biol, PMID 37009488

PXD038233 Dataset with its publication pending (from PRIDE)
Dataset title: Target identification of methyl bestatin
Possible reference: Yang, M. et al. (2021) Identification and biochemical characterisation of a novel methionine aminopeptidase from the taiga tick Ixodes persulcatus., Ticks Tick Borne Dis, PMID 33002807

PXD038232 Dataset with its publication pending (from PRIDE)
Dataset title: Assigning functionality to cysteines by base editing of cancer dependency genes
Possible reference: Li, H. et al. (2023) Assigning functionality to cysteines by base editing of cancer dependency genes., Nat Chem Biol, PMID 37783940

PXD038225 no publication (from MassIVE)
Dataset title: Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency
Possible reference: Forny, P. et al. (2023) Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency., Nat Metab, PMID 36717752

PXD038217 no publication (from MassIVE)
Dataset title: The NFIB/CARM1 Partnership is a Therapeutic Target for Small Cell Lung Cancer
Possible reference: Gao, G. et al. (2023) The NFIB/CARM1 partnership is a driver in preclinical models of small cell lung cancer., Nat Commun, PMID 36690626

PXD038201 Dataset with its publication pending (from PRIDE)
Dataset title: A CRISPR/Cas9-mediated screen identifies regulators of early plasma cell differentiation
Possible reference: Xiong, E. et al. (2022) A CRISPR/Cas9-mediated screen identifies determinants of early plasma cell differentiation., Front Immunol, PMID 36685499

PXD038191 Dataset with its publication pending (from PRIDE)
Dataset title: Modelling organ-specific metastatic colonization of cholangiocarcinoma organoids in decellularized lung and lymph nodes
Possible reference: van Tienderen, GS. et al. (2022) Modelling metastatic colonization of cholangiocarcinoma organoids in decellularized lung and lymph nodes., Front Oncol, PMID 36741736

PXD038174 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of various stages of fermentation of pea isolate in presence of Aspergillus oryzae
Possible reference: Das, PP. et al. (2023) Snapshot of proteomic changes in Aspergillus oryzae during various stages of fermentative processing of pea protein isolate., Food Chem (Oxf), PMID 36925614

PXD038157 Dataset with its publication pending (from PRIDE)
Dataset title: Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and C53-mediated autophagy
Possible reference: Picchianti, L. et al. (2023) Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy., EMBO J, PMID 36762703

PXD038149 Dataset with its publication pending (from PRIDE)
Dataset title: Proteotranscriptomic analysis of advanced colorectal cancer patient derived organoids for drug sensitivity prediction
Possible reference: Papaccio, F. et al. (2023) "Proteotranscriptomic analysis of advanced colorectal cancer patient derived organoids for drug sensitivity prediction"., J Exp Clin Cancer Res, PMID 36604765

PXD038141 no publication (from MassIVE)
Dataset title: A ubiquitin-based effector-to-inhibitor switch coordinates brain, craniofacial, and skin development
Possible reference: Asmar, AJ. et al. (2023) A ubiquitin-based effector-to-inhibitor switch coordinates early brain, craniofacial, and skin development., Nat Commun, PMID 37495603

PXD038131 Dataset with its publication pending (from PRIDE)
Dataset title: LC-MS/MS of Pseudoregma bambucicola salivary gland and saliva
Possible reference: Zhang, H. et al. (2022) Transcriptomic and proteomic analyses provide insights into host adaptation of a bamboo-feeding aphid., Front Plant Sci, PMID 36714746

PXD038119 Dataset with its publication pending (from PRIDE)
Dataset title: Characteristics of Mycobacterium tuberculosis PtpA interaction and activity on the alpha subunit of human mitochondrial trifunctional protein, a key enzyme of lipid metabolism
Possible reference: Margenat, M. et al. (2023) Characteristics of Mycobacterium tuberculosis PtpA interaction and activity on the alpha subunit of human mitochondrial trifunctional protein, a key enzyme of lipid metabolism., Front Cell Infect Microbiol, PMID 37424790

PXD038104 Dataset with its publication pending (from PRIDE)
Dataset title: Bacterial host adaptation through sequence and structural variations of a single type III effector gene
Possible reference: Lauber, E. et al. (2024) Bacterial host adaptation through sequence and structural variations of a single type III effector gene., iScience, PMID 38439954

PXD038097 Dataset with its publication pending (from jPOST)
Dataset title: Secreted dengue virus NS1 is predominantly dimeric and in complex with high-density lipoprotein
Possible reference: Chew, BLA. et al. (2024) Secreted dengue virus NS1 from infection is predominantly dimeric and in complex with high-density lipoprotein., Elife, PMID 38787378

PXD038087 no publication (from MassIVE)
Dataset title: Comparative proteomic analysis revealing ActJ-regulated proteins in Sinorhizobium meliloti
Possible reference: Albicoro, FJ. et al. (2023) Comparative Proteomic Analysis Revealing ActJ-Regulated Proteins in Sinorhizobium meliloti., J Proteome Res, PMID 37017314

PXD038085 Dataset with its publication pending (from iProX)
Dataset title: Comprehensive analysis of ovarian granulosa cell proteomics and phosphoproteomics in PCOS patients without insulin resistance
Possible reference: Yang, X. et al. (2024) Comprehensive analysis of ovarian granulosa cell proteomics and phosphoproteomics in PCOS patients without insulin resistance., Mol Hum Reprod, PMID 38291901

PXD038075 Dataset with its publication pending (from PRIDE)
Dataset title: A viral ADP-ribosyltransferase attaches RNA chains to host proteins
Possible reference: Wolfram-Schauerte, M. et al. (2023) A viral ADP-ribosyltransferase attaches RNA chains to host proteins., Nature, PMID 37587340

PXD038038 Dataset with its publication pending (from PRIDE)
Dataset title: Revealing Corynebacterium glutamicum proteoforms through top-down proteomics
Possible reference: Melo, RM. et al. (2023) Revealing Corynebacterium glutamicum proteoforms through top-down proteomics., Sci Rep, PMID 36788287

PXD038027 Dataset with its publication pending (from PRIDE)
Dataset title: Protocol for cell surface biotinylation of magnetic labeled and captured human peripheral blood mononuclear cells
Possible reference: Ayaz-Guner, S. et al. (2022) Protocol for cell surface biotinylation of magnetic labeled and captured human peripheral blood mononuclear cells., STAR Protoc, PMID 36595912

PXD038001 Dataset with its publication pending (from PRIDE)
Dataset title: An integrated multi-omics analysis of identiﬁes distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa
Possible reference: Yang, Y. et al. (2023) An integrated multi-omics analysis of identifies distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa., PLoS Pathog, PMID 37643174

PXD037995 Dataset with its publication pending (from PRIDE)
Dataset title: Folding stabilities of ribosome-bound nascent polypeptides probed by mass spectrometry
Possible reference: Tan, R. et al. (2023) Folding stabilities of ribosome-bound nascent polypeptides probed by mass spectrometry., Proc Natl Acad Sci U S A, PMID 37552756

PXD037992 Dataset with its publication pending (from PRIDE)
Dataset title: The Small GTPase Rab7 Regulates Release of Mitochondria in Extracellular Vesicles in Response to Lysosomal Dysfunction
Possible reference: Liang, W. et al. (2023) The Small GTPase Rab7 Regulates Release of Mitochondria in Extracellular Vesicles in Response to Lysosomal Dysfunction., bioRxiv, PMID 36824711

PXD037975 Dataset with its publication pending (from jPOST)
Dataset title: Chronic Strongyloides stercoralis infection increases Ruminococcus torques group and alter microbiome proteome in ivermectin treatment
Possible reference: Tran, NTD. et al. (2023) Chronic Strongyloides stercoralis infection increases presence of the Ruminococcus torques group in the gut and alters the microbial proteome., Sci Rep, PMID 36918707

PXD037973 Dataset with its publication pending (from iProX)
Dataset title: Proteolysis-assisted cyclization facilitates site-centric target deconvolution of isothiocyanates
Possible reference: He, J. et al. (2026) Proteolysis-Assisted Cyclization Facilitates Site-Centric Target Deconvolution of Isothiocyanates., Angew Chem Int Ed Engl, PMID 42116263

PXD037971 Dataset with its publication pending (from iProX)
Dataset title: Subcellular Localization Shapes the Fate of RNA Polymerase III
Possible reference: Tian, K. et al. (2023) Subcellular localization shapes the fate of RNA polymerase III., Cell Rep, PMID 37556328

PXD037957 Dataset with its publication pending (from PRIDE)
Dataset title: Mining Nudibranch Symbionts for Biosynthesis of novel Secondary Metabolites
Possible reference: Elsaeed, E. et al. (2023) Mining Chromodoris quadricolor symbionts for biosynthesis of novel secondary metabolites., Mar Genomics, PMID 36738602

PXD037944 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteome analysis of different Saccharomyces cerevisiae strains during growth on sucrose and glucose
Possible reference: Soares Rodrigues, CI. et al. (2023) Comparative proteome analysis of different Saccharomyces cerevisiae strains during growth on sucrose and glucose., Sci Rep, PMID 36746999

PXD037942 Dataset with its publication pending (from PRIDE)
Dataset title: Thermal proteome profiling in Cryptosporidium parvum
Possible reference: Hanna, JC. et al. (2023) Mode of action studies confirm on-target engagement of lysyl-tRNA synthetase inhibitor and lead to new selection marker for Cryptosporidium., Front Cell Infect Microbiol, PMID 37600947

PXD037926 Dataset with its publication pending (from PRIDE)
Dataset title: Endothelial OTUD1 promotes Ang II-induced vascular remodeling by deubiquitinating SMAD3
Possible reference: Huang, Z. et al. (2023) Mouse endothelial OTUD1 promotes angiotensin II-induced vascular remodeling by deubiquitinating SMAD3., EMBO Rep, PMID 36579465

PXD037922 Dataset with its publication pending (from PRIDE)
Dataset title: DRAK2 alters IL-2 sensitivity and Treg development
Possible reference: Mandarano, AH. et al. (2023) DRAK2 contributes to type 1 diabetes by negatively regulating IL-2 sensitivity to alter regulatory T�cell development., Cell Rep, PMID 36773294

PXD037918 Dataset with its publication pending (from PRIDE)
Dataset title: Citrullinated glucose-regulated protein 78 is a candidate target for cancer immunotherapy
Possible reference: Brentville, VA. et al. (2022) Citrullinated glucose-regulated protein 78 is a candidate target for melanoma immunotherapy., Front Immunol, PMID 36544781

PXD037906 Dataset with its publication pending (from PRIDE)
Dataset title: Human Tim8a, Tim8b and Tim13 are auxiliary assembly factors of mature Complex IV
Possible reference: Anderson, AJ. et al. (2023) Human Tim8a, Tim8b and Tim13 are auxiliary assembly factors of mature Complex IV., EMBO Rep, PMID 37272231

PXD037895 Dataset with its publication pending (from PRIDE)
Dataset title: A Selective Small-Molecule STAT5 PROTAC Degrader Capable of Achieving Tumor Regression In Vivo
Possible reference: Kaneshige, A. et al. (2023) A selective small-molecule STAT5 PROTAC degrader capable of achieving tumor regression in vivo., Nat Chem Biol, PMID 36732620

PXD037892 Dataset with its publication pending (from PRIDE)
Dataset title: The Fgf/Erf/NCoR1/2 repressive axis controls trophoblast cell fate
Possible reference: Lackner, A. et al. (2023) The Fgf/Erf/NCoR1/2 repressive axis controls trophoblast cell fate., Nat Commun, PMID 37137875

PXD037883 Dataset with its publication pending (from iProX)
Dataset title: DIA mass spectrometry analysis of carotid body tumors revealed the potential mechanism and molecular differences among Shamblin classifications
Possible reference: Lv, Y. et al. (2023) Proteomics analysis of carotid body tumor revealed potential mechanisms and molecular differences among Shamblin classifications., Exp Biol Med (Maywood), PMID 37845830

PXD037875 Dataset with its publication pending (from PRIDE)
Dataset title: Coordinate control of endoplasmic reticulum chaperone biosynthesis and peptide hormone secretion revealed by a Î²-cell model of Prader-Willi syndrome
Possible reference: Koppes, EA. et al. (2023) Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones., PLoS Genet, PMID 37068109

PXD037859 Dataset with its publication pending (from PRIDE)
Dataset title: Synapse integrity and function: dependence on protein synthesis and identification of potential failure points
Possible reference: Cohen, LD. et al. (2022) Synapse integrity and function: Dependence on protein synthesis and identification of potential failure points., Front Mol Neurosci, PMID 36583084

PXD037847 Dataset with its publication pending (from PRIDE)
Dataset title: Environmental gradients reveal stress hubs predating plant terrestrialization
Possible reference: Dadras, A. et al. (2023) Environmental gradients reveal stress hubs pre-dating plant terrestrialization., Nat Plants, PMID 37640935

PXD037846 Dataset with its publication pending (from PRIDE)
Dataset title: Acclimation strategies of the green alga Chlorella vulgaris to different light regimes revealed by physiologic and comparative proteomic analysis
Possible reference: Cecchin, M. et al. (2023) Acclimation strategies of the green alga Chlorella vulgaris to different light regimes revealed by physiological and comparative proteomic analyses., J Exp Bot, PMID 37155956

PXD037844 Dataset with its publication pending (from PRIDE)
Dataset title: Human Beta Defensin-2-mediated protection of human skin barrier in vitro; a mechanistic evaluation
Possible reference: Shelley, JR. et al. (2023) A mechanistic evaluation of human beta defensin 2 mediated protection of human skin barrier in vitro., Sci Rep, PMID 36755116

PXD037804 Dataset with its publication pending (from PRIDE)
Dataset title: Physiology of trans-translation deficiency in Bacillus subtilis – a comparative proteomics study
Possible reference: V�zquez-Hern�ndez, M. et al. (2023) Physiology of trans-translation deficiency in Bacillus subtilis - a comparative proteomics study., Proteomics, PMID 37496314

PXD037803 Dataset with its publication pending (from PRIDE)
Dataset title: Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics
Possible reference: Gueto-Tettay, C. et al. (2023) Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics., PLoS Comput Biol, PMID 36668672

PXD037795 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles from Trypanosoma cruzi-dendritic cell interaction show modulatory properties and confer resistance to lethal infection as a cell-free based therapy strategy
Possible reference: Gutierrez, BC. et al. (2022) Extracellular vesicles from Trypanosoma cruzi-dendritic cell interaction show modulatory properties and confer resistance to lethal infection as a cell-free based therapy strategy., Front Cell Infect Microbiol, PMID 36467728

PXD037790 Dataset with its publication pending (from jPOST)
Dataset title: The Liquid Chromatography/Tandem Mass Spectrometry-Based Quantification of Angiotensin Ⅱ
Possible reference: He, C. et al. (2020) Development of a novel nanoflow liquid chromatography-parallel reaction monitoring mass spectrometry-based method for quantification of angiotensin peptides in HUVEC cultures., PeerJ, PMID 32983648

PXD037779 no publication (from MassIVE)
Dataset title: MHC Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T cell epitopes specific to seasonal coronaviruses and epitopes cross-reactive with SARS-CoV-2
Possible reference: Becerra-Artiles, A. et al. (2022) Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2., bioRxiv, PMID 36482973

PXD037755 Dataset with its publication pending (from PRIDE)
Dataset title: Key changes in bovine milk immunoglobulin G during lactation: NeuAc sialylation is a hallmark of colostrum immunoglobulin G N-glycosylation Key changes in bovine milk immunoglobulin G during lactation: NeuAc sialylation is a hallmark of colostrum immunogl
Possible reference: Gazi, I. et al. (2023) Key changes in bovine milk immunoglobulin G during lactation: NeuAc sialylation is a hallmark of colostrum immunoglobulin G N-glycosylation., Glycobiology, PMID 36611013

PXD037754 Dataset with its publication pending (from PRIDE)
Dataset title: P2X7 signaling drives Th1 cell differentiation through metabolic reprogramming for aerobic glycolysis
Possible reference: de Salles, �M. et al. (2023) P2RX7 signaling drives the differentiation of Th1 cells through metabolic reprogramming for aerobic glycolysis., Front Immunol, PMID 36993971

PXD037741 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins
Possible reference: Groh, C. et al. (2023) Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins., Life Sci Alliance, PMID 36941057

PXD037736 Dataset with its publication pending (from PRIDE)
Dataset title: Coupled induction of prophage and virulence factors during tick transmission of the Lyme disease spirochete
Possible reference: Wachter, J. et al. (2023) Coupled induction of prophage and virulence factors during tick transmission of the Lyme disease spirochete., Nat Commun, PMID 36639656

PXD037687 Dataset with its publication pending (from jPOST)
Dataset title: A multiplexed microflow LC-MS/MS-PRM assay for serologic quantification of IgG N- and HPX O- glycoforms in liver fibrosis
Possible reference: Panigrahi, A. et al. (2023) A multiplexed microflow LC-MS/MS-PRM assay for serologic quantification of IgG N- and HPX O- glycoforms in liver fibrosis., Sci Rep, PMID 36635317

PXD037682 Dataset with its publication pending (from PRIDE)
Dataset title: ALSPAC human inflammation plasma proteomics
Possible reference: Tsang, RSM. et al. (2025) Inflammation proteomic profiling of psychosis in young adults: Findings from the ALSPAC birth cohort., Psychoneuroendocrinology, PMID 39442229

PXD037668 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular Docking and Proteomics Reveals the Synergistic Antibacterial Mechanism of Theaflavin with Î²-lactam Antibiotics Against MRSA
Possible reference: Guan, S. et al. (2022) Molecular docking and proteomics reveals the synergistic antibacterial mechanism of theaflavin with β-lactam antibiotics against MRSA., Front Microbiol, PMID 36452924

PXD037667 Dataset with its publication pending (from PRIDE)
Dataset title: Curcuminoid Supplementation in Canine Diabetic Mellitus and its Complications using Proteomic Analysis
Possible reference: Suemanotham, N. et al. (2022) Curcuminoid supplementation in canine diabetic mellitus and its complications using proteomic analysis., Front Vet Sci, PMID 36619946

PXD037657 Dataset with its publication pending (from PRIDE)
Dataset title: Lipid metabolism reprogramming and Trastuzumab resistance in Breast cancer cell lines overexpressing the ERBB2 membrane receptor.
Possible reference: Cortese, K. et al. (2023) Lipid Metabolism Reprogramming and Trastuzumab Resistance in Breast Cancer Cell Lines Overexpressing the ERBB2 Membrane Receptor., Membranes (Basel), PMID 37367744

PXD037644 Dataset with its publication pending (from jPOST)
Dataset title: Motif-targeting phosphoproteome analysis of cancer cells for profiling kinase inhibitors.
Possible reference: Ogata, K. et al. (2022) Motif-Targeting Phosphoproteome Analysis of Cancer Cells for Profiling Kinase Inhibitors., Cancers (Basel), PMID 36612075

PXD037643 no publication (from MassIVE)
Dataset title: Lipo-chitooligosaccharides induce specialized fungal metabolite profiles that modulate bacterial growth.
Possible reference: Rush, TA. et al. (2022) Lipo-Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles That Modulate Bacterial Growth., mSystems, PMID 36453934

PXD037629 Dataset with its publication pending (from PRIDE)
Dataset title: Specific milk composition in miR-30b-transgenic mice associated to offspring early gut maturation with lasting consequences on their growth
Possible reference: Le Guillou, S. et al. (2023) Specific Milk Composition of miR-30b Transgenic Mice Associated with Early Duodenum Maturation in Offspring with Lasting Consequences for Growth., J Nutr, PMID 37543213

PXD037621 Dataset with its publication pending (from PRIDE)
Dataset title: BLIMP1 induces cancer immune evasion by modulating the USP22-SPI1-PD-L1 axis in hepatocellular carcinoma cells
Possible reference: Li, Q. et al. (2022) PRDM1/BLIMP1 induces cancer immune evasion by modulating the USP22-SPI1-PD-L1 axis in hepatocellular carcinoma cells., Nat Commun, PMID 36509766

PXD037611 no publication (from MassIVE)
Dataset title: Ammonium Sulfate-based Prefractionation Improved Carbonylated Proteome Coverage in Arabidopsis thaliana Leaf Extract
Possible reference: Tola, AJ. et al. (2023) Ammonium sulfate-based prefractionation improved proteome coverage and detection of carbonylated proteins in Arabidopsis thaliana leaf extract., Planta, PMID 36808312

PXD037601 Dataset with its publication pending (from PRIDE)
Dataset title: Functional annotation of proteins for signaling network inference in non-model species
Possible reference: Van den Broeck, L. et al. (2023) Functional annotation of proteins for signaling network inference in non-model species., Nat Commun, PMID 37537196

PXD037590 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics analysis of zebrafish spinal cord regeneration
Possible reference: Salisbury, JP. et al. (2015) The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation., BMC Genomics, PMID 25879418

PXD037572 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of Eya3 binding partners
Possible reference: Wiedner, HJ. et al. (2023) RBFOX2 regulated EYA3 isoforms partner with SIX4 or ZBTB1 to control transcription during myogenesis., iScience, PMID 38026174

PXD037570 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of the proteolytic signature in CVB3-infected cell
Possible reference: Vlok, M. et al. (2024) Identification of the proteolytic signature in CVB3-infected cells., J Virol, PMID 38953667

PXD037545 Dataset with its publication pending (from PRIDE)
Dataset title: The ribosome quality control factor Asc1 determines the fate of HSP70 mRNA on and off the ribosome
Possible reference: Alagar Boopathy, LR. et al. (2023) The ribosome quality control factor Asc1 determines the fate of HSP70 mRNA on and off the ribosome., Nucleic Acids Res, PMID 37158240

PXD037533 no publication (from MassIVE)
Dataset title: Scribe: next-generation library searching for DDA experiments
Possible reference: Searle, BC. et al. (2023) Scribe: Next Generation Library Searching for DDA Experiments., J Proteome Res, PMID 36695531

PXD037532 no publication (from MassIVE)
Dataset title: Improved Structural Characterization of Glycerophospholipids and Sphingomyelins with Real-Time Library Searching
Possible reference: Brademan, DR. et al. (2023) Improved Structural Characterization of Glycerophospholipids and Sphingomyelins with Real-Time Library Searching., Anal Chem, PMID 37172325

PXD037528 Dataset with its publication pending (from PRIDE)
Dataset title: SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9
Possible reference: Schmidt, N. et al. (2023) SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9., Cell, PMID 37794589

PXD037525 Dataset with its publication pending (from PRIDE)
Dataset title: Site-Selective Photocatalytic Functionalization of Peptides and Proteins at Selenocysteine
Possible reference: Dowman, LJ. et al. (2022) Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine., Nat Commun, PMID 36371402

PXD037524 Dataset with its publication pending (from PRIDE)
Dataset title: Myeloperoxidase is a Critical Mediator of Anthracycline-induced Cardiomyopathy
Possible reference: Nettersheim, FS. et al. (2023) Myeloperoxidase is a critical mediator of anthracycline-induced cardiomyopathy., Basic Res Cardiol, PMID 37656254

PXD037515 no publication (from MassIVE)
Dataset title: Proteome wide analysis of hydrogen peroxide-induced protein carbonylation in Arabidopsis thaliana
Possible reference: Fangue-Yapseu, GY. et al. (2022) Proteome-wide analysis of hydrogen peroxide-induced protein carbonylation in Arabidopsis thaliana., Front Plant Sci, PMID 36544875

PXD037514 no publication (from MassIVE)
Dataset title: Comprehensive and quantitative analysis of the changes in proteomic and phosphoproteomic profiles during stimulation and repression of steroidogenesis in MA-10 Leydig cells.
Possible reference: Demmouche, ZB. et al. (2022) Comprehensive and Quantitative Analysis of the Changes in Proteomic and Phosphoproteomic Profiles during Stimulation and Repression of Steroidogenesis in MA-10 Leydig Cells., Int J Mol Sci, PMID 36361638

PXD037509 Dataset with its publication pending (from PRIDE)
Dataset title: Complete integration of carbene-transfer chemistry into biosynthesis
Possible reference: Huang, J. et al. (2023) Complete integration of carbene-transfer chemistry into biosynthesis., Nature, PMID 37138074

PXD037507 Dataset with its publication pending (from PRIDE)
Dataset title: A Subtractive Proteomics Approach for the Identification of Immunodominant Acinetobacter baumannii Vaccine Candidate Proteins
Possible reference: Acar, MB. et al. (2022) A subtractive proteomics approach for the identification of immunodominant Acinetobacter baumannii vaccine candidate proteins., Front Immunol, PMID 36439128

PXD037490 Dataset with its publication pending (from PRIDE)
Dataset title: Synaptic vesicle proteins and ATG9A self-organize in distinct vesicle phases within synapsin condensates
Possible reference: Park, D. et al. (2023) Synaptic vesicle proteins and ATG9A self-organize in distinct vesicle phases within synapsin condensates., Nat Commun, PMID 36709207

PXD037488 Dataset with its publication pending (from PRIDE)
Dataset title: Multigenerational effect of heat stress on the Drosophila melanogaster sperm proteome
Possible reference: Khan, S. et al. (2024) Multigenerational Effect of Heat Stress on the Drosophila melanogaster Sperm Proteome., J Proteome Res, PMID 38743012

PXD037464 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamic partitioning of branched-chain amino acids- derived nitrogen supports renal cancer progression
Possible reference: Sciacovelli, M. et al. (2022) Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression., Nat Commun, PMID 36539415

PXD037445 no publication (from MassIVE)
Dataset title: The influence of iron availability on protein carbonylation in Arabidopsis thaliana plant
Possible reference: Tola, AJ. et al. (2023) Iron Availability Influences Protein Carbonylation in Arabidopsis thaliana Plants., Int J Mol Sci, PMID 37298684

PXD037423 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of Plasma Membrane Proteins in Stylosanthes Leaves and Roots Using Simplified Enrichment Method
Possible reference: Yang, L. et al. (2022) Characterization of plasma membrane proteins in stylosanthes leaves and roots using simplified enrichment method with a nonionic detergent., Front Plant Sci, PMID 36589080

PXD037391 Dataset with its publication pending (from PRIDE)
Dataset title: Oxidized thioredoxin-1 restrains the NLRP1 inflammasome
Possible reference: Ball, DP. et al. (2022) Oxidized thioredoxin-1 restrains the NLRP1 inflammasome., Sci Immunol, PMID 36332009

PXD037381 Dataset with its publication pending (from PRIDE)
Dataset title: Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation
Possible reference: Caligaris, M. et al. (2023) Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation., Elife, PMID 36749016

PXD037376 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting CHAF1B enhances interferon activity in myeloproliferative neoplasms
Possible reference: Saleiro, D. et al. (2023) Targeting CHAF1B Enhances IFN Activity against Myeloproliferative Neoplasm Cells., Cancer Res Commun, PMID 37377894

PXD037351 Dataset with its publication pending (from iProX)
Dataset title: AggLink probe for aggregated proteome
Possible reference: Shen, D. et al. (2023) Developing an Affinity-Based Chemical Proteomics Method to In Situ Capture Amorphous Aggregated Proteome and Profile Its Heterogeneity in Stressed Cells., Anal Chem, PMID 37017602

PXD037350 Dataset with its publication pending (from iProX)
Dataset title: Multi-Comparative Thermal Proteome Profiling Uncovers New O-GlcNAc Proteins in System-Wide
Possible reference: Wang, G. et al. (2023) Multi-comparative Thermal Proteome Profiling Uncovers New O-GlcNAc Proteins in a System-wide Method., Anal Chem, PMID 36580660

PXD037346 Dataset with its publication pending (from PRIDE)
Dataset title: A proteomic analysis shows stimulation of light reactions and inhibition of Calvin cycle in skin chloroplasts of ripe red grape berries
Possible reference: Teixeira, A. et al. (2022) A proteomic analysis shows the stimulation of light reactions and inhibition of the Calvin cycle in the skin chloroplasts of ripe red grape berries., Front Plant Sci, PMID 36388544

PXD037337 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics explored the feasibility of curcumin as anticancer copper ionophore
Possible reference: Yang, Y. et al. (2022) Proteomics revealed the crosstalk between copper stress and cuproptosis, and explored the feasibility of curcumin as anticancer copper ionophore., Free Radic Biol Med, PMID 36395954

PXD037335 Dataset with its publication pending (from PRIDE)
Dataset title: Target of L-menthol in keratinocytes
Possible reference: Wang, Z. et al. (2022) Targeting the transcription factor HES1 by L-menthol restores protein phosphatase 6 in keratinocytes in models of psoriasis., Nat Commun, PMID 36535970

PXD037321 Dataset with its publication pending (from PRIDE)
Dataset title: Î²-OHB Reduces Reinstatement of Cocaine Conditioned Place Preference Through Hippocampal CaMKII-Î± Î²-Hydroxybutyrylation
Possible reference: Li, H. et al. (2022) β-hydroxybutyrate reduces reinstatement of cocaine conditioned place preference through hippocampal CaMKII-α β-hydroxybutyrylation., Cell Rep, PMID 36450263

PXD037305 no publication (from MassIVE)
Dataset title: Urinary Proteome of Chronic Kidney Disease of Unknown Etiology (CKDu)
Possible reference: Kolli, RT. et al. (2023) The urinary proteome infers dysregulation of mitochondrial, lysosomal, and protein reabsorption processes in chronic kidney disease of unknown etiology (CKDu)., Am J Physiol Renal Physiol, PMID 36794752

PXD037303 Dataset with its publication pending (from iProX)
Dataset title: Integrative analysis of proteomics and transcriptomics of longissimus dorsi of the Different Feeding Systems the Yaks
Possible reference: Ma, X. et al. (2023) Integrative Analysis of Proteomics and Transcriptomics of Longissimus dorsi with Different Feeding Systems in Yaks., Foods, PMID 36673349

PXD037302 Dataset with its publication pending (from iProX)
Dataset title: Excessive sulfur oxidation in endoplasmic reticulum drives an inflammatory reaction of chondrocytes in aging mice
Possible reference: Chen, K. et al. (2022) Excessive sulfur oxidation in endoplasmic reticulum drives an inflammatory reaction of chondrocytes in aging mice., Front Pharmacol, PMID 36353501

PXD037299 no publication (from MassIVE)
Dataset title: KIBRA repairs synaptic plasticity and promotes resilience to tauopathy-related memory loss
Possible reference: Kauwe, G. et al. (2023) KIBRA repairs synaptic plasticity and promotes resilience to tauopathy-related memory loss., bioRxiv, PMID 37398236

PXD037298 Dataset with its publication pending (from jPOST)
Dataset title: Impact of internal fragments on top-down analysis of intact proteins by 193 nm UVPD
Possible reference: Dunham, SD. et al. (2023) Impact of Internal Fragments on Top-Down Analysis of Intact Proteins by 193 nm UVPD., J Proteome Res, PMID 36503236

PXD037291 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteome and phosphoproteome datasets of DNA replication and mitosis in Saccharomyces cerevisiae
Possible reference: Rossio, V. et al. (2022) Quantitative proteome and phosphoproteome datasets of DNA replication and mitosis in Saccharomyces cerevisiae., Data Brief, PMID 36425962

PXD037281 Dataset with its publication pending (from PRIDE)
Dataset title: Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides
Possible reference: Reķēna, A. et al. (2023) Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides., PLoS Comput Biol, PMID 37099621

PXD037278 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics revealed the crosstalk between copper stress and cuproptosis
Possible reference: Yang, Y. et al. (2022) Proteomics revealed the crosstalk between copper stress and cuproptosis, and explored the feasibility of curcumin as anticancer copper ionophore., Free Radic Biol Med, PMID 36395954

PXD037263 Dataset with its publication pending (from PRIDE)
Dataset title: The dimeric deubiquitinase Usp28 integrates 53bp1 and Myc functions to limit DNA damage
Possible reference: Jin, C. et al. (2024) The dimeric deubiquitinase USP28 integrates 53BP1 and MYC functions to limit DNA damage., Nucleic Acids Res, PMID 38227944

PXD037253 Dataset with its publication pending (from PRIDE)
Dataset title: Growth Signaling Autonomy in Circulating Tumor Cells Aids Metastatic Seeding
Possible reference: Sinha, S. et al. (2024) Growth signaling autonomy in circulating tumor cells aids metastatic seeding., PNAS Nexus, PMID 38312224

PXD037250 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic and in silico analyses of the influence of dextran synthesis on the adaptation of Leuconostoc lactis AV1n to temperature change
Possible reference: Besrour-Aouam, N. et al. (2022) Proteomic and in silico analyses of dextran synthesis influence on Leuconostoc lactis AV1n adaptation to temperature change., Front Microbiol, PMID 36713162

PXD037230 Dataset with its publication pending (from PRIDE)
Dataset title: Scleraxis-lineage cells are required for tendon homeostasis and their depletion induces an accelerated extracellular matrix aging phenotype
Possible reference: Korcari, A. et al. (2023) Scleraxis-lineage cells are required for tendon homeostasis and their depletion induces an accelerated extracellular matrix aging phenotype., Elife, PMID 36656751

PXD037226 Dataset with its publication pending (from jPOST)
Dataset title: Enabling the Photo-crosslinking and Photo-sensitizing Chemistry for Synthetic Fluorescent Protein Chromophore
Possible reference: Feng, H. et al. (2023) Enabling Photo-Crosslinking and Photo-Sensitizing Properties for Synthetic Fluorescent Protein Chromophores., Angew Chem Int Ed Engl, PMID 36370037

PXD037225 no publication (from MassIVE)
Dataset title: Surfaceome analysis of extracellular vesicles from senescent cells uncovers uptake repressor DPP4
Possible reference: Meng, Q. et al. (2023) Surfaceome analysis of extracellular vesicles from senescent cells uncovers uptake repressor DPP4., Proc Natl Acad Sci U S A, PMID 37862381

PXD037218 Dataset with its publication pending (from jPOST)
Dataset title: Metaproteomic analysis of gut resistome in the cecal microbiota of fattening pigs raised without antibiotics
Possible reference: Buthasane, P. et al. (2023) Metaproteomic Analysis of Gut Resistome in the Cecal Microbiota of Fattening Pigs Raised without Antibiotics., Microbiol Spectr, PMID 37439677

PXD037209 Dataset with its publication pending (from iProX)
Dataset title: Design, Construction and Functional Characterization of a tRNA Neochromosome in Yeast
Possible reference: Schindler, D. et al. (2023) Design, construction, and functional characterization of a tRNA neochromosome in yeast., Cell, PMID 37944512

PXD037203 no publication (from MassIVE)
Dataset title: Newly synthesized glycoproteins during ex vivo lung perfusion
Possible reference: Ling, Z. et al. (2023) Newly synthesized glycoprotein profiling to identify molecular signatures of warm ischemic injury in donor lungs., Am J Physiol Lung Cell Mol Physiol, PMID 37130807

PXD037200 (from jPOST)
Dataset title: Proteomic analysis of ascites from LC and GC patients
Possible reference: Bateman, RM. et al. (2016) 36th International Symposium on Intensive Care and Emergency Medicine : Brussels, Belgium. 15-18 March 2016., Crit Care, PMID 27885969

PXD037181 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of acrosin and acrosin binding protein as novel CRISP2 interacting proteins in boar spermatozoa
Possible reference: Zhang, M. et al. (2023) Characterization of acrosin and acrosin binding protein as novel CRISP2 interacting proteins in boar spermatozoa., Andrology, PMID 36815564

PXD037176 Dataset with its publication pending (from PRIDE)
Dataset title: Inactivation of Influenza A virus under expiratory aerosol conditions is mediated by structural protein changes, as determined by whole virus mass-spectrometry.
Possible reference: David, SC. et al. (2023) Inactivation mechanisms of influenza A virus under pH conditions encountered in aerosol particles as revealed by whole-virus HDX-MS., mSphere, PMID 37594288

PXD037155 Dataset with its publication pending (from PRIDE)
Dataset title: Lineage-specific oncogenes drive growth of major forms of human cancer using common downstream mechanisms
Possible reference: Kauko, O. et al. (2025) Diverse oncogenes use common mechanisms to drive growth of major forms of human cancer., Sci Adv, PMID 40834066

PXD037154 Dataset with its publication pending (from PRIDE)
Dataset title: PARP1 proximity proteomics reveals interaction partners at stressed replication forks
Possible reference: Mosler, T. et al. (2022) PARP1 proximity proteomics reveals interaction partners at stressed replication forks., Nucleic Acids Res, PMID 36350633

PXD037153 Dataset with its publication pending (from PRIDE)
Dataset title: Nonionic surfactants can modify the thermal stability of globular and membrane proteins interfering with the thermal proteome profiling principles to identify protein targets
Possible reference: Berlin, E. et al. (2023) Nonionic Surfactants can Modify the Thermal Stability of Globular and Membrane Proteins Interfering with the Thermal Proteome Profiling Principles to Identify Protein Targets., Anal Chem, PMID 36779864

PXD037150 Dataset with its publication pending (from PRIDE)
Dataset title: Interplay between acetylation and ubiquitination of Isw1 confers multidrug resistance in Cryptococcus neoformans
Possible reference: Meng, Y. et al. (2024) Interplay between acetylation and ubiquitination of imitation switch chromatin remodeler Isw1 confers multidrug resistance in Cryptococcus neoformans., Elife, PMID 38251723

PXD037143 Dataset with its publication pending (from PRIDE)
Dataset title: Triap1 upregulation promotes escape from mitotic slippage-induced G1 arrest
Possible reference: Pavani, M. et al. (2023) Triap1 upregulation promotes escape from mitotic-slippage-induced G1 arrest., Cell Rep, PMID 36917609

PXD037140 Dataset with its publication pending (from PRIDE)
Dataset title: H11-induced immune protection is predominantly linked to N-glycan moieties
Possible reference: Wang, C. et al. (2022) H11-induced immunoprotection is predominantly linked to N-glycan moieties during Haemonchus contortus infection., Front Immunol, PMID 36405717

PXD037134 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive glycoprofiling of oral tumours associates N-glycosylation with lymph node metastasis and patient survival
Possible reference: Carnielli, CM. et al. (2023) Comprehensive Glycoprofiling of Oral Tumors Associates N-Glycosylation With Lymph Node Metastasis and Patient Survival., Mol Cell Proteomics, PMID 37268159

PXD037126 no publication (from MassIVE)
Dataset title: Integrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation
Possible reference: Chiu, CC. et al. (2023) Integrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation., BMC Plant Biol, PMID 36869316

PXD037111 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic dataset of the moss Physcomitrium patens PpRALF knockout lines
Possible reference: Mamaeva, A. et al. (2022) Quantitative proteomic dataset of the moss Physcomitrium patens SMG1 KO mutant line., Data Brief, PMID 34977295

PXD037108 Dataset with its publication pending (from PRIDE)
Dataset title: Termination of STING responses is mediated via ESCRT-dependent degradation
Possible reference: Gentili, M. et al. (2023) ESCRT-dependent STING degradation inhibits steady-state and cGAMP-induced signalling., Nat Commun, PMID 36739287

PXD037101 Dataset with its publication pending (from PRIDE)
Dataset title: Amino Acids Downregulate SIRT4 to Detoxify Ammonia through the Urea Cycle
Possible reference: Hu, SH. et al. (2023) Amino acids downregulate SIRT4 to detoxify ammonia through the urea cycle., Nat Metab, PMID 37081161

PXD037098 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omics Analyses Reveal Sex Differences in Mouse Renal Proximal Tubules
Possible reference: Chen, L. et al. (2023) Multiomics Analyses Reveal Sex Differences in Mouse Renal Proximal Subsegments., J Am Soc Nephrol, PMID 36758122

PXD037085 no publication (from MassIVE)
Dataset title: The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids
Possible reference: Muenzner, J. et al. (2024) Natural proteome diversity links aneuploidy tolerance to protein turnover., Nature, PMID 38778096

PXD037079 Dataset with its publication pending (from iProX)
Dataset title: TMT-Based Quantitative Proteomics Reveals the Targets of Andrographolide on LPS-induced Liver Injury
Possible reference: Ge, S. et al. (2023) TMT-based quantitative proteomics reveals the targets of andrographolide on LPS-induced liver injury., BMC Vet Res, PMID 37817228

PXD037077 no publication (from MassIVE)
Dataset title: Cell State Dependent Effects of Bmal1 on Melanoma Immunity and Tumorigenicity
Possible reference: Zhang, X. et al. (2024) Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity., Nat Commun, PMID 38245503

PXD037071 Dataset with its publication pending (from jPOST)
Dataset title: Enabling the Photo-crosslinking and Photo-sensitizing Chemistry for Synthetic Fluorescent Protein Chromophore
Possible reference: Feng, H. et al. (2023) Enabling Photo-Crosslinking and Photo-Sensitizing Properties for Synthetic Fluorescent Protein Chromophores., Angew Chem Int Ed Engl, PMID 36370037

PXD037063 Dataset with its publication pending (from PRIDE)
Dataset title: Calliactis polypus acontia venom
Possible reference: Smith, HL. et al. (2023) Acontia, a Specialised Defensive Structure, Has Low Venom Complexity in Calliactis polypus., Toxins (Basel), PMID 36977109

PXD037043 Dataset with its publication pending (from PRIDE)
Dataset title: McIdas localizes at centrioles and controls centriole numbers through PLK4-dependent phosphorylation
Possible reference: Arbi, M. et al. (2026) McIdas localizes to centrioles and controls centriole numbers through PLK4-dependent phosphorylation., EMBO Rep, PMID 41644695

PXD037040 Dataset with its publication pending (from PRIDE)
Dataset title: Tryptase regulation of joint lubrication and inflammation in osteoarthritis
Possible reference: Das, N. et al. (2023) Tryptase β regulation of joint lubrication and inflammation via proteoglycan-4 in osteoarthritis., Nat Commun, PMID 37024468

PXD037037 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanisms of stop codon readthrough mitigation reveal principles of GCN1 mediated translational quality control
Possible reference: M�ller, MBD. et al. (2023) Mechanisms of readthrough mitigation reveal principles of GCN1-mediated translational quality control., Cell, PMID 37339632

PXD037030 Dataset with its publication pending (from PRIDE)
Dataset title: Structural Assessment of the Full-Length Tumor Suppressor Protein p53 by Mass Spectrometry-Guided Computational Modeling
Possible reference: Di Ianni, A. et al. (2023) Structural assessment of the full-length wild-type tumor suppressor protein p53 by mass spectrometry-guided computational modeling., Sci Rep, PMID 37231156

PXD037017 Dataset with its publication pending (from iProX)
Dataset title: O-GlcNAcylation determines the biological function of YTHDF proteins
Possible reference: Chen, Y. et al. (2023) O-GlcNAcylation determines the translational regulation and phase separation of YTHDF proteins., Nat Cell Biol, PMID 37945829

PXD037002 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated Proteomic and Metabolomic Profiling of Urine of Renal Anemia Patients Uncovers Molecular Mechanisms of Roxadustat
Possible reference: You, X. et al. (2023) Integrated proteomic and metabolomic profiling of urine of renal anemia patients uncovers the molecular mechanisms of roxadustat., Mol Omics, PMID 37039271

PXD036995 Dataset with its publication pending (from PRIDE)
Dataset title: Tyrosine phosphorylation regulates RIPK1 activity to limit cell death and inflammation
Possible reference: Tu, H. et al. (2022) Tyrosine phosphorylation regulates RIPK1 activity to limit cell death and inflammation., Nat Commun, PMID 36329033

PXD036993 Dataset with its publication pending (from PRIDE)
Dataset title: Muscle stem cell maintenance and regeneration of skeletal muscle require functional motor innervation
Possible reference: Coletti, C. et al. (2022) Exercise-mediated reinnervation of skeletal muscle in elderly people: An update., Eur J Transl Myol, PMID 35234025

PXD036982 Dataset with its publication pending (from PRIDE)
Dataset title: All-in-One Digital Microfluidics Pipeline for Proteomic Sample Preparation and Analysis
Possible reference: Peng, J. et al. (2023) All-in-One digital microfluidics pipeline for proteomic sample preparation and analysis., Chem Sci, PMID 36937585

PXD036976 Dataset with its publication pending (from PRIDE)
Dataset title: Liver RBFOX2 regulates cholesterol homeostasis via Scarb1 alternative splicing in mice
Possible reference: Paterson, HAB. et al. (2022) Liver RBFOX2 regulates cholesterol homeostasis via Scarb1 alternative splicing in mice., Nat Metab, PMID 36536133

PXD036954 Dataset with its publication pending (from jPOST)
Dataset title: Identification of novel kinases of Tau using fluorescence complementation mass spectrometry (FCMS)
Possible reference: Kao, DS. et al. (2022) Identification of Novel Kinases of Tau Using Fluorescence Complementation Mass Spectrometry (FCMS)., Mol Cell Proteomics, PMID 36379402

PXD036953 Dataset with its publication pending (from PRIDE)
Dataset title: The interactome of flavin adenine dinucleotide (FAD) with RNA-binding proteins
Possible reference: Prokofeva, P. et al. (2022) Merits of Diazirine Photo-Immobilization for Target Profiling of Natural Products and Cofactors., ACS Chem Biol, PMID 36302507

PXD036946 Dataset with its publication pending (from PRIDE)
Dataset title: BioID of 41 ASD-risk genes to identify protein-protein interaction networks and shared pathways
Possible reference: Murtaza, N. et al. (2022) Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies., Cell Rep, PMID 36417873

PXD036940 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular matrix educates a tumor macrophage phenotype found in ovarian cancer metastasis
Possible reference: Puttock, EH. et al. (2023) Extracellular matrix educates an immunoregulatory tumor macrophage phenotype found in ovarian cancer metastasis., Nat Commun, PMID 37188691

PXD036934 Dataset with its publication pending (from PRIDE)
Dataset title: Structural and functional analysis of peptides derived from KEX2-processed repeat proteins in agaricomycetes using reverse genetics and peptidomics
Possible reference: Vogt, E. et al. (2022) Structural and Functional Analysis of Peptides Derived from KEX2-Processed Repeat Proteins in Agaricomycetes Using Reverse Genetics and Peptidomics., Microbiol Spectr, PMID 36314921

PXD036900 Dataset with its publication pending (from PRIDE)
Dataset title: Biomarkers found in the tumor interstitial fluid may help explain the differential behavior among keratinocyte carcinomas
Possible reference: Matas-Nadal, C. et al. (2023) Biomarkers Found in the Tumor Interstitial Fluid may Help Explain the Differential Behavior Among Keratinocyte Carcinomas., Mol Cell Proteomics, PMID 37059366

PXD036891 Dataset with its publication pending (from PRIDE)
Dataset title: A proteomic signature for human papillomavirus-associated oropharyngeal squamous cell carcinoma predicts patients at high risk of recurrence
Possible reference: Jackson, CC. et al. (2025) A Proteomic Signature for Human Papillomavirus-Associated Oropharyngeal Squamous Cell Carcinoma Predicts Patients at High Risk of Recurrence., Cancer Res Commun, PMID 40014866

PXD036890 Dataset with its publication pending (from PRIDE)
Dataset title: RNP remodeling during RNA virus replication through phosphoregulation of SR proteins revealed by metabolic labeling
Possible reference: Lee, KM. et al. (2025) Subversion of phosphorylated SR proteins by enterovirus A71 in IRES-dependent translation revealed by RNA-interactome analysis., PLoS Pathog, PMID 40522993

PXD036888 Dataset with its publication pending (from PRIDE)
Dataset title: N-acetyltransferase NAT10 Controls Cell Fates
Possible reference: Hu, Z. et al. (2024) N-acetyltransferase NAT10 controls cell fates via connecting mRNA cytidine acetylation to chromatin signaling., Sci Adv, PMID 38215194

PXD036880 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analyses of brassinosteroids mutants in response to salt stress in Arabidopsis
Possible reference: Feng, L. et al. (2023) Integrative transcriptomic and proteomic analyses reveal a positive role of BES1 in salt tolerance in Arabidopsis., Front Plant Sci, PMID 36938058

PXD036870 Dataset with its publication pending (from iProX)
Dataset title: Chlamydomonas reinhardtii cc125 Cd stress
Possible reference: Yu, Z. et al. (2019) Sensitivity of Chlamydomonas reinhardtii to cadmium stress is associated with phototaxis., Environ Sci Process Impacts, PMID 31120077

PXD036865 Dataset with its publication pending (from PRIDE)
Dataset title: Selective PROTAC-mediated degradation of SMARCA2 is efficacious in SMARCA4 mutant cancers
Possible reference: Cantley, J. et al. (2022) Selective PROTAC-mediated degradation of SMARCA2 is efficacious in SMARCA4 mutant cancers., Nat Commun, PMID 36357397

PXD036859 Dataset with its publication pending (from PRIDE)
Dataset title: Production and properties of adhesin-free gingipain proteinase RgpA
Possible reference: Mahmud, ASM. et al. (2023) Production and properties of adhesin-free gingipain proteinase RgpA., Sci Rep, PMID 37402780

PXD036849 no publication (from MassIVE)
Dataset title: Comprehensive characterization of the Hsp70 interactome reveals novel client proteins and interactions mediated by post-translational modifications
Possible reference: Nitika, . et al. (2022) Comprehensive characterization of the Hsp70 interactome reveals novel client proteins and interactions mediated by posttranslational modifications., PLoS Biol, PMID 36269765

PXD036811 Dataset with its publication pending (from PRIDE)
Dataset title: Microbial Peptides Activate Tumor-Infiltrating Lymphocytes in Glioblastoma
Possible reference: Naghavian, R. et al. (2023) Microbial peptides activate tumour-infiltrating lymphocytes in glioblastoma., Nature, PMID 37198490

PXD036809 Dataset with its publication pending (from PRIDE)
Dataset title: The histone chaperone NASP maintains H3-H4 reservoirs in the early Drosophila embryo
Possible reference: Tirgar, R. et al. (2023) The histone chaperone NASP maintains H3-H4 reservoirs in the early Drosophila embryo., PLoS Genet, PMID 36930688

PXD036792 Dataset with its publication pending (from PRIDE)
Dataset title: Interactome dynamics of RAF1-BRAF kinase monomers and dimers
Possible reference: Iglesias-Martinez, LF. et al. (2023) Interactome dynamics of RAF1-BRAF kinase monomers and dimers., Sci Data, PMID 37045861

PXD036789 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of skeletal muscles from wild type and transgenic mice carrying recessive Ryr1 mutations
Possible reference: Eckhardt, J. et al. (2023) Quantitative proteomic analysis of skeletal muscles from wild-type and transgenic mice carrying recessive Ryr1 mutations linked to congenital myopathies., Elife, PMID 36862731

PXD036785 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-Omics analysis revealed a significant alteration of critical metabolic pathways due to sorafenib-resistance in Hep3B cell lines
Possible reference: Abushawish, KYI. et al. (2022) Multi-Omics Analysis Revealed a Significant Alteration of Critical Metabolic Pathways Due to Sorafenib-Resistance in Hep3B Cell Lines., Int J Mol Sci, PMID 36233276

PXD036782 Dataset with its publication pending (from PRIDE)
Dataset title: DLST mutations in pheochromocytoma and paraganglioma cause proteome hyposuccinylation and metabolic remodeling
Possible reference: Mellid, S. et al. (2023) DLST mutations in pheochromocytoma and paraganglioma cause proteome hyposuccinylation and metabolic remodeling., Cancer Commun (Lond), PMID 37139660

PXD036766 Dataset with its publication pending (from jPOST)
Dataset title: TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells
Possible reference: Kitajima, H. et al. (2023) TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells., Cell Death Dis, PMID 37443145

PXD036761 Dataset with its publication pending (from PanoramaPublic)
Dataset title: The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effector
Possible reference: Yu, G. et al. (2022) The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effector., EMBO J, PMID 36314733

PXD036760 Dataset with its publication pending (from iProX)
Dataset title: Characteristics of Proteome Changes in Brain Regions of Chronic Ketamine-Induced Schizophrenia Mice
Possible reference: Xiao, L. et al. (2024) Proteomic Characteristics of the Prefrontal Cortex and Hippocampus in Mice with Chronic Ketamine-Induced Anxiety and Cognitive Impairment., Neuroscience, PMID 38266908

PXD036755 Dataset with its publication pending (from iProX)
Dataset title: Canopy light distribution effects on light use efficiency in wheat and its mechanism
Possible reference: Reynolds, M. et al. (2012) Achieving yield gains in wheat., Plant Cell Environ, PMID 22860982

PXD036744 Dataset with its publication pending (from PRIDE)
Dataset title: Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines.
Possible reference: Sunna, S. et al. (2023) Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines., Mol Cell Proteomics, PMID 37061046

PXD036737 Dataset with its publication pending (from PRIDE)
Dataset title: Arginine limitation causes a directed DNA sequence evolution response in colorectal cancer cells
Possible reference: Hsu, DJ. et al. (2023) Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells., Sci Adv, PMID 36608131

PXD036733 Dataset with its publication pending (from jPOST)
Dataset title: A robust glycoproteomics platform reveals a tetra-antennary site-specific glycan capping with sialyl-Lewis antigen for early detection of gastric cancer
Possible reference: Liu, L. et al. (2024) Robust Glycoproteomics Platform Reveals a Tetra-Antennary Site-Specific Glycan Capping with Sialyl-Lewis Antigen for Early Detection of Gastric Cancer., Adv Sci (Weinh), PMID 38084450

PXD036684 no publication (from MassIVE)
Dataset title: Tumor-produced and aging-associated oncometabolite methylmalonic acid promotes cancer-associated fibroblast activation to drive metastatic progression
Possible reference: Li, Z. et al. (2022) Tumor-produced and aging-associated oncometabolite methylmalonic acid promotes cancer-associated fibroblast activation to drive metastatic progression., Nat Commun, PMID 36266345

PXD036679 Dataset with its publication pending (from PRIDE)
Dataset title: Macrophage infectivity potentiator protein, a peptidyl prolyl cis/trans isomerase, essential for Coxiella burnetii growth and pathogenesis
Possible reference: Debowski, AW. et al. (2023) Macrophage infectivity potentiator protein, a peptidyl prolyl cis-trans isomerase, essential for Coxiella burnetii growth and pathogenesis., PLoS Pathog, PMID 37399210

PXD036676 Dataset with its publication pending (from PRIDE)
Dataset title: Staphylococcus aureus prophage-encoded protein causes abortive infection and provides population immunity against kayviruses
Possible reference: Kuntov�, L. et al. (2023) Staphylococcus aureus Prophage-Encoded Protein Causes Abortive Infection and Provides Population Immunity against Kayviruses., mBio, PMID 36779718

PXD036674 Dataset with its publication pending (from PRIDE)
Dataset title: MYC multimers shield stalled replication forks from RNA polymerase
Possible reference: Solvie, D. et al. (2022) MYC multimers shield stalled replication forks from RNA polymerase., Nature, PMID 36424410

PXD036659 Dataset with its publication pending (from PRIDE)
Dataset title: On the relationship between metabolic capacities and in vivo viscoelastic properties of the liver
Possible reference: Shahryari, M. et al. (2022) On the relationship between metabolic capacities and in vivo viscoelastic properties of the liver., Front Bioeng Biotechnol, PMID 36698634

PXD036616 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of Drosophila Clueless differentially affects the mitochondrial proteome compared to loss of Sod2 and Pink1
Possible reference: Sen, A. et al. (2022) Loss of Drosophila Clueless differentially affects the mitochondrial proteome compared to loss of Sod2 and Pink1., Front Physiol, PMID 36388112

PXD036614 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omic profiling of breast cancer cells uncovers stress MAPK-associated sensitivity to AKT degradation
Possible reference: Erickson, EC. et al. (2024) Multiomic profiling of breast cancer cells uncovers stress MAPK-associated sensitivity to AKT degradation., Sci Signal, PMID 38412255

PXD036604 Dataset with its publication pending (from jPOST)
Dataset title: Proteogenomic Landscape and Clinical Characterization of GH-Producing Pituitary Adenoma
Possible reference: Yamato, A. et al. (2022) Proteogenomic landscape and clinical characterization of GH-producing pituitary adenomas/somatotroph pituitary neuroendocrine tumors., Commun Biol, PMID 36435867

PXD036601 Dataset with its publication pending (from jPOST)
Dataset title: EVTOP: extracellular vesicle to phosphoproteomics with microliters of biofluids
Possible reference: Sun, J. et al. (2023) Profiling Phosphoproteome Landscape in Circulating Extracellular Vesicles from Microliters of Biofluids through Functionally Tunable Paramagnetic Separation., Angew Chem Int Ed Engl, PMID 37216424

PXD036589 Dataset with its publication pending (from PRIDE)
Dataset title: PPARÎ³ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation
Possible reference: Madsen, MS. et al. (2022) PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation., Nat Commun, PMID 36402763

PXD036586 Dataset with its publication pending (from PRIDE)
Dataset title: Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation
Possible reference: Li, B. et al. (2023) Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation., Nat Commun, PMID 36801853

PXD036578 Dataset with its publication pending (from PRIDE)
Dataset title: Investigating the effects of glyphosate on the bumblebee proteome and microbiota
Possible reference: Cullen, MG. et al. (2023) Investigating the effects of glyphosate on the bumblebee proteome and microbiota., Sci Total Environ, PMID 36566850

PXD036569 Dataset with its publication pending (from PRIDE)
Dataset title: SITE-SPECIFIC ACTIVITY-BASED PROTEIN PROFILING USING PHOSPHONATE HANDLES
Possible reference: van Bergen, W. et al. (2023) Site-Specific Activity-Based Protein Profiling Using Phosphonate Handles., Mol Cell Proteomics, PMID 36435334

PXD036566 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative analysis of DDA- and DIA-PASEF methods for proteomics analysis of human valve interstitial cells and osteoblasts during osteogenic differentiation
Possible reference: Lobov, A. et al. (2025) Similar, but not the same: multiomics comparison of human valve interstitial cells and osteoblast osteogenic differentiation expanded with an estimation of data-dependent and data-independent PASEF proteomics., Gigascience, PMID 39798943

PXD036559 Dataset with its publication pending (from PRIDE)
Dataset title: ER stress and dsRNA sensing with Rt3D and palbociclib - Immunopeptidome
Possible reference: Roulstone, V. et al. (2025) Palbociclib and dsRNA sensor co-operate to enhance anti-cancer effects through ER stress and modulation of immune evasion., Nat Commun, PMID 40413207

PXD036550 Dataset with its publication pending (from iProX)
Dataset title: Metabolomics-based study of metabolic defects in neonates
Possible reference: Troisi, J. et al. (2018) A metabolomics-based approach for non-invasive screening of fetal central nervous system anomalies., Metabolomics, PMID 30830338

PXD036534 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic analysis of near isogenic lines for qDSI.4B.1 QTL on short arm of chromosome 4B conferring drought tolerance in wheat
Possible reference: Nouraei, S. et al. (2024) Proteomic analysis of near-isogenic lines reveals key biomarkers on wheat chromosome 4B conferring drought tolerance., Plant Genome, PMID 37199103

PXD036528 Dataset with its publication pending (from PRIDE)
Dataset title: The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors
Possible reference: Wang, H. et al. (2022) The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors., Nat Commun, PMID 36171202

PXD036511 Dataset with its publication pending (from PRIDE)
Dataset title: ER-Golgi membrane contact sites control the formation of plasma membrane lipid nanodomains required for anthrax intoxication
Possible reference: Anwar, MU. et al. (2022) ER-Golgi-localized proteins TMED2 and TMED10 control the formation of plasma membrane lipid nanodomains., Dev Cell, PMID 36174556

PXD036505 Dataset with its publication pending (from PRIDE)
Dataset title: Global analysis of lysine 2-hydroxyisobutyrylation in Glycine max
Possible reference: Zhao, W. et al. (2023) Proteomic analysis of protein lysine 2-hydroxyisobutyrylation�(Khib) in soybean leaves., BMC Plant Biol, PMID 36631736

PXD036484 no publication (from MassIVE)
Dataset title: Integrated Proteomics Reveals Alterations in Sarcomere Composition and Developmental Processes during Postnatal Swine Heart Development
Possible reference: Aballo, TJ. et al. (2023) Integrated proteomics reveals alterations in sarcomere composition and developmental processes during postnatal swine heart development., J Mol Cell Cardiol, PMID 36657638

PXD036475 Dataset with its publication pending (from PRIDE)
Dataset title: Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)
Possible reference: Chihara, K. et al. (2022) Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)., RNA, PMID 36328526

PXD036471 Dataset with its publication pending (from PRIDE)
Dataset title: Alternative Splicing of HDAC7 Regulates its Interaction with 14-3-3 Proteins to Alter Histone Marks and Target Gene Expression
Possible reference: Agosto, LM. et al. (2023) Alternative splicing of HDAC7 regulates its interaction with 14-3-3 proteins to alter histone marks and target gene expression., Cell Rep, PMID 36933216

PXD036459 Dataset with its publication pending (from iProX)
Dataset title: The proteomics of Coreius guichenoti
Possible reference: Duan, Y. et al. (2022) Studies on the molecular level changes and potential resistance mechanism of Coreius guichenoti under temperature stimulation., Front Genet, PMID 36263436

PXD036457 Dataset with its publication pending (from PRIDE)
Dataset title: Super-killer CTLs are generated by single gene deletion of Bach2
Possible reference: Barton, PR. et al. (2022) Super-killer CTLs are generated by single gene deletion of Bach2., Eur J Immunol, PMID 36086884

PXD036450 Dataset with its publication pending (from PRIDE)
Dataset title: Diadenosine tetraphosphate as a cosubstrate for AMPylation mediated by FICD
Possible reference: Frese, M. et al. (2023) The Alarmone Diadenosine Tetraphosphate as a Cosubstrate for Protein AMPylation., Angew Chem Int Ed Engl, PMID 36524454

PXD036446 Dataset with its publication pending (from PRIDE)
Dataset title: HDX-MS of AcrIF9 and AcrIF2 binding to CRISPR IF Csy complex
Possible reference: Patterson, A. et al. (2022) Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex., Nucleic Acids Res, PMID 36215034

PXD036431 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of cuticle protein in Nilaparvata lugens
Possible reference: Pan, PL. et al. (2018) A comprehensive omics analysis and functional survey of cuticular proteins in the brown planthopper., Proc Natl Acad Sci U S A, PMID 29712872

PXD036423 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Atlas of Obesity and Type 2 Diabetes in Cynomolgus Monkeys
Possible reference: Zhang, X. et al. (2023) A transcriptomic and proteomic atlas of obesity and type 2 diabetes in cynomolgus monkeys., Cell Rep, PMID 37556324

PXD036418 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of HeLa cells after stable transfection with the Chlamydia trachomatis CT143 gene
Possible reference: Gong, D. et al. (2025) Proteomic analysis of HeLa cells after stable transfection with the Chlamydia trachomatis CT143 gene., Gene, PMID 39374816

PXD036417 Dataset with its publication pending (from PRIDE)
Dataset title: Counterintuitive structural and functional effects due to naturally-occurring mutations targeting the active site of the disease-associated NQO1 enzyme
Possible reference: Pacheco-Garc�a, JL. et al. (2023) Counterintuitive structural and functional effects due to naturally occurring mutations targeting the active site of the disease-associated NQO1 enzyme., FEBS J, PMID 36378023

PXD036406 Dataset with its publication pending (from jPOST)
Dataset title: Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome
Possible reference: Rahman, S. et al. (2022) Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome., Proc Natl Acad Sci U S A, PMID 36095189

PXD036399 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of NDUFS4 KO hearts
Possible reference: Khumalo, SG. et al. (2026) SWATH-MS reveals tissue-specific proteomic changes in a Leigh syndrome mouse model., Mol Genet Metab, PMID 41506052

PXD036390 Dataset with its publication pending (from jPOST)
Dataset title: Monitoring Autophagic Flux in vivo Revealed its Physiological Response and Significance of Heterogeneity in Pancreatic Beta Cells
Possible reference: Aoyama, S. et al. (2023) Monitoring autophagic flux in�vivo revealed its physiological response and significance of heterogeneity in pancreatic beta cells., Cell Chem Biol, PMID 36944338

PXD036387 Dataset with its publication pending (from iProX)
Dataset title: Proteome data of tobacco infected by Ralstonia solanacearum
Possible reference: Wang, B. et al. (2021) Proteomic Analysis of Potato Responding to the Invasion of Ralstonia solanacearum UW551 and Its Type III Secretion System Mutant., Mol Plant Microbe Interact, PMID 33332146

PXD036373 no publication (from MassIVE)
Dataset title: Temporal phosphoproteomics reveals WEE1-dependent control of 53BP1 pathway I
Possible reference: Petrosius, V. et al. (2023) Temporal phosphoproteomics reveals WEE1-dependent control of 53BP1 pathway., iScience, PMID 36632060

PXD036366 Dataset with its publication pending (from PRIDE)
Dataset title: CMTM4 is a subunit of the IL-17 receptor and mediates autoimmune pathology
Possible reference: Knizkova, D. et al. (2022) CMTM4 is a subunit of the IL-17 receptor and mediates autoimmune pathology., Nat Immunol, PMID 36271145

PXD036364 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics analyses reveal the novel targets of spermine alleviating diabetic cardiomyopathy
Possible reference: Sun, J. et al. (2022) Proteomic and metabolomic analyses reveal the novel targets of spermine for alleviating diabetic cardiomyopathy in type II diabetic mice., Front Cardiovasc Med, PMID 36312255

PXD036301 Dataset with its publication pending (from PRIDE)
Dataset title: Endogenous alpha-synuclein is essential for the transfer of pathology by exosomes, following PFF inoculation in vivo.
Possible reference: Melachroinou, K. et al. (2024) Endogenous Alpha-Synuclein is Essential for the Transfer of Pathology by Exosome-Enriched Extracellular Vesicles, Following Inoculation with Preformed Fibrils in vivo., Aging Dis, PMID 37548944

PXD036283 Dataset with its publication pending (from PRIDE)
Dataset title: Repurposing of Amisulpride, a known antipsychotic drug, to target synovial fibroblasts activation in arthritis.
Possible reference: Papadopoulou, D. et al. (2023) Repurposing the antipsychotic drug amisulpride for targeting synovial fibroblast activation in arthritis., JCI Insight, PMID 37014697

PXD036268 Dataset with its publication pending (from PRIDE)
Dataset title: One-pot comparative analysis and characterization of MCF-7 and MCF-10A cell lines
Possible reference: Sarkate, AP. et al. (2021) One pot synthesis, in silico study and evaluation of some novel flavonoids as potent topoisomerase II inhibitors., Bioorg Med Chem Lett, PMID 33689875

PXD036243 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of universally applicable and species-specific marker peptides for Bacillus anthracis
Possible reference: Witt, N. et al. (2022) Identification of Universally Applicable and Species-Specific Marker Peptides for Bacillus anthracis., Life (Basel), PMID 36294983

PXD036233 no publication (from MassIVE)
Dataset title: Alternative proteoforms and proteoform-dependent assemblies in humans and plants
Possible reference: McWhite, CD. et al. (2024) Alternative proteoforms and proteoform-dependent assemblies in humans and plants., Mol Syst Biol, PMID 38918600

PXD036227 Dataset with its publication pending (from PRIDE)
Dataset title: Chaperone-mediated autophagy promotes PCa survival during ARPI through selective proteome remodeling
Possible reference: Nikesitch, N. et al. (2023) Chaperone-mediated autophagy promotes PCa survival during ARPI through selective proteome remodeling., Oncogene, PMID 36611121

PXD036212 Dataset with its publication pending (from jPOST)
Dataset title: Physiological and Proteomic Responses of Cassava to Short-term Extreme Cool and Hot Temperature
Possible reference: Santanoo, S. et al. (2022) Physiological and Proteomic Responses of Cassava to Short-Term Extreme Cool and Hot Temperature., Plants (Basel), PMID 36079689

PXD036208 Dataset with its publication pending (from iProX)
Dataset title: Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway
Possible reference: Shi, H. et al. (2023) Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway., Proteomics, PMID 36254857

PXD036191 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery of a small molecule inhibitor of the UBE2F-CRL5 axis that induces apoptosis and G2/M arrest and confers radiosensitization
Possible reference: Xu, T. et al. (2022) A small molecule inhibitor of the UBE2F-CRL5 axis induces apoptosis and radiosensitization in lung cancer., Signal Transduct Target Ther, PMID 36253371

PXD036170 Dataset with its publication pending (from PRIDE)
Dataset title: Redirecting the neo-substrate specificity of Cereblon-targeting PROTACs to Helios
Possible reference: Verano, AL. et al. (2022) Redirecting the Neo-Substrate Specificity of Cereblon-Targeting PROTACs to Helios., ACS Chem Biol, PMID 36007246

PXD036164 Dataset with its publication pending (from PRIDE)
Dataset title: proteomic analysis of the formalin-fixed paraffin embedded (FFPE) renal tissue between steroid-sensitive and steroid-resistant (SR) children FSGS patients
Possible reference: Ni, J. et al. (2022) Comparative proteomic analysis of children FSGS FFPE tissues., BMC Pediatr, PMID 36503536

PXD036163 Dataset with its publication pending (from PRIDE)
Dataset title: Metabolic and Morphotypic Trade-offs within the Eco-Evolutionary Dynamics of Escherichia coli
Possible reference: Zlatkov, N. et al. (2022) Metabolic and Morphotypic Trade-Offs within the Eco-Evolutionary Dynamics of Escherichia coli., Microbiol Spectr, PMID 36169422

PXD036161 Dataset with its publication pending (from PRIDE)
Dataset title: High-throughput proteomics of the 26 medically most important elapids and vipers from sub-Saharan Africa
Possible reference: Nguyen, GTT. et al. (2022) High-throughput proteomics and in vitro functional characterization of the 26 medically most important elapids and vipers from sub-Saharan Africa., Gigascience, PMID 36509548

PXD036160 Dataset with its publication pending (from PRIDE)
Dataset title: Differential virulence of Aggregatibacter actinomycetemcomitans serotypes explained by exoproteome heterogeneity
Possible reference: Fu, Y. et al. (2023) Differential Virulence of Aggregatibacter actinomycetemcomitans Serotypes Explained by Exoproteome Heterogeneity., Microbiol Spectr, PMID 36541765

PXD036145 Xiaowei Gao, Bhagyashree N. Swarge, Winfried Roseboom, Yan Wang, Henk L. Dekker, Peter Setlow, Stanley Brul and Gertjan Kramer. settings Open AccessArticle Changes in the Spore Proteome of Bacillus cereus in Response to Introduction of Plasmids. Microorga (from MassIVE)
Dataset title: Changes in the spore proteome of Bacillus cereus in response to introduction of plasmids.
Possible reference: Gao, X. et al. (2022) Changes in the Spore Proteome of Bacillus cereus in Response to Introduction of Plasmids., Microorganisms, PMID 36144297

PXD036143 no publication (from MassIVE)
Dataset title: Comprehensive discovery of the accessible primary amino group containing segments from cell surface proteins by fine-tuning high-throughput biotinylation method
Possible reference: Lang�, T. et al. (2022) Comprehensive Discovery of the Accessible Primary Amino Group-Containing Segments from Cell Surface Proteins by Fine-Tuning a High-Throughput Biotinylation Method., Int J Mol Sci, PMID 36613715

PXD036121 Dataset with its publication pending (from iProX)
Dataset title: Dual-species proteomics and targeted intervention of animal-pathogen interactions
Possible reference: Liu, YS. et al. (2025) Dual-species proteomics and targeted intervention of animal-pathogen interactions., J Adv Res, PMID 39233003

PXD036106 Dataset with its publication pending (from PRIDE)
Dataset title: Extended DNA threading through a dual-engine motor module in the activating signal co-integrator complex
Possible reference: Jia, J. et al. (2023) Extended DNA threading through a dual-engine motor module of the activating signal co-integrator 1 complex., Nat Commun, PMID 37019967

PXD036095 Dataset with its publication pending (from PRIDE)
Dataset title: Putative N-glycoprotein markers of MCF-7/ADR cancer stem cells from N-glycoproteomics characterization of the whole cell lysate
Possible reference: Yang, H. et al. (2021) Putative N-glycoprotein markers of MCF-7/ADR cancer stem cells from N-glycoproteomics characterization of the whole cell lysate., Talanta, PMID 34074422

PXD036093 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics Reveals the Potential Mechanism of Tanshinone IIA Promoting the Ex Vivo Expansion of Human Bone Marrow Mesenchymal Stem Cells.
Possible reference: Yuan, P. et al. (2022) Proteomics reveals the potential mechanism of Tanshinone IIA in promoting the Ex�Vivo expansion of human bone marrow mesenchymal stem cells., Regen Ther, PMID 36475023

PXD036088 no publication (from PanoramaPublic)
Dataset title: Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei
Possible reference: Fu, JY. et al. (2022) Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei., Front Microbiol, PMID 36419437

PXD036076 Dataset with its publication pending (from PRIDE)
Dataset title: Ligand-induced shifts in conformational ensembles that predict transcriptional activation
Possible reference: Khan, SH. et al. (2022) Ligand-induced shifts in conformational ensembles that describe transcriptional activation., Elife, PMID 36222302

PXD036025 Dataset with its publication pending (from PRIDE)
Dataset title: Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants and therapeutically-relevant pathways
Possible reference: Soltis, AR. et al. (2022) Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants, and therapeutically relevant pathways., Cell Rep Med, PMID 36384096

PXD036023 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Landscape of Human Spermatozoa: Optimized Extraction Method and Application
Possible reference: Luo, M. et al. (2022) Proteomic Landscape of Human Spermatozoa: Optimized Extraction Method and Application., Cells, PMID 36552826

PXD036011 Dataset with its publication pending (from PRIDE)
Dataset title: Dual-omics reveals the different roles of Î±1 and Î²-adrenergic receptors in acute sympathetic stress-induced cardiac inflammation
Possible reference: Zhang, D. et al. (2023) Dual-omics reveals temporal differences in acute sympathetic stress-induced cardiac inflammation following α1 and β-adrenergic receptors activation., Acta Pharmacol Sin, PMID 36737635

PXD036006 Dataset with its publication pending (from PRIDE)
Dataset title: Ctenopharyngodon idella, CIK cells, pull-down MS
Possible reference: Su, H. et al. (2020) Grass Carp Reovirus Major Outer Capsid Protein VP4 Interacts with RNA Sensor RIG-I to Suppress Interferon Response., Biomolecules, PMID 32268551

PXD035996 Dataset with its publication pending (from PRIDE)
Dataset title: KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA-DNA triplexes and HP1 binding
Possible reference: Zhang, X. et al. (2022) KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA-DNA triplexes and HP1 binding., Nat Cell Biol, PMID 36266489

PXD035978 Dataset with its publication pending (from PRIDE)
Dataset title: Campylobacter jejuni MOMP carbene footprinting
Possible reference: Okoye, JC. et al. (2022) Ferric quinate (QPLEX) interacts with the major outer membrane protein (MOMP) of Campylobacter jejuni and enters through the porin channel into the periplasmic space., Comput Struct Biotechnol J, PMID 36212543

PXD035973 Dataset with its publication pending (from PRIDE)
Dataset title: ELTD1 is present in extracellular vesicles derived from endothelial cells as a cleaved extracellular domain which induces in vivo angiogenesis
Possible reference: Sheldon, H. et al. (2022) ELTD1 is present in extracellular vesicles derived from endothelial cells as a cleaved extracellular domain which induces in vivo angiogenesis., J Extracell Biol, PMID 38939053

PXD035965 Dataset with its publication pending (from PRIDE)
Dataset title: Systemic response in hybrid poplar tolerance to aggressive Phytophthora species
Possible reference: Cerny, M. et al. (2022) Defense mechanisms promoting tolerance to aggressive Phytophthora species in hybrid poplar., Front Plant Sci, PMID 36325556

PXD035956 Dataset with its publication pending (from PRIDE)
Dataset title: Defense mechanisms promoting tolerance to aggressive Phytophthora species in hybrid poplar
Possible reference: Cerny, M. et al. (2022) Defense mechanisms promoting tolerance to aggressive Phytophthora species in hybrid poplar., Front Plant Sci, PMID 36325556

PXD035931 Dataset with its publication pending (from PRIDE)
Dataset title: A seed-like proteome in oil-rich tubers
Possible reference: Niemeyer, PW. et al. (2022) A seed-like proteome in oil-rich tubers., Plant J, PMID 36050843

PXD035906 Dataset with its publication pending (from jPOST)
Dataset title: Serum peptidome profiles in metastatic and non-metastatic feline mammary carcinoma
Possible reference: Paphussaro, W. et al. (2024) Analysis of serum peptidome profiles of non-metastatic and metastatic feline mammary carcinoma using liquid chromatography-tandem mass spectrometry., BMC Vet Res, PMID 38951817

PXD035904 no publication (from MassIVE)
Dataset title: Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry
Possible reference: Roberts, DS. et al. (2022) Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry., bioRxiv, PMID 35475171

PXD035897 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteome dataset profiling UBC4 and UBC5 deletion strains in Saccharomyces cerevisiae
Possible reference: Rossio, V. et al. (2022) Quantitative proteome dataset profiling of UBC4 and UBC5 deletion strains in Saccharomyces cerevisiae., Data Brief, PMID 36426069

PXD035896 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteome and phosphoproteome datasets of DNA replication and mitosis in Saccharomyces cerevisiae
Possible reference: Rossio, V. et al. (2022) Quantitative proteome and phosphoproteome datasets of DNA replication and mitosis in Saccharomyces cerevisiae., Data Brief, PMID 36425962

PXD035892 Dataset with its publication pending (from PRIDE)
Dataset title: The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site usage in Arabidopsis
Possible reference: Diego-Martin, B. et al. (2022) The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated�+1 nucleosome positioning and transcription start site determination in Arabidopsis., Nucleic Acids Res, PMID 36189880

PXD035889 Dataset with its publication pending (from PRIDE)
Dataset title: Deficiency of the frontotemporal dementia gene GRN results in gangliosidosis
Possible reference: Boland, S. et al. (2022) Deficiency of the frontotemporal dementia gene GRN results in gangliosidosis., Nat Commun, PMID 36207292

PXD035877 Dataset with its publication pending (from PRIDE)
Dataset title: A method for targeting a specified segment of DNA to a bacterial microorganelle
Possible reference: Otoničar, J. et al. (2022) A method for targeting a specified segment of DNA to a bacterial microorganelle., Nucleic Acids Res, PMID 36029110

PXD035873 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated omics reveal time-resolved insights into T4 phage infection of E. coli on proteome and transcriptome level
Possible reference: Wolfram-Schauerte, M. et al. (2022) Integrated Omics Reveal Time-Resolved Insights into T4 Phage Infection of E. coli on Proteome and Transcriptome Levels., Viruses, PMID 36423111

PXD035871 Dataset with its publication pending (from PRIDE)
Dataset title: Complexome Profiling of the thylakoid proteome from Arabidopsis thaliana
Possible reference: Schr�der, L. et al. (2022) The photosynthesis apparatus of European mistletoe (Viscum album)., Plant Physiol, PMID 35976139

PXD035852 Dataset with its publication pending (from PRIDE)
Dataset title: Fine-tuning of mTOR signaling by the UBE4B-KLHL22 E3 ubiquitin ligase cascade in brain development
Possible reference: Kong, X. et al. (2022) Fine-tuning of mTOR signaling by the UBE4B-KLHL22 E3 ubiquitin ligase cascade in brain development., Development, PMID 36440598

PXD035835 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated proteomics and metabolomics analysis of rice leaves in response to rice straw return
Possible reference: Yan, S. et al. (2022) Integrated proteomics and metabolomics analysis of rice leaves in response to rice straw return., Front Plant Sci, PMID 36176680

PXD035828 Dataset with its publication pending (from jPOST)
Dataset title: Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells
Possible reference: Zhao, L. et al. (2024) Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells., Nat Commun, PMID 39333085

PXD035827 no publication (from MassIVE)
Dataset title: Proteome phenotypes discriminate growing location and malting traits in field-grown barley
Possible reference: Bahmani, M. et al. (2022) Proteome Phenotypes Discriminate the Growing Location and Malting Traits in Field-Grown Barley., J Agric Food Chem, PMID 35981222

PXD035826 Dataset with its publication pending (from jPOST)
Dataset title: In-Depth In Vivo Crosslinking in Minutes by a Compact, Membrane- Permeable, and Alkynyl-Enrichable Crosslinker
Possible reference: Gao, H. et al. (2022) In-Depth In Vivo Crosslinking in Minutes by a Compact, Membrane-Permeable, and Alkynyl-Enrichable Crosslinker., Anal Chem, PMID 35575683

PXD035825 Dataset with its publication pending (from PRIDE)
Dataset title: Complexome Profiling of the thylakoid proteome from Viscum album
Possible reference: Schr�der, L. et al. (2022) The photosynthesis apparatus of European mistletoe (Viscum album)., Plant Physiol, PMID 35976139

PXD035818 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of Phosphorylation-dependent Antibody Binding to Cancer-mutated Linkers of C2H2 Zinc Finger Proteins by Intact Transition Epitope Mapping - Thermodynamic Weak-force Order Analysis.
Possible reference: Scherf, M. et al. (2023) Characterization of Phosphorylation-Dependent Antibody Binding to Cancer-Mutated Linkers of C2H2 Zinc Finger Proteins by Intact Transition Epitope Mapping-Thermodynamic Weak-Force Order Analysis., J Am Soc Mass Spectrom, PMID 36656134

PXD035809 Dataset with its publication pending (from PRIDE)
Dataset title: Bifidobacterium infantis utilizes N-acetylglucosamine nitrogen
Possible reference: Li, S. et al. (2023) Bifidobacterium infantis utilizes N-acetylglucosamine-containing human milk oligosaccharides as a nitrogen source., Gut Microbes, PMID 37609905

PXD035802 Dataset with its publication pending (from PRIDE)
Dataset title: Mycobacterium tuberculosis modified proteome under oxidative stress
Possible reference: Choudhary, E. et al. (2022) Deciphering the Proteomic Landscape of Mycobacterium tuberculosis in Response to Acid and Oxidative Stresses., ACS Omega, PMID 35936415

PXD035792 Dataset with its publication pending (from jPOST)
Dataset title: Proteome changes in cassava cv. Kasetsart 50 in response to Sri Lankan cassava mosaic virus
Possible reference: Siriwan, W. et al. (2022) Analysis of proteomic changes in cassava cv. Kasetsart 50 caused by Sri Lankan cassava mosaic virus infection., BMC Plant Biol, PMID 36494781

PXD035780 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of human and microbial salivary proteomes in children offers insights on the molecular pathogenesis of molar-incisor hypomineralization
Possible reference: Pappa, E. et al. (2022) Analysis of Human and Microbial Salivary Proteomes in Children Offers Insights on the Molecular Pathogenesis of Molar-Incisor Hypomineralization., Biomedicines, PMID 36140166

PXD035775 Dataset with its publication pending (from PRIDE)
Dataset title: Deciphering O-glycoprotease substrate preferences with O-Pair Search
Possible reference: Riley, NM. et al. (2022) Deciphering O-glycoprotease substrate preferences with O-Pair Search., Mol Omics, PMID 36373229

PXD035774 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation of binding preference of different microtubes for nanoproteomics sample preparation
Possible reference: Zhang, Z. et al. (2023) Evaluation of the Binding Preference of Microtubes for Nanoproteomics Sample Preparation., J Proteome Res, PMID 36455010

PXD035761 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of putative reader proteins of RNA 5-methylcytosine and its derivatives in Caenorhabditis elegans
Possible reference: Navarro, IC. et al. (2022) Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA., Wellcome Open Res, PMID 37475875

PXD035750 Dataset with its publication pending (from PRIDE)
Dataset title: DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts
Possible reference: Goyal, A. et al. (2023) DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts., Nat Commun, PMID 37872136

PXD035748 Dataset with its publication pending (from PRIDE)
Dataset title: DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts
Possible reference: Goyal, A. et al. (2023) DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts., Nat Commun, PMID 37872136

PXD035731 Dataset with its publication pending (from jPOST)
Dataset title: iSDAC: in situ digestion of alcohol-fixed cells
Possible reference: Hatano, A. et al. (2023) In situ digestion of alcohol-fixed cells for quantitative proteomics., J Biochem, PMID 36455924

PXD035719 Dataset with its publication pending (from PRIDE)
Dataset title: Mass spectrometry identification of biomarkers in extracellular vesicles from Plasmodium vivax liver hypnozoite infections
Possible reference: Gualdr�n-L�pez, M. et al. (2022) Mass Spectrometry Identification of Biomarkers in Extracellular Vesicles From Plasmodium vivax Liver Hypnozoite Infections., Mol Cell Proteomics, PMID 36030044

PXD035712 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart
Possible reference: Caudal, A. et al. (2022) Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart., Nat Cardiovasc Res, PMID 36405497

PXD035696 Dataset with its publication pending (from PRIDE)
Dataset title: Distinct transcriptome, translatome, and proteome reprogramming during the oocyte-to-embryo transition
Possible reference: Zhang, H. et al. (2023) Stable maternal proteins underlie distinct transcriptome, translatome, and proteome reprogramming during mouse oocyte-to-embryo transition., Genome Biol, PMID 37443062

PXD035694 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of regenerating island-derived protein 3E in dogs
Possible reference: Peters, LM. et al. (2022) Identification of regenerating island-derived protein 3E in dogs., Front Vet Sci, PMID 36387376

PXD035677 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of stably expressed reference genes for expression studies in Arabidopsis thaliana using mass spectrometry-based label-free quantification
Possible reference: Cheng, SS. et al. (2022) Identification of stably expressed reference genes for expression studies in Arabidopsis thaliana using mass spectrometry-based label-free quantification., Front Plant Sci, PMID 36247637

PXD035673 Dataset with its publication pending (from PRIDE)
Dataset title: Exosome proteomics reveals the deregulation of coagulation, complement and lipid metabolism proteins in gestational diabetes mellitus
Possible reference: Bernea, EG. et al. (2022) Exosome Proteomics Reveals the Deregulation of Coagulation, Complement and Lipid Metabolism Proteins in Gestational Diabetes Mellitus., Molecules, PMID 36080270

PXD035668 Dataset with its publication pending (from PRIDE)
Dataset title: Disordered region encodes Î±-crystallin chaperone activity toward lens client Î³D-crystallin
Possible reference: Woods, CN. et al. (2023) Disordered region encodes α-crystallin chaperone activity toward lens client γD-crystallin., Proc Natl Acad Sci U S A, PMID 36719917

PXD035665 Dataset with its publication pending (from PRIDE)
Dataset title: Deep single-shot nanoLCMS proteome profiling with 1500 bar UHPLC system, long fully porous columns, and HRAM MS
Possible reference: Zheng, R. et al. (2022) Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS., J Proteome Res, PMID 36068014

PXD035662 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of MRSA252 secretome and membrane vesicles
Possible reference: Uppu, DS. et al. (2023) Contribution of Extracellular Membrane Vesicles To the Secretome of Staphylococcus aureus., mBio, PMID 36744901

PXD035653 Dataset with its publication pending (from PRIDE)
Dataset title: Non-enzymatic acetylation inhibits glycolytic enzymes in Escherichia coli
Possible reference: Schastnaya, E. et al. (2023) Non-enzymatic acetylation inhibits glycolytic enzymes in Escherichia coli., Cell Rep, PMID 36640332

PXD035636 no publication (from MassIVE)
Dataset title: Evaluation of quantification and normalization strategies for phosphoprotein phosphatase affinity proteomics: application to breast cancer signaling
Possible reference: Brauer, BL. et al. (2023) Evaluation of Quantification and Normalization Strategies for Phosphoprotein Phosphatase Affinity Proteomics: Application to Breast Cancer Signaling., J Proteome Res, PMID 36448918

PXD035628 Dataset with its publication pending (from PRIDE)
Dataset title: Structural perturbation at the N-terminal domain of human phosphoglycerate kinase 1 reduces the kinetic stability and unfolding cooperativity of a two-domain enzyme
Possible reference: Pacheco-Garc�a, JL. et al. (2022) Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core., Sci Rep, PMID 36229482

PXD035622 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart
Possible reference: Caudal, A. et al. (2022) Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart., Nat Cardiovasc Res, PMID 36405497

PXD035618 Dataset with its publication pending (from PRIDE)
Dataset title: Insights into the digestive gland of Mytilus coruscus under heat stress using TMT-based proteomics
Possible reference: Xu, L. et al. (2023) Insights into the Response in Digestive Gland of Mytilus coruscus under Heat Stress Using TMT-Based Proteomics., Animals (Basel), PMID 37508026

PXD035607 no publication (from MassIVE)
Dataset title: Untargeted Metabolomics and Lipidomics Reveal Complex Pathways Spurred by Activation of Acid Resistance Mechanisms in Escherichia coli
Possible reference: Gold, A. et al. (2022) More than Meets the Eye: Untargeted Metabolomics and Lipidomics Reveal Complex Pathways Spurred by Activation of Acid Resistance Mechanisms in Escherichia coli., J Proteome Res, PMID 36322795

PXD035605 no publication (from MassIVE)
Dataset title: Loss of TMEM65 causes mitochondrial disease mediated by mitochondrial calcium
Possible reference: Zhang, Y. et al. (2026) Loss of TMEM65 in mice causes mitochondrial disease mediated by mitochondrial Ca2., Nat Commun, PMID 41980949

PXD035600 no publication (from MassIVE)
Dataset title: Data-Independent Acquisition and Quantification of Extracellular Matrix from Human Lung in Chronic Inflammation-Associated Carcinomas
Possible reference: Bons, J. et al. (2023) Data-independent acquisition and quantification of extracellular matrix from human lung in chronic inflammation-associated carcinomas., Proteomics, PMID 36228107

PXD035597 Dataset with its publication pending (from jPOST)
Dataset title: The Liquid Chromatography/Tandem Mass Spectrometry-Based Quantification of Angiotensin Peptides
Possible reference: He, C. et al. (2020) Development of a novel nanoflow liquid chromatography-parallel reaction monitoring mass spectrometry-based method for quantification of angiotensin peptides in HUVEC cultures., PeerJ, PMID 32983648

PXD035587 Dataset with its publication pending (from PRIDE)
Dataset title: Unique Ligand and Kinase-Independent Roles of the Insulin Receptor in Regulation of Cell Cycle, Senescence and Apoptosis
Possible reference: Nagao, H. et al. (2023) Unique ligand and kinase-independent roles of the insulin receptor in regulation of cell cycle, senescence and apoptosis., Nat Commun, PMID 36599833

PXD035578 Dataset with its publication pending (from PRIDE)
Dataset title: Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis
Possible reference: Zhong, Z. et al. (2022) Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis., Nat Commun, PMID 36379930

PXD035577 Dataset with its publication pending (from PRIDE)
Dataset title: Age-related decline in the resistance of mice to bacterial infection and in LPS/TLR4 pathway-dependent neutrophil responses
Possible reference: Hornigold, K. et al. (2022) Age-related decline in the resistance of mice to bacterial infection and in LPS/TLR4 pathway-dependent neutrophil responses., Front Immunol, PMID 36090969

PXD035532 Dataset with its publication pending (from PRIDE)
Dataset title: A metabolic map of the DNA damage response identifies PRDX1 in nuclear ROS scavenging and aspartate synthesis
Possible reference: Moretton, A. et al. (2023) A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability., Mol Syst Biol, PMID 37259925

PXD035516 no publication (from MassIVE)
Dataset title: Regulation of PaRBOH1-mediated ROS production
Possible reference: Nickolov, K. et al. (2022) Regulation of PaRBOH1-mediated ROS production in Norway spruce by Ca2+ binding and phosphorylation., Front Plant Sci, PMID 36311083

PXD035506 no publication (from MassIVE)
Dataset title: Regulation of PaRBOH1-mediated ROS production
Possible reference: Nickolov, K. et al. (2022) Regulation of PaRBOH1-mediated ROS production in Norway spruce by Ca2+ binding and phosphorylation., Front Plant Sci, PMID 36311083

PXD035482 Dataset with its publication pending (from PRIDE)
Dataset title: The Legionella pneumophila effector DenR hijacks host NRas signaling during infection
Possible reference: Lehman, SS. et al. (2024) The Legionella pneumophila effector DenR hijacks the host NRas proto-oncoprotein to downregulate MAPK signaling., Cell Rep, PMID 38568811

PXD035478 Dataset with its publication pending (from PRIDE)
Dataset title: Immunization of mice with virus-like vesicles of Kaposi sarcoma-associated herpesvirus reveals a role of ORF4 in complement-mediated neutralization
Possible reference: Lam, AK. et al. (2023) Immunization of Mice with Virus-Like Vesicles of Kaposi Sarcoma-Associated Herpesvirus Reveals a Role for Antibodies Targeting ORF4 in Activating Complement-Mediated Neutralization., J Virol, PMID 36757205

PXD035477 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of the interactome profiling of Mycoplasma DnaK in cancer cell reveals interference with key cellular pathways
Possible reference: Curreli, S. et al. (2022) Characterization of the interactome profiling of Mycoplasma fermentans DnaK in cancer cells reveals interference with key cellular pathways., Front Microbiol, PMID 36386669

PXD035462 Dataset with its publication pending (from jPOST)
Dataset title: Identification of novel kinases of Tau using fluorescence complementation mass spectrometry (FCMS)
Possible reference: Kao, DS. et al. (2022) Identification of Novel Kinases of Tau Using Fluorescence Complementation Mass Spectrometry (FCMS)., Mol Cell Proteomics, PMID 36379402

PXD035451 Dataset with its publication pending (from PRIDE)
Dataset title: SARS-CoV-2 hijacks p38Î²/MAPK11 to promote virus replication
Possible reference: Higgins, CA. et al. (2023) SARS-CoV-2 hijacks p38β/MAPK11 to promote virus replication., mBio, PMID 37345956

PXD035450 Dataset with its publication pending (from PRIDE)
Dataset title: TFEB AND TFE3 DRIVE KIDNEY CYSTOGENESIS AND TUMORIGENESIS
Possible reference: Di Malta, C. et al. (2023) TFEB and TFE3 drive kidney cystogenesis and�tumorigenesis., EMBO Mol Med, PMID 36987696

PXD035448 Dataset with its publication pending (from PRIDE)
Dataset title: Tropodithietic acid, a multifunctional antimicrobial, facilitates adaption and colonization of the producer, Phaeobacter piscinae S26
Possible reference: Lindqvist, LL. et al. (2023) Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae., mSphere, PMID 36622251

PXD035433 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted cross-linker delivery for in situ mapping of protein conformations and interactions in mitochondria
Possible reference: Chen, Y. et al. (2023) Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria., Nat Commun, PMID 37391416

PXD035420 Dataset with its publication pending (from PRIDE)
Dataset title: Substrate spectrum of PPM1D in the cellular response to DNA double strand breaks
Possible reference: Gr�f, JF. et al. (2022) Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks., iScience, PMID 36060052

PXD035418 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation and physiological function of proteins for heat tolerance in cowpea (Vigna unguiculata) genotypes under controlled and field conditions
Possible reference: Selinga, TI. et al. (2022) Regulation and physiological function of proteins for heat tolerance in cowpea (Vigna unguiculata) genotypes under controlled and field conditions., Front Plant Sci, PMID 36072323

PXD035413 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex
Possible reference: Soni, K. et al. (2023) Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex., Nat Commun, PMID 36774373

PXD035400 Dataset with its publication pending (from PRIDE)
Dataset title: Selective inhibitors of SARM1 targeting an allosteric cysteine in the autoregulatory ARM domain
Possible reference: Feldman, HC. et al. (2022) Selective inhibitors of SARM1 targeting an allosteric cysteine in the autoregulatory ARM domain., Proc Natl Acad Sci U S A, PMID 35994671

PXD035399 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells
Possible reference: Ternet, C. et al. (2023) Analysis of context-specific KRAS-effector (sub)complexes in Caco-2 cells., Life Sci Alliance, PMID 36894174

PXD035398 Dataset with its publication pending (from PRIDE)
Dataset title: Diptoindonesin G is a middle domain HSP90 modulator for cancer treatment
Possible reference: Donahue, K. et al. (2022) Diptoindonesin G is a middle domain HSP90 modulator for cancer treatment., J Biol Chem, PMID 36395883

PXD035394 Dataset with its publication pending (from PRIDE)
Dataset title: Nuclear myosin VI maintains replication fork stability
Possible reference: Shi, J. et al. (2023) Nuclear myosin VI maintains replication fork stability., Nat Commun, PMID 37355687

PXD035390 Dataset with its publication pending (from iProX)
Dataset title: Proteomics and Phosphoproteomics of Cymbidium sinense Leaf Variegation Mutant
Possible reference: Gao, J. et al. (2024) Phosphorylation of 399S at CsHsp70 of Cymbidium sinense is essential to maintain chlorophyll stability., Plant Physiol Biochem, PMID 38744085

PXD035385 Dataset with its publication pending (from iProX)
Dataset title: Vibrio alginolyticus strain: ZJ-T
Possible reference: Deng, Y. et al. (2016) The RNA Chaperone Hfq Is Involved in Colony Morphology, Nutrient Utilization and Oxidative and Envelope Stress Response in Vibrio alginolyticus., PLoS One, PMID 27685640

PXD035376 Dataset with its publication pending (from jPOST)
Dataset title: Brain proteomics in GLUT1-deltaGFAP mice
Possible reference: Ardanaz, CG. et al. (2024) Astrocytic GLUT1 reduction paradoxically improves central and peripheral glucose homeostasis., Sci Adv, PMID 39423276

PXD035359 no publication (from MassIVE)
Dataset title: Identifying natural bioactive peptides from the ink by-product of common octopus (Octopus vulgaris) using proteomics
Possible reference: Imran, MAS. et al. (2023) Insights into Common Octopus (Octopus vulgaris) Ink Proteome and Bioactive Peptides Using Proteomic Approaches., Mar Drugs, PMID 37103345

PXD035356 no publication (from MassIVE)
Dataset title: Identifying natural bioactive peptides from the common octopus (Octopus vulgaris Cuvier, 1797) skin mucus by-products using proteogenomic analysis
Possible reference: P�rez-Polo, S. et al. (2023) Identifying Natural Bioactive Peptides from the Common Octopus (Octopus vulgaris Cuvier, 1797) Skin Mucus By-Products Using Proteogenomic Analysis., Int J Mol Sci, PMID 37108304

PXD035355 Dataset with its publication pending (from jPOST)
Dataset title: Enhanced protein-protein interaction network construction promoted by in vivo cross-linking
Possible reference: Zhao, L. et al. (2022) Enhanced protein-protein interaction network construction promoted by in vivo cross-linking with acid-cleavable click-chemistry enrichment., Front Chem, PMID 36479438

PXD035346 Dataset with its publication pending (from PRIDE)
Dataset title: Branch point evolution controls species-specific alternative splicing and regulates long term potentiation
Possible reference: Franz, A. et al. (2023) Branch point strength controls species-specific CAMK2B alternative splicing and regulates LTP., Life Sci Alliance, PMID 36543542

PXD035317 Dataset with its publication pending (from jPOST)
Dataset title: Enhanced protein-protein interaction network construction promoted by in vivo cross-linking with acid-cleavable click chemistry enrichment
Possible reference: Zhao, L. et al. (2022) Enhanced protein-protein interaction network construction promoted by in vivo cross-linking with acid-cleavable click-chemistry enrichment., Front Chem, PMID 36479438

PXD035313 Dataset with its publication pending (from iProX)
Dataset title: Quantitative proteomic analysis of ClpX in Synechocystis
Possible reference: Zhang, Y. et al. (2022) Proteomic analysis of the regulatory networks of ClpX in a model cyanobacterium Synechocystis sp. PCC 6803., Front Plant Sci, PMID 36247581

PXD035312 no publication (from MassIVE)
Dataset title: Vitamin C modulates the levels of several proteins of the mitochondrial complex III and its activity in the mouse liver
Possible reference: Aumailley, L. et al. (2022) Vitamin C modulates the levels of several proteins of the mitochondrial complex III and its activity in the mouse liver., Redox Biol, PMID 36179436

PXD035301 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative analyses of the N-glycoproteomes in HCT116 cancer cells and their non-tumorigenic DNMT1/3b double knockout (DKO1) cells and insight into the Mannose-6-phosphate pathway
Possible reference: Chen, M. et al. (2023) Comparative site-specific N-glycoproteome analysis reveals aberrant N-glycosylation and gives insights into mannose-6-phosphate pathway in cancer., Commun Biol, PMID 36639722

PXD035254 Dataset with its publication pending (from PRIDE)
Dataset title: IFITM3 restricts virus-induced inflammatory cytokine production by limiting Nogo-B mediated TLR responses
Possible reference: Clement, M. et al. (2022) IFITM3 restricts virus-induced inflammatory cytokine production by limiting Nogo-B mediated TLR responses., Nat Commun, PMID 36075894

PXD035244 Dataset with its publication pending (from PRIDE)
Dataset title: Small Extracellular Vesicles from Hypoxic Triple-Negative Breast Cancer Cells induce Oxygen-dependent Cell Invasion
Possible reference: Pachane, BC. et al. (2022) Small Extracellular Vesicles from Hypoxic Triple-Negative Breast Cancer Cells Induce Oxygen-Dependent Cell Invasion., Int J Mol Sci, PMID 36293503

PXD035199 Dataset with its publication pending (from PRIDE)
Dataset title: Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics
Possible reference: Dhondt, B. et al. (2023) Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics., J Extracell Vesicles, PMID 37202906

PXD035192 Dataset with its publication pending (from PRIDE)
Dataset title: Yeast Mitochondrial Derived Vesicles (MDVs) have membrane potential and contain a functional ATP synthase
Possible reference: Hazan Ben-Menachem, R. et al. (2023) Mitochondrial-derived vesicles retain membrane potential and contain a functional ATP synthase., EMBO Rep, PMID 36929726

PXD035189 no publication (from MassIVE)
Dataset title: CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1
Possible reference: Hluch�, M. et al. (2022) CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1., Nature, PMID 36104565

PXD035166 Dataset with its publication pending (from iProX)
Dataset title: Genetic code expansion reveals aminoacylated lysine ubiquitination mediated by UBE2W
Possible reference: Zang, J. et al. (2023) Genetic code expansion reveals aminoacylated lysine ubiquitination mediated by UBE2W., Nat Struct Mol Biol, PMID 36593310

PXD035156 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic analysis for a putative 2, 3-bisphosphoglycerate-dependent phosphoglycerate mutase in Acidovorax citrulli
Possible reference: Lee, J. et al. (2022) A putative 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase is involved in the virulence, carbohydrate metabolism, biofilm formation, twitching halo, and osmotic tolerance in Acidovorax citrulli., Front Plant Sci, PMID 36438092

PXD035140 Dataset with its publication pending (from PRIDE)
Dataset title: Different SWI/SNF complexes coordinately promote R-loop- and RAD52- dependent transcription-coupled homologous recombination
Possible reference: Dav�-Mart�nez, C. et al. (2023) Different SWI/SNF complexes coordinately promote R-loop- and RAD52-dependent transcription-coupled homologous recombination., Nucleic Acids Res, PMID 37470997

PXD035138 Dataset with its publication pending (from PRIDE)
Dataset title: Evidence for a widespread third system for bacterial polysaccharide export across the outer membrane comprising a composite OPX/Î²-barrel translocon
Possible reference: Schwabe, J. et al. (2022) Evidence for a Widespread Third System for Bacterial Polysaccharide Export across the Outer Membrane Comprising a Composite OPX/β-Barrel Translocon., mBio, PMID 35972145

PXD035133 Dataset with its publication pending (from iProX)
Dataset title: Characterization the phosphate response 2-dependent and independent Pi-starvation response secretome in rice
Possible reference: Du, Z. et al. (2022) Characterization of the PHOSPHATE RESPONSE 2-dependent and -independent Pi-starvation response secretome in rice., J Exp Bot, PMID 35994773

PXD035125 Dataset with its publication pending (from PRIDE)
Dataset title: �The EGFR/ErbB inhibitor neratinib promotes apoptosis and clearance by airway macrophages
Possible reference: Herman, KD. et al. (2022) The EGFR/ErbB inhibitor neratinib modifies the neutrophil phosphoproteome and promotes apoptosis and clearance by airway macrophages., Front Immunol, PMID 35967296

PXD035121 Dataset with its publication pending (from PRIDE)
Dataset title: Cardiac perilipin 5 promotes physiological cardioprotective hypertrophy through increased calcium handling and cardiomyocyte contractility
Possible reference: Cinato, M. et al. (2023) Cardiac Plin5 interacts with SERCA2 and promotes calcium handling and cardiomyocyte contractility., Life Sci Alliance, PMID 36717246

PXD035109 Dataset with its publication pending (from PRIDE)
Dataset title: The Holdup Multiplex, an assay for high-throughput measurement of protein-ligand affinity constants using a mass-spectrometry readout
Possible reference: Delalande, F. et al. (2025) Holdup Multiplex Assay for High-Throughput Measurement of Protein-Ligand Affinity Constants Using a Mass Spectrometry Readout., J Am Chem Soc, PMID 40129024

PXD035107 Dataset with its publication pending (from PRIDE)
Dataset title: Global phosphoproteomic profiling of skeletal muscle in ovarian-hormone deficient mice
Possible reference: Peyton, MP. et al. (2022) Global phosphoproteomic profiling of skeletal muscle in ovarian hormone-deficient mice., Physiol Genomics, PMID 36062884

PXD035100 Dataset with its publication pending (from PRIDE)
Dataset title: ALK fusion NSCLC oncogenes promote survival and inhibit NK cell responses via SERPINB4 expression
Possible reference: Chuang, TP. et al. (2023) ALK fusion NSCLC oncogenes promote survival and inhibit NK cell responses via SERPINB4 expression., Proc Natl Acad Sci U S A, PMID 36791109

PXD035095 no publication (from MassIVE)
Dataset title: Witch Nails Krt90whnl A spontaneous mouse mutation affecting nail growth and development
Possible reference: Sundberg, JP. et al. (2022) Witch Nails (Krt90whnl): A spontaneous mouse mutation affecting nail growth and development., PLoS One, PMID 36374931

PXD035082 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of the secretome of a esxaA mutant Mycobacterium tuberculosis strain
Possible reference: Tschumi, A. et al. (2012) Functional analyses of mycobacterial lipoprotein diacylglyceryl transferase and comparative secretome analysis of a mycobacterial lgt mutant., J Bacteriol, PMID 22609911

PXD035078 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation of absorbent cotton for glycopeptide enrichment
Possible reference: Xin, M. et al. (2022) Evaluation of absorbent cotton for glycopeptide enrichment., Anal Bioanal Chem, PMID 36181511

PXD035076 Dataset with its publication pending (from PRIDE)
Dataset title: Phenylalanine Impairs Insulin Signaling and Inhibits Glucose Uptake Through Modification of IRÎ²
Possible reference: Zhou, Q. et al. (2022) Phenylalanine impairs insulin signaling and inhibits glucose uptake through modification of IRβ., Nat Commun, PMID 35879296

PXD035065 Dataset with its publication pending (from PRIDE)
Dataset title: Salt and metal tolerance involves formation of guttation droplets in species of the Aspergillus versicolor complex
Possible reference: Harpke, M. et al. (2022) Salt and Metal Tolerance Involves Formation of Guttation Droplets in Species of the Aspergillus versicolor Complex., Genes (Basel), PMID 36140799

PXD035059 Dataset with its publication pending (from iProX)
Dataset title: Sunflower seed proteome analysis by iTRAQ
Possible reference: Yang, C. et al. (2017) iTRAQ-based proteomics of sunflower cultivars differing in resistance to parasitic weed Orobanche cumana., Proteomics, PMID 28618117

PXD035058 Dataset with its publication pending (from iProX)
Dataset title: Bioinformatics and quantitative proteomics-based identification of gastric adenocarcinoma-related proteins and analysis of PGRN function
Possible reference: Liu, W. et al. (2024) Bioinformatics- and quantitative proteomics-based identification of gastric adenocarcinoma-related proteins and analysis., Am J Cancer Res, PMID 39659938

PXD035046 no publication (from MassIVE)
Dataset title: Rapid Monocyte Recruitment Dictates the Therapeutic Efficacy of Focal Radiotherapy
Possible reference: Tadepalli, S. et al. (2023) Rapid recruitment and IFN-I-mediated activation of monocytes dictate focal radiotherapy efficacy., Sci Immunol, PMID 37294749

PXD035045 Dataset with its publication pending (from PRIDE)
Dataset title: Ubiquitinome profiling reveals in vivo UBE2D3 targets and implicates UBE2D3 in protein quality control.
Possible reference: Yal�in, Z. et al. (2023) Ubiquitinome Profiling Reveals in�Vivo UBE2D3 Targets and Implicates UBE2D3 in Protein Quality Control., Mol Cell Proteomics, PMID 37059365

PXD035030 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive analysis of platelet glycoprotein IbÎ± glycosylation.
Possible reference: Hollenhorst, MA. et al. (2023) Comprehensive analysis of platelet glycoprotein Ibα ectodomain glycosylation., J Thromb Haemost, PMID 36740532

PXD035001 Dataset with its publication pending (from PRIDE)
Dataset title: Heat shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition
Possible reference: Lu, S. et al. (2022) Heat-shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition., Nat Cell Biol, PMID 36075972

PXD034999 Dataset with its publication pending (from PRIDE)
Dataset title: The UAS domain of UBXN7 interacts with RNF111 RING domain
Possible reference: Amhaz, S. et al. (2023) The UAS thioredoxin-like domain of UBXN7 regulates E3 ubiquitin ligase activity of RNF111/Arkadia., BMC Biol, PMID 37024974

PXD034987 Dataset with its publication pending (from PRIDE)
Dataset title: The proteomic responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to subminimal-inhibitory concentrations of meropenem revealed by quantitative tandem mass spectrometry
Possible reference: Salv�-Serra, F. et al. (2022) Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics., Front Microbiol, PMID 36845973

PXD034968 Dataset with its publication pending (from PRIDE)
Dataset title: iBench Ground Truth Validation Tool
Possible reference: Cormican, JA. et al. (2023) iBench: A ground truth approach for advanced validation of mass spectrometry identification method., Proteomics, PMID 36189881

PXD034953 no publication (from MassIVE)
Dataset title: Tan_V-ATPase_mEAK-7_interaction_2022
Possible reference: Tan, YZ. et al. (2022) CryoEM of endogenous mammalian V-ATPase interacting with the TLDc protein mEAK-7., Life Sci Alliance, PMID 35794005

PXD034945 no publication (from MassIVE)
Dataset title: Small changes in phospho-occupancy at the kinetochore-microtubule interface drive mitotic fidelity
Possible reference: Kucharski, TJ. et al. (2022) Small changes in phospho-occupancy at the kinetochore-microtubule interface drive mitotic fidelity., J Cell Biol, PMID 35878017

PXD034937 Dataset with its publication pending (from PRIDE)
Dataset title: Thermal proteome profiling of MMV897615
Possible reference: Bopp, S. et al. (2023) Potent acyl-CoA synthetase 10 inhibitors kill Plasmodium falciparum by disrupting triglyceride formation., Nat Commun, PMID 36927839

PXD034922 Dataset with its publication pending (from PRIDE)
Dataset title: Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import
Possible reference: Nashed, S. et al. (2023) Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import., PLoS Genet, PMID 37585488

PXD034911 Dataset with its publication pending (from PRIDE)
Dataset title: TNAP - a potential cytokine in the cerebral inflammation in Spastic Cerebral Palsy
Possible reference: Wang, XK. et al. (2022) TNAP-a potential cytokine in the cerebral inflammation in spastic cerebral palsy., Front Mol Neurosci, PMID 36187348

PXD034908 Dataset with its publication pending (from PRIDE)
Dataset title: The muscle proteome reflects changes in mitochondrial function, cellular stress and proteolysis after 14 days of unilateral lower limb immobilization in active young men
Possible reference: Doering, TM. et al. (2022) The muscle proteome reflects changes in mitochondrial function, cellular stress and proteolysis after 14 days of unilateral lower limb immobilization in active young men., PLoS One, PMID 36048851

PXD034901 Dataset with its publication pending (from PRIDE)
Dataset title: Acetylation of p62 regulates base excision repair through interaction with APE1
Possible reference: Li, M. et al. (2022) Acetylation of p62 regulates base excision repair through interaction with APE1., Cell Rep, PMID 35858573

PXD034899 Dataset with its publication pending (from PRIDE)
Dataset title: Acetylation of p62 regulates base excision repair through interaction with APE1
Possible reference: Li, M. et al. (2022) Acetylation of p62 regulates base excision repair through interaction with APE1., Cell Rep, PMID 35858573

PXD034891 Dataset with its publication pending (from PRIDE)
Dataset title: Label-free quantitative SWATH-MS proteomic analysis of adult myocardial slices in vitro after biomimetic electromechanical stimulation
Possible reference: Zabielska-Kaczorowska, MA. et al. (2022) Label-free quantitative SWATH-MS proteomic analysis of adult myocardial slices in vitro after biomimetic electromechanical stimulation., Sci Rep, PMID 36192624

PXD034886 Dataset with its publication pending (from PRIDE)
Dataset title: Sortilin-driven cancer secretome in HCC
Possible reference: Chan, KK. et al. (2023) Sortilin-Driven Cancer Secretome Enhances Tumorigenic Properties of Hepatocellular Carcinoma via de Novo Lipogenesis., Am J Pathol, PMID 37673328

PXD034881 no publication (from MassIVE)
Dataset title: Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei
Possible reference: Fu, JY. et al. (2022) Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei., Front Microbiol, PMID 36419437

PXD034880 no publication (from MassIVE)
Dataset title: Regulation of urea cycle by reversible high stoichiometry lysine succinylation
Possible reference: Zhang, R. et al. (2024) Regulation of urea cycle by reversible high-stoichiometry lysine succinylation., Nat Metab, PMID 38448615

PXD034879 no publication (from MassIVE)
Dataset title: Variation in milk proteins across lactation in Pongo pygmaeus and Gorilla gorilla
Possible reference: Cleland, TP. et al. (2022) Variation in Milk Proteins Across Lactation in Pongo pygmaeus and Gorilla gorilla., J Proteome Res, PMID 36278968

PXD034875 Dataset with its publication pending (from PRIDE)
Dataset title: Structure of the human FERRY Rab5 effector complex
Possible reference: Quentin, D. et al. (2023) Structural basis of mRNA binding by the human FERRY Rab5 effector complex., Mol Cell, PMID 37267906

PXD034862 no publication (from MassIVE)
Dataset title: High sensitivity limited material proteomics empowered by data-independent acquisition on linear ion traps
Possible reference: Phlairaharn, T. et al. (2022) High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps., J Proteome Res, PMID 36287219

PXD034860 no publication (from MassIVE)
Dataset title: Synovial fluid proteomics from serial aspiration of ACL injured knees identifies candidate biomarkers for osteoarthritis
Possible reference: Rai, MF. et al. (2023) Synovial Fluid Proteomics From Serial Aspirations of ACL-Injured Knees Identifies Candidate Biomarkers., Am J Sports Med, PMID 37191559

PXD034845 Dataset with its publication pending (from PRIDE)
Dataset title: Oxonium Ion-Guided Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro
Possible reference: Mukherjee, S. et al. (2023) Oxonium Ion-Guided Optimization of Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro., Mol Cell Proteomics, PMID 36549589

PXD034838 no publication (from MassIVE)
Dataset title: Proteomic analysis of prostate cancer FFPE samples reveals markers of disease progression and aggressiveness
Possible reference: Lygirou, V. et al. (2022) Proteomic Analysis of Prostate Cancer FFPE Samples Reveals Markers of Disease Progression and Aggressiveness., Cancers (Basel), PMID 35954429

PXD034829 Dataset with its publication pending (from PRIDE)
Dataset title: Intestinal epithelial c-Maf expression determines enterocyte differentiation and nutrient uptake
Possible reference: Cosovanu, C. et al. (2022) Intestinal epithelial c-Maf expression determines enterocyte differentiation and nutrient uptake in mice., J Exp Med, PMID 36121416

PXD034805 Dataset with its publication pending (from PRIDE)
Dataset title: A mass spectrometry-based approach for the identification of KpnÎ²1 binding partners in cancer cells
Possible reference: Okpara, MO. et al. (2022) A mass spectrometry-based approach for the identification of Kpnβ1 binding partners in cancer cells., Sci Rep, PMID 36418423

PXD034801 no publication (from MassIVE)
Dataset title: Lack of TRPV1 Channel Modulates Mouse Gene Expression and Liver Proteome with Glucose Metabolism Changes
Possible reference: Lacerda, JT. et al. (2022) Lack of TRPV1 Channel Modulates Mouse Gene Expression and Liver Proteome with Glucose Metabolism Changes., Int J Mol Sci, PMID 35806020

PXD034773 Dataset with its publication pending (from PRIDE)
Dataset title: Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes
Possible reference: Racle, J. et al. (2023) Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes., Immunity, PMID 37023751

PXD034771 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibition of mammalian mtDNA transcription in liver reprograms metabolism to reverse diet-induced obesity and hepatosteatosis
Possible reference: Jiang, S. et al. (2024) Inhibition of mammalian mtDNA transcription acts paradoxically to reverse diet-induced hepatosteatosis and obesity., Nat Metab, PMID 38689023

PXD034768 Dataset with its publication pending (from jPOST)
Dataset title: Suborganelle-specific protein complexes analysis enabled by in-vivo crosslinking coupled with proximal labeling
Possible reference: An, Y. et al. (2022) Suborganelle-Specific Protein Complex Analysis Enabled by in Vivo Cross-Linking Coupled with Proximal Labeling., Anal Chem, PMID 36004751

PXD034712 Dataset with its publication pending (from PRIDE)
Dataset title: Compounds activating VCP D1 ATPase enhance both autophagic and proteasomal neurotoxic protein clearance
Possible reference: Wrobel, L. et al. (2022) Compounds activating VCP D1 ATPase enhance both autophagic and proteasomal neurotoxic protein clearance., Nat Commun, PMID 35842429

PXD034644 Dataset with its publication pending (from PRIDE)
Dataset title: N-acetylcysteine overcomes NF1-loss driven resistance to PI3K alpha inhibition in breast cancer.
Possible reference: Auf der Maur, P. et al. (2023) N-acetylcysteine overcomes NF1 loss-driven resistance to PI3Kα inhibition in breast cancer., Cell Rep Med, PMID 37044095

PXD034641 Dataset with its publication pending (from PRIDE)
Dataset title: Effect of iron-limitation, elevated temperature and florfenicol antibiotics on the subcellular proteomes and the vesiculation of the fish pathogen Aeromonas salmonicida
Possible reference: Kroniger, T. et al. (2022) Effect of Iron Limitation, Elevated Temperature, and Florfenicol on the Proteome and Vesiculation of the Fish Pathogen Aeromonas salmonicida., Microorganisms, PMID 36144337

PXD034635 no publication (from MassIVE)
Dataset title: Protein nonadditivity and stability contribute to heterosis in Arabidopsis hybrids and allotetraploids
Possible reference: June, V. et al. (2023) Protein nonadditive expression and solubility contribute to heterosis in Arabidopsis hybrids and allotetraploids., Front Plant Sci, PMID 37780492

PXD034604 Dataset with its publication pending (from PRIDE)
Dataset title: Cardioviruses’ leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic
Possible reference: Lizcano-Perret, B. et al. (2022) Cardiovirus leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic., PLoS Pathog, PMID 36508477

PXD034596 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of fibroblasts differentiates patients with severe, intermediate and mild spinal muscular atrophy
Possible reference: Brown, SJ. et al. (2022) The Proteome Signatures of Fibroblasts from Patients with Severe, Intermediate and Mild Spinal Muscular Atrophy Show Limited Overlap., Cells, PMID 36078032

PXD034565 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteome dynamics of Streptomyces rimosus during submerged growth and antibiotic production
Possible reference: Šarić, E. et al. (2022) Phosphoproteome Dynamics of Streptomyces rimosus during Submerged Growth and Antibiotic Production., mSystems, PMID 36094082

PXD034562 Dataset with its publication pending (from PRIDE)
Dataset title: Deciphering the involvement of the Hippo pathway co - regulators, YAP/TAZ in invadopodia formation and matrix degradation
Possible reference: Venghateri, JB. et al. (2023) Deciphering the involvement of the Hippo pathway co-regulators, YAP/TAZ in invadopodia formation and matrix degradation., Cell Death Dis, PMID 37185904

PXD034517 Dataset with its publication pending (from PRIDE)
Dataset title: MYC sensitises cells to apoptosis by driving energetic demand
Possible reference: Edwards-Hicks, J. et al. (2022) MYC sensitises cells to apoptosis by driving energetic demand., Nat Commun, PMID 35945217

PXD034511 Dataset with its publication pending (from PRIDE)
Dataset title: A complex epigenome-splicing crosstalk governs epithelial to mesenchymal transition in metastasis and brain development
Possible reference: Sahu, SK. et al. (2022) A complex epigenome-splicing crosstalk governs epithelial-to-mesenchymal transition in metastasis and brain development., Nat Cell Biol, PMID 35941369

PXD034505 no publication (from MassIVE)
Dataset title: TXNRD1 drives innate immune response in senescent cells and promotes age-associated inflammation
Possible reference: Hao, X. et al. (2024) TXNRD1 drives the innate immune response in senescent cells with implications for age-associated inflammation., Nat Aging, PMID 38267705

PXD034498 no publication (from MassIVE)
Dataset title: Quantitative Proteomics and Network Analysis of Differentially Expressed Proteins in proteomes of icefish muscle mitochondria compared with closely related red-blooded species
Possible reference: Katyal, G. et al. (2022) Quantitative Proteomics and Network Analysis of Differentially Expressed Proteins in Proteomes of Icefish Muscle Mitochondria Compared with Closely Related Red-Blooded Species., Biology (Basel), PMID 35892974

PXD034491 Dataset with its publication pending (from PRIDE)
Dataset title: TurboID identification of evolutionarily divergent components of the nuclear pore complex in the malaria model Plasmodium berghei
Possible reference: Ambekar, SV. et al. (2022) TurboID Identification of Evolutionarily Divergent Components of the Nuclear Pore Complex in the Malaria Model Plasmodium berghei., mBio, PMID 36040030

PXD034482 no publication (from MassIVE)
Dataset title: A naturally occurring variant of SHLP2 is a protective factor in Parkinson disease
Possible reference: Kim, SJ. et al. (2024) A naturally occurring variant of SHLP2 is a protective factor in Parkinson's disease., Mol Psychiatry, PMID 38167865

PXD034476 Dataset with its publication pending (from PRIDE)
Dataset title: Deep Proteome profiling reveals signatures of age and sex differences in paw skin and sciatic nerve of na�ve mice
Possible reference: Xian, F. et al. (2022) Deep proteome profiling reveals signatures of age and sex differences in paw skin and sciatic nerve of na�ve mice., Elife, PMID 36448997

PXD034471 Dataset with its publication pending (from PRIDE)
Dataset title: Coordinate control of endoplasmic reticulum chaperone biosynthesis and peptide hormone secretion revealed by a Î²-cell model of Prader-Willi syndrome
Possible reference: Koppes, EA. et al. (2023) Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones., PLoS Genet, PMID 37068109

PXD034464 Dataset with its publication pending (from PRIDE)
Dataset title: Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts
Possible reference: Price, AM. et al. (2022) Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts., PLoS Pathog, PMID 36095031

PXD034448 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components
Possible reference: Ugur, E. et al. (2023) Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components., Nucleic Acids Res, PMID 36806742

PXD034444 Dataset with its publication pending (from PRIDE)
Dataset title: Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities
Possible reference: Zhang, Y. et al. (2023) Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities., Nat Struct Mol Biol, PMID 37488358

PXD034440 Dataset with its publication pending (from PRIDE)
Dataset title: Chemical degradation of BTK/TEC as a novel approach to inhibit platelet function.
Possible reference: Trory, JS. et al. (2023) Chemical degradation of BTK/TEC as a novel approach to inhibit platelet function., Blood Adv, PMID 36342848

PXD034424 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring Effectiveness of KEAP1-based PROTAC Strategy
Possible reference: Chen, J. et al. (2025) Advances in KEAP1-based PROTACs as emerging therapeutic modalities: Structural basis and progress., Redox Biol, PMID 40714402

PXD034423 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring Effectiveness of KEAP1-based PROTAC Strategy
Possible reference: Chen, J. et al. (2025) Advances in KEAP1-based PROTACs as emerging therapeutic modalities: Structural basis and progress., Redox Biol, PMID 40714402

PXD034417 Dataset with its publication pending (from PRIDE)
Dataset title: Engineering consortia by polymeric microbial swarmbots
Possible reference: Wang, L. et al. (2022) Engineering consortia by polymeric microbial swarmbots., Nat Commun, PMID 35790722

PXD034409 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic Profiling of Cutaneous Melanoma Identifies Novel Molecular Signatures of Tumour Metastasis
Possible reference: Maus, RLG. et al. (2019) Identification of novel, immune-mediating extracellular vesicles in human lymphatic effluent draining primary cutaneous melanoma., Oncoimmunology, PMID 31741769

PXD034383 Dataset with its publication pending (from PRIDE)
Dataset title: Venom dynamics across populations of Nematostella
Possible reference: Smith, EG. et al. (2023) Micro and macroevolution of sea anemone venom phenotype., Nat Commun, PMID 36646703

PXD034378 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring Effectiveness of KEAP1-based PROTAC Strategy
Possible reference: Chen, J. et al. (2025) Advances in KEAP1-based PROTACs as emerging therapeutic modalities: Structural basis and progress., Redox Biol, PMID 40714402

PXD034370 Dataset with its publication pending (from PRIDE)
Dataset title: Microscopy-based functional single cell proteomic profiling of cells with abnormal DNA damage response dynamics
Possible reference: Su, PR. et al. (2022) Microscopy-based single-cell proteomic profiling reveals heterogeneity in DNA damage response dynamics., Cell Rep Methods, PMID 35784653

PXD034355 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteomic analysis of neoadjuvant breast cancer reveals a subset of patients with increased sensitivity to paclitaxel driven by CDK4 and Filamin A.
Possible reference: Mouron, S. et al. (2022) Phosphoproteomic analysis of neoadjuvant breast cancer suggests that increased sensitivity to paclitaxel is driven by CDK4 and filamin A., Nat Commun, PMID 36477027

PXD034351 Dataset with its publication pending (from PRIDE)
Dataset title: System-wide profiling of drug residence time by proteome integral solubility alteration assay
Possible reference: Sabatier, P. et al. (2022) System-Wide Profiling by Proteome Integral Solubility Alteration Assay of Drug Residence Times for Target Characterization., Anal Chem, PMID 36377428

PXD034341 Dataset with its publication pending (from PRIDE)
Dataset title: m6a methylation orchestrates IMP1 regulation of microtubules during human neuronal differentiation
Possible reference: Klein, P. et al. (2024) m6a methylation orchestrates IMP1 regulation of microtubules during human neuronal differentiation., Nat Commun, PMID 38844464

PXD034275 no publication (from MassIVE)
Dataset title: In-depth Analysis of the Sirtuin 5-regulated Mouse Brain Acylome using Library-free Data-Independent Acquisitions
Possible reference: Bons, J. et al. (2023) In-depth analysis of the Sirtuin 5-regulated mouse brain malonylome and succinylome using library-free data-independent acquisitions., Proteomics, PMID 36479818

PXD034273 no publication (from MassIVE)
Dataset title: Isolation of intact and active FoF1 ATP synthase using a FLAG-tagged subunit from the cyanobacterium Synechocystis sp. PCC 6803
Possible reference: Song, K. et al. (2022) Isolation of intact and active FoF1 ATP synthase using a FLAG-tagged subunit from the cyanobacterium Synechocystis sp. PCC 6803., STAR Protoc, PMID 36039073

PXD034271 no publication (from MassIVE)
Dataset title: Sleep prevents brain phosphoproteome disruption to safguard survival
Possible reference: Ma, J. et al. (2025) Sleep prevents brain phosphoproteome disruption to safeguard survival., Cell Discov, PMID 40555714

PXD034268 Dataset with its publication pending (from iProX)
Dataset title: Aeromonas hydrophila NJ-35 proteome
Possible reference: Liu, J. et al. (2018) Tetrahymena thermophila Predation Enhances Environmental Adaptation of the Carp Pathogenic Strain Aeromonas hydrophila NJ-35., Front Cell Infect Microbiol, PMID 29594069

PXD034263 Dataset with its publication pending (from iProX)
Dataset title: Comprehensive molecular characterization of clinical responses to PD-1 inhibition in hepatocellular carcinoma
Possible reference: Sangsuwannukul, T. et al. (2025) T cell exhaustion in poorly immunogenic HCC is partially rescued by checkpoint blockade but suppressed by oncolytic virotherapy., Mol Ther, PMID 40898614

PXD034244 Dataset with its publication pending (from PRIDE)
Dataset title: Transcriptome and proteome profiling of activated cardiac fibroblasts supports target prioritization in cardiac fibrosis
Possible reference: Moita, MR. et al. (2022) Transcriptome and proteome profiling of activated cardiac fibroblasts supports target prioritization in cardiac fibrosis., Front Cardiovasc Med, PMID 36531712

PXD034242 Dataset with its publication pending (from PRIDE)
Dataset title: The non-classical major-histocompatibility-complex II protein SLA-DM is crucial for African swine fever virus replication
Possible reference: Pannhorst, K. et al. (2023) The non-classical major histocompatibility complex II protein SLA-DM is crucial for African swine fever virus replication., Sci Rep, PMID 37604847

PXD034233 Dataset with its publication pending (from iProX)
Dataset title: Significant alterations of sphingolipid metabolism in GC discovered by lipidome pseudotargeted metabolomics
Possible reference: Zeng, J. et al. (2022) Lipid metabolism characterization in gastric cancer identifies signatures to predict prognostic and therapeutic responses., Front Genet, PMID 36406121

PXD034231 Dataset with its publication pending (from jPOST)
Dataset title: Mitochondrial protein import stress regulates the LC3 lipidation step of mitophagy through NLRX1 and RRBP1
Possible reference: Killackey, SA. et al. (2022) Mitochondrial protein import stress regulates the LC3 lipidation step of mitophagy through NLRX1 and RRBP1., Mol Cell, PMID 35752171

PXD034226 Dataset with its publication pending (from iProX)
Dataset title: Proteome analysis of two Eucalyptus species during the somatic embryogenesis
Possible reference: Chen, S. et al. (2024) Integration analysis of transcriptome and proteome profiles brings new insights of somatic embryogenesis of two eucalyptus species., BMC Plant Biol, PMID 38877454

PXD034214 Dataset with its publication pending (from PRIDE)
Dataset title: Plasma glycoproteomics delivers high-specificity disease biomarkers by detecting site-specific glycosylation abnormalities
Possible reference: Wessels, HJCT. et al. (2024) Plasma glycoproteomics delivers high-specificity disease biomarkers by detecting site-specific glycosylation abnormalities., J Adv Res, PMID 37683725

PXD034202 Dataset with its publication pending (from jPOST)
Dataset title: Tape Stripped Stratum Corneum Samples are Suitable for Diagnosis and Comprehensive Proteomic Investigation in Mycosis Fungoides
Possible reference: Qureshi, HA. et al. (2023) Tape stripped stratum corneum samples are suitable for diagnosis and comprehensive proteomic investigation in mycosis fungoides., Proteomics Clin Appl, PMID 36824058

PXD034187 Dataset with its publication pending (from PRIDE)
Dataset title: HBO1 Catalyzes Lysine Benzoylation in Mammalian Cells
Possible reference: Tan, D. et al. (2022) HBO1 catalyzes lysine benzoylation in mammalian cells., iScience, PMID 36388951

PXD034174 Dataset with its publication pending (from PRIDE)
Dataset title: Physiological constraints dictate toxin spatial heterogeneity in snake venom glands
Possible reference: Kazandjian, TD. et al. (2022) Physiological constraints dictate toxin spatial heterogeneity in snake venom glands., BMC Biol, PMID 35761243

PXD034173 Dataset with its publication pending (from PRIDE)
Dataset title: The type-A response regulators negatively mediate heat stress response by altering redox homeostasis in Arabidopsis
Possible reference: Jindal, S. et al. (2022) Type-A response regulators negatively mediate heat stress response by altering redox homeostasis in Arabidopsis., Front Plant Sci, PMID 36212299

PXD034167 Dataset with its publication pending (from PRIDE)
Dataset title: The Plasmodium falciparum Nuclear Protein Phosphatase NIF4 is Required for Efficient Merozoite Invasion and Regulates Artemisinin Sensitivity
Possible reference: Zhu, X. et al. (2022) The Plasmodium falciparum Nuclear Protein Phosphatase NIF4 Is Required for Efficient Merozoite Invasion and Regulates Artemisinin Sensitivity., mBio, PMID 35938722

PXD034156 Dataset with its publication pending (from PRIDE)
Dataset title: DYRK1A regulates B cell class switch recombination through phosphorylation of MSH6
Possible reference: Stoler-Barak, L. et al. (2023) B cell class switch recombination is regulated by DYRK1A through MSH6 phosphorylation., Nat Commun, PMID 36927854

PXD034132 Dataset with its publication pending (from PRIDE)
Dataset title: Novel Venetin-1 nanoparticle from earthworm coelomic fluid as a promising agent for the treatment of non-small cell lung cancer
Possible reference: Rybicka, M. et al. (2022) Novel Venetin-1 nanoparticle from earthworm coelomic fluid as a promising agent for the treatment of non-small cell lung cancer., Sci Rep, PMID 36323731

PXD034128 Dataset with its publication pending (from PRIDE)
Dataset title: Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF
Possible reference: Skowronek, P. et al. (2022) Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF., Mol Cell Proteomics, PMID 35944843

PXD034126 Dataset with its publication pending (from iProX)
Dataset title: Protein Identification of Capsaicin in RAW264.7 cells
Possible reference: Zhang, Z. et al. (2024) Alcohol inducing macrophage M2b polarization in colitis by modulating the TRPV1-MAPK/NF-κB pathways., Phytomedicine, PMID 38810558

PXD034121 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic response of A549 lung cancer cell line to Venetin-1
Possible reference: Czaplewska, P. et al. (2023) Proteomic response of A549 lung cancer cell line to protein-polysaccharide complex Venetin-1 isolated from earthworm coelomic fluid., Front Mol Biosci, PMID 37377864

PXD034111 Dataset with its publication pending (from jPOST)
Dataset title: Plasmodium falciparum S-adenosylmethionine synthetase is essential for parasite survival through a complex interaction network with cytoplasmic and nuclear proteins
Possible reference: Musabyimana, JP. et al. (2022) Plasmodium falciparum S-Adenosylmethionine Synthetase Is Essential for Parasite Survival through a Complex Interaction Network with Cytoplasmic and Nuclear Proteins., Microorganisms, PMID 35889137

PXD034107 Dataset with its publication pending (from PRIDE)
Dataset title: Nematode gene annotation by machine learning assisted proteotranscriptomics enables proteome-wide evolutionary analysis
Possible reference: Ceron-Noriega, A. et al. (2023) Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis., Genome Res, PMID 36653121

PXD034102 Dataset with its publication pending (from PRIDE)
Dataset title: Aberrant expression of transglutaminase 2 in pancreas and thymus of NOD mice underscores the importance of deamidation in neoantigen generation.
Possible reference: Callebaut, A. et al. (2022) Aberrant expression of transglutaminase 2 in pancreas and thymus of NOD mice underscores the importance of deamidation in neoantigen generation., Front Endocrinol (Lausanne), PMID 35966081

PXD034098 Dataset with its publication pending (from PRIDE)
Dataset title:   Cyclin A and Cks1 promote kinase consensus switching to non-proline directed CDK1 phosphorylation
Possible reference: Al-Rawi, A. et al. (2023) Cyclin A and Cks1 promote kinase consensus switching to non-proline-directed CDK1 phosphorylation., Cell Rep, PMID 36840943

PXD034076 Dataset with its publication pending (from PRIDE)
Dataset title: Bioactive insulin-loaded electrospun wound dressings for localized drug delivery and stimulation of protein expression associated with wound healing
Possible reference: Walther, M. et al. (2023) Bioactive Insulin-Loaded Electrospun Wound Dressings for Localized Drug Delivery and Stimulation of Protein Expression Associated with Wound Healing., Mol Pharm, PMID 36538353

PXD034065 Dataset with its publication pending (from PRIDE)
Dataset title: Chitotriosidase 1 in the cerebrospinal fluid as a putative biomarker for HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) progression
Possible reference: Gomes, YCP. et al. (2022) Chitotriosidase 1 in the cerebrospinal fluid as a putative biomarker for HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) progression., Front Immunol, PMID 36052089

PXD034041 Dataset with its publication pending (from jPOST)
Dataset title: Apically-located P4-ATPase1-Lem1 complex flips phosphatidylserine and regulates motility-dependent invasion and egress in Toxoplasma gondii
Possible reference: Chen, K. et al. (2023) Apically-located P4-ATPase1-Lem1 complex internalizes phosphatidylserine and regulates motility-dependent invasion and egress in Toxoplasma gondii., Comput Struct Biotechnol J, PMID 36936814

PXD034040 no publication (from MassIVE)
Dataset title: MRG proteins are shared by multiple protein complexes with distinct functions.
Possible reference: Devoucoux, M. et al. (2022) MRG Proteins Are Shared by Multiple Protein Complexes With Distinct Functions., Mol Cell Proteomics, PMID 35636729

PXD034033 Dataset with its publication pending (from jPOST)
Dataset title: Phosphorylation barcodes encoded by CXCR3 agonists direct biased chemokine signaling
Possible reference: Eiger, DS. et al. (2023) Phosphorylation barcodes direct biased chemokine signaling at CXCR3., bioRxiv, PMID 36993369

PXD034031 Dataset with its publication pending (from jPOST)
Dataset title: Plasma membrane-associated proteins identified in Arabidopsis wild type, lbr2-2 and bak1-4 mutants treated with LPSs from Pseudomonas syringae and Xanthomonas campestris
Possible reference: Offor, BC. et al. (2022) Plasma Membrane-Associated Proteins Identified in Arabidopsis Wild Type, lbr2-2 and bak1-4 Mutants Treated with LPSs from Pseudomonas syringae and Xanthomonas campestris., Membranes (Basel), PMID 35736313

PXD034028 Dataset with its publication pending (from PRIDE)
Dataset title: Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation
Possible reference: Palhano Zanela, TM. et al. (2023) Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation., Structure, PMID 36870334

PXD034027 Dataset with its publication pending (from PRIDE)
Dataset title: DISCO-MS: Proteomics of spatially identified tissues in whole organs and organisms
Possible reference: Bhatia, HS. et al. (2022) Spatial proteomics in three-dimensional intact specimens., Cell, PMID 36563667

PXD034026 Dataset with its publication pending (from jPOST)
Dataset title: A cell type-specific proteomics uncovers a guard cell-specific RAF15-SnRK2.6/OST1 kinase cascade
Possible reference: Wang, H. et al. (2023) Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells., J Integr Plant Biol, PMID 37226855

PXD034022 Dataset with its publication pending (from PRIDE)
Dataset title: SimPLIT: Simplified sample preparation for large-scale isobaric tagging proteomics
Possible reference: Sialana, FJ. et al. (2022) SimPLIT: Simplified Sample Preparation for Large-Scale Isobaric Tagging Proteomics., J Proteome Res, PMID 35848491

PXD034018 Dataset with its publication pending (from jPOST)
Dataset title: Absolute quantification of ribosome subunits
Possible reference: Waite, CJ. et al. (2021) Resource Allocation During the Transition to Diazotrophy in Klebsiella oxytoca., Front Microbiol, PMID 34434180

PXD034014 Dataset with its publication pending (from PRIDE)
Dataset title: The small RNA Teg41 is a pleiotropic regulator of virulence in Staphylococcus aureus
Possible reference: Briaud, P. et al. (2022) The Small RNA Teg41 Is a Pleiotropic Regulator of Virulence in Staphylococcus aureus., Infect Immun, PMID 36214557

PXD034010 Dataset with its publication pending (from PRIDE)
Dataset title: Posttranslational splicing modifications as a key mechanism in cytarabine resistance in AML
Possible reference: Morales, ML. et al. (2023) Posttranslational splicing modifications as a key mechanism in cytarabine resistance in acute myeloid leukemia., Leukemia, PMID 37422594

PXD034002 Dataset with its publication pending (from iProX)
Dataset title: Caffeine alleviates high altitude pulmonary edema via mitochondrial quality control process
Possible reference: Tian, L. et al. (2023) Low-dose of caffeine alleviates high altitude pulmonary edema via regulating mitochondrial quality control process in AT1 cells., Front Pharmacol, PMID 37081967

PXD033999 no publication (from MassIVE)
Dataset title: GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins
Possible reference: Arif, A. et al. (2022) GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins., Nature, PMID 35772669

PXD033978 Dataset with its publication pending (from PRIDE)
Dataset title: Charting the proteoform landscape of serum proteins in individual donors by high-resolution native mass spectrometry
Possible reference: Cramer, DAT. et al. (2022) Charting the Proteoform Landscape of Serum Proteins in Individual Donors by High-Resolution Native Mass Spectrometry., Anal Chem, PMID 36074704

PXD033971 Dataset with its publication pending (from PRIDE)
Dataset title: Hypoxia increases the methylated histones to prevent histone clipping and redistribution of heterochromatin during Raf-induced senescence.
Possible reference: Chang, S. et al. (2025) Hypoxia increases methylated histones to prevent histone clipping and heterochromatin redistribution during Raf-induced senescence., Nucleic Acids Res, PMID 39660649

PXD033969 Dataset with its publication pending (from PRIDE)
Dataset title: Milk proteins as a feed restriction signature in dairy cows
Possible reference: Leduc, A. et al. (2022) Milk proteins as a feed restriction signature indicating the metabolic adaptation of dairy cows., Sci Rep, PMID 36344510

PXD033957 Dataset with its publication pending (from PRIDE)
Dataset title: The Plasmodium falciparum Nuclear Protein Phosphatase NIF4 is Required for Efficient Merozoite Invasion and Regulates Artemisinin Sensitivity
Possible reference: Zhu, X. et al. (2022) The Plasmodium falciparum Nuclear Protein Phosphatase NIF4 Is Required for Efficient Merozoite Invasion and Regulates Artemisinin Sensitivity., mBio, PMID 35938722

PXD033942 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of myeloid-derived growth factor as a mechanically-induced, growth-promoting angiocrine signal for human hepatocytes
Possible reference: Gro�e-Segerath, L. et al. (2024) Identification of myeloid-derived growth factor as a mechanically-induced, growth-promoting angiocrine signal for human hepatocytes., Nat Commun, PMID 38316785

PXD033940 Dataset with its publication pending (from PRIDE)
Dataset title: An optimized proteomics approach reveals novel alternative proteins in mouse liver development
Possible reference: Yang, Y. et al. (2023) An Optimized Proteomics Approach Reveals Novel Alternative Proteins in Mouse Liver Development., Mol Cell Proteomics, PMID 36494044

PXD033923 Dataset with its publication pending (from PRIDE)
Dataset title: The Human Nse5 Orthologue SIMC1 Localizes SMC5/6 to Polyomavirus Replication Centers
Possible reference: Oravcov�, M. et al. (2022) The Nse5/6-like SIMC1-SLF2 complex localizes SMC5/6 to viral replication centers., Elife, PMID 36373674

PXD033905 Dataset with its publication pending (from PRIDE)
Dataset title: Data from a proteomic comparative analysis highlight differential adaptation of Lactobacillus delbrueckii subsp. bulgaricus to cow milk versus to soy milk environments
Possible reference: Jan, G. et al. (2022) Data from a proteomic comparative analysis highlight differential adaptation of Lactobacillus delbrueckii subsp. bulgaricus to cow milk versus to soy milk environments., Data Brief, PMID 36426081

PXD033901 Dataset with its publication pending (from PRIDE)
Dataset title: Optogenetic rejuvenation of mitochondrial membrane potential extends C. elegans lifespan
Possible reference: Berry, BJ. et al. (2023) Optogenetic rejuvenation of mitochondrial membrane potential extends C. elegans lifespan., Nat Aging, PMID 36873708

PXD033887 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of the wood decay fungus Fomitopsis pinicola is altered by substrate
Possible reference: Sabat, G. et al. (2022) Proteome of the Wood Decay Fungus Fomitopsis pinicola Is Altered by Substrate., Microbiol Resour Announc, PMID 35969048

PXD033868 Dataset with its publication pending (from PRIDE)
Dataset title: MS�Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
Possible reference: Declercq, A. et al. (2022) MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates., Mol Cell Proteomics, PMID 35803561

PXD033863 Dataset with its publication pending (from PRIDE)
Dataset title: Sox9 directs divergent epigenomic states in brain tumor subtypes
Possible reference: Sardar, D. et al. (2022) Sox9 directs divergent epigenomic states in brain tumor subtypes., Proc Natl Acad Sci U S A, PMID 35858326

PXD033858 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic network of antibiotic-induced outer membrane vesicles released by extensively drug-resistant Elizabethkingia anophelis
Possible reference: Chiang, MH. et al. (2022) Proteomic Network of Antibiotic-Induced Outer Membrane Vesicles Released by Extensively Drug-Resistant Elizabethkingia anophelis., Microbiol Spectr, PMID 35852325

PXD033843 Dataset with its publication pending (from PRIDE)
Dataset title: Duplicated ribosomal protein paralogs promote alternative translation and drug resistance
Possible reference: Malik Ghulam, M. et al. (2022) Duplicated ribosomal protein paralogs promote alternative translation and drug resistance., Nat Commun, PMID 35999447

PXD033836 Dataset with its publication pending (from PRIDE)
Dataset title: The DREAM complex functions as conserved master regulator of somatic DNA repair capacities
Possible reference: Bujarrabal-Dueso, A. et al. (2023) The DREAM complex functions as conserved master regulator of somatic DNA-repair capacities., Nat Struct Mol Biol, PMID 36959262

PXD033787 no publication (from MassIVE)
Dataset title: Coenzyme A binding sites induce proximal acylation across protein families
Possible reference: Carrico, C. et al. (2023) Coenzyme A binding sites induce proximal acylation across protein families., Sci Rep, PMID 36977698

PXD033762 Dataset with its publication pending (from PRIDE)
Dataset title: Mebendazole Inhibits Histoplasma capsulatum In Vitro Growth and Decreases Mitochondrion and Cytoskeleton Protein Levels
Possible reference: Almeida, MA. et al. (2023) Mebendazole Inhibits Histoplasma capsulatum In Vitro Growth and Decreases Mitochondrion and Cytoskeleton Protein Levels., J Fungi (Basel), PMID 36983553

PXD033755 Dataset with its publication pending (from iProX)
Dataset title: Proteome-wide analysis of protein thermal stability in Arabidopsis
Possible reference: Volkening, JD. et al. (2019) Proteome-wide Analysis of Protein Thermal Stability in the Model Higher Plant Arabidopsis thaliana., Mol Cell Proteomics, PMID 30401684

PXD033752 Dataset with its publication pending (from PRIDE)
Dataset title: Salivary orosomucoid 1 as a biomarker of hepatitis B associated hepatocellular carcinoma
Possible reference: He, J. et al. (2022) Salivary orosomucoid 1 as a biomarker of hepatitis B associated hepatocellular carcinoma., Sci Rep, PMID 36096917

PXD033741 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Characterization of Epithelial Ovarian Cancer Delineates Molecular Signatures and Therapeutic Targets in Distinct Histological Subtypes
Possible reference: Gong, TT. et al. (2023) Proteomic characterization of epithelial ovarian cancer delineates molecular signatures and therapeutic targets in distinct histological subtypes., Nat Commun, PMID 38016970

PXD033731 Dataset with its publication pending (from jPOST)
Dataset title: TRIM22 negatively regulates MHC-II expression
Possible reference: Inoue, A. et al. (2022) TRIM22 negatively regulates MHC-II expression., Biochim Biophys Acta Mol Cell Res, PMID 35777501

PXD033728 Dataset with its publication pending (from iProX)
Dataset title: Serum Exosome Proteome Differentiate Early Stage Liver Fibrosis
Possible reference: Ye, B. et al. (2022) Differential proteomic analysis of plasma-derived exosomes as diagnostic biomarkers for chronic HBV-related liver disease., Sci Rep, PMID 36002595

PXD033722 . . . (from MassIVE)
Dataset title: Proteome Remodeling of the Eye Lens at 50 Years Identified with Data-Independent Acquisition
Possible reference: Cantrell, LS. et al. (2023) Proteome Remodeling of the Eye Lens at 50�Years Identified With Data-Independent Acquisition., Mol Cell Proteomics, PMID 36470534

PXD033692 Dataset with its publication pending (from PRIDE)
Dataset title: Metaexoproteomics identifies active plant-microbe interactions operating in the rhizosphere
Possible reference: Lidbury, IDEA. et al. (2022) Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions., mSystems, PMID 35862821

PXD033687 Dataset with its publication pending (from PRIDE)
Dataset title: METATAXONOMIC AND METAPROTEOMIC PROFILING OF THE ORAL MICROBIOME IN ORAL LICHEN PLANUS
Possible reference: Bankvall, M. et al. (2023) Metataxonomic and metaproteomic profiling of the oral microbiome in oral lichen planus - a pilot study., J Oral Microbiol, PMID 36605405

PXD033673 Dataset with its publication pending (from PRIDE)
Dataset title: Neddylation tunes peripheral blood mononuclear cells immune response in COVID-19 patients
Possible reference: Serrano-Maci�, M. et al. (2022) Neddylation tunes peripheral blood mononuclear cells immune response in COVID-19 patients., Cell Death Discov, PMID 35831294

PXD033661 Dataset with its publication pending (from PRIDE)
Dataset title: Persistent Dysfunction of Innate Immune and Clotting Factors Detected in Saliva and Blood Plasma after COVID-19
Possible reference: Jang, H. et al. (2023) Persistent immune and clotting dysfunction detected in saliva and blood plasma after COVID-19., Heliyon, PMID 37483779

PXD033654 no publication (from MassIVE)
Dataset title: Streptomyces tenebrarius proteomics
Possible reference: Linardi, D. et al. (2022) Proteomining-Based Elucidation of Natural Product Biosynthetic Pathways in Streptomyces., Front Microbiol, PMID 35898901

PXD033644 Dataset with its publication pending (from PRIDE)
Dataset title: Transforming chemical proteomics into high-throughput method using SP2E workflow.
Possible reference: Becker, T. et al. (2022) Transforming Chemical Proteomics Enrichment into a High-Throughput Method Using an SP2E Workflow., JACS Au, PMID 35911458

PXD033616 Dataset with its publication pending (from PRIDE)
Dataset title: Druggable Serine Proteases of Leishmania by Activity‐Based Protein Profiling
Possible reference: Porta, EOJ. et al. (2022) Discovery of Leishmania Druggable Serine Proteases by Activity-Based Protein Profiling., Front Pharmacol, PMID 35910377

PXD033586 Dataset with its publication pending (from PRIDE)
Dataset title: The marine Bacteroidetes Muricauda sp. MAR_2010_75 digests diatom Î²-mannan
Possible reference: Beidler, I. et al. (2023) Marine bacteroidetes use a conserved enzymatic cascade to digest diatom β-mannan., ISME J, PMID 36411326

PXD033583 Dataset with its publication pending (from PRIDE)
Dataset title: RcgA and RcgR, two novel proteins involved in conjugative transfer of rhizobial plasmids
Possible reference: Castellani, LG. et al. (2022) RcgA and RcgR, Two Novel Proteins Involved in the Conjugative Transfer of Rhizobial Plasmids., mBio, PMID 36073816

PXD033571 no publication (from MassIVE)
Dataset title: Shared and distinctive neighborhoods of emerin and LBR revealed by proximity labeling and quantitative proteomics
Possible reference: Cheng, LC. et al. (2022) Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics., J Proteome Res, PMID 35972904

PXD033553 Dataset with its publication pending (from PRIDE)
Dataset title: Role of the two-component system CiaRH in the regulation of efflux pump SatAB and its correlation with fluoroquinolones susceptibility
Possible reference: Yang, X. et al. (2022) Role of the Two-Component System CiaRH in the Regulation of Efflux Pump SatAB and Its Correlation with Fluoroquinolone Susceptibility., Microbiol Spectr, PMID 35638854

PXD033545 Dataset with its publication pending (from PRIDE)
Dataset title: Naringenin Suppresses BEAS-2B-derived Exosomal Cargoes Disorder Caused by Cigarette Smoke Extract thereby Inhibiting M1 Macrophage Polarization
Possible reference: Chen, Z. et al. (2022) Naringenin suppresses BEAS-2B-derived extracellular vesicular cargoes disorder caused by cigarette smoke extract thereby inhibiting M1 macrophage polarization., Front Immunol, PMID 35924248

PXD033530 Dataset with its publication pending (from PRIDE)
Dataset title: PARP1-SNAI2 Transcription Axis Drives Resistance to PARP Inhibitor, Talazoparib
Possible reference: Ding, X. et al. (2022) PARP1-SNAI2 transcription axis drives resistance to PARP inhibitor, Talazoparib., Sci Rep, PMID 35864202

PXD033528 Dataset with its publication pending (from PRIDE)
Dataset title: A Conformation specific Nanobody Targeting the NMN-activated State of SARM1
Possible reference: Hou, YN. et al. (2022) A conformation-specific nanobody targeting the nicotinamide mononucleotide-activated state of SARM1., Nat Commun, PMID 36550129

PXD033509 Dataset with its publication pending (from PRIDE)
Dataset title: Interacting partners of Trypanosoma brucei RBSR1 and RBSR2
Possible reference: Waithaka, A. et al. (2022) Sequences and proteins that influence mRNA processing in Trypanosoma brucei: Evolutionary conservation of SR-domain and PTB protein functions., PLoS Negl Trop Dis, PMID 36288402

PXD033507 Dataset with its publication pending (from PRIDE)
Dataset title: Aedes aegypti CLIPB9 activates prophenoloxidase-3 in the presence of CLIPA14 after fungal infection
Possible reference: Ji, Y. et al. (2022) Aedes aegypti CLIPB9 activates prophenoloxidase-3 in the presence of CLIPA14 after fungal infection., Front Immunol, PMID 35967454

PXD033506 Dataset with its publication pending (from PRIDE)
Dataset title: GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance
Possible reference: Chen, W. et al. (2022) GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance., Nat Commun, PMID 36085149

PXD033488 Dataset with its publication pending (from PRIDE)
Dataset title: Human RIPK3 C-lobe phosphorylation is essential for necroptotic signaling
Possible reference: Meng, Y. et al. (2022) Human RIPK3 C-lobe phosphorylation is essential for necroptotic signaling., Cell Death Dis, PMID 35739084

PXD033476 Dataset with its publication pending (from PRIDE)
Dataset title: A proteomics approach reveals digestive and nutritional responses to food intake in anadromous Coilia nasus
Possible reference: Ma, F. et al. (2022) A proteomics approach reveals digestive and nutritional responses to food intake in anadromous Coilia nasus., Comp Biochem Physiol Part D Genomics Proteomics, PMID 35594610

PXD033468 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery and characterization of a new class of O-linking oligosaccharyltransferase from bacteria in the Moraxellaceae family
Possible reference: Knoot, CJ. et al. (2023) Discovery and characterization of a new class of O-linking oligosaccharyltransferases from the Moraxellaceae family., Glycobiology, PMID 36239418

PXD033461 Dataset with its publication pending (from iProX)
Dataset title: Proteomic and Phosphoproteomic Analyses Reveal Gibel Carp Responses to Cyprinid Herpesvirus 2 Infection
Possible reference: Xu, C. et al. (2022) Proteomic and Phosphoproteomic Analyses Reveal Gibel Carp Responses to Cyprinid Herpesvirus 2 Infection., J Proteome Res, PMID 35792615

PXD033459 Dataset with its publication pending (from PRIDE)
Dataset title: Native SEC-MS of the human HT29 colon adenocarcinoma cell line treated with the HSP90 inhibitor tanespimycin (17-AAG)
Possible reference: Samant, RS. et al. (2023) Native Size-Exclusion Chromatography-Based Mass Spectrometry Reveals New Components of the Early Heat Shock Protein 90 Inhibition Response Among Limited Global Changes., Mol Cell Proteomics, PMID 36549590

PXD033458 no publication (from MassIVE)
Dataset title: Histone malonylation is regulated by SIRT5 and KAT2A
Possible reference: Zhang, R. et al. (2023) Histone malonylation is regulated by SIRT5 and KAT2A., iScience, PMID 36879797

PXD033452 Dataset with its publication pending (from PRIDE)
Dataset title: SARS-CoV-2 proteins BioID in HEK293
Possible reference: Terracciano, R. et al. (2021) Mapping the SARS-CoV-2-Host Protein-Protein Interactome by Affinity Purification Mass Spectrometry and Proximity-Dependent Biotin Labeling: A Rational and Straightforward Route to Discover Host-Directed Anti-SARS-CoV-2 Therapeutics., Int J Mol Sci, PMID 33430309

PXD033449 Dataset with its publication pending (from PRIDE)
Dataset title: Integrative proteomic and physiological analyses of the molecular response to dessication-stress in Auricularia fibrillifera
Possible reference: Guo, H. et al. (2022) Integrative proteomic and physiological analyses of the molecular response to dessication-stress in Auricularia fibrillifera., Front Plant Sci, PMID 36212373

PXD033446 Dataset with its publication pending (from PRIDE)
Dataset title: Functional crosstalk between the cohesin loader and chromatin remodelers
Possible reference: Mu�oz, S. et al. (2022) Functional crosstalk between the cohesin loader and chromatin remodelers., Nat Commun, PMID 36509793

PXD033440 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of colonic primary cilia promotes inflammation and carcinogenesis
Possible reference: Paul, C. et al. (2022) Loss of primary cilia promotes inflammation and carcinogenesis., EMBO Rep, PMID 36281991

PXD033418 Dataset with its publication pending (from PRIDE)
Dataset title: Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits
Possible reference: Sasson, G. et al. (2022) Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits., ISME J, PMID 35974086

PXD033412 Dataset with its publication pending (from PRIDE)
Dataset title: Hepatic urea, creatinine and uric acid metabolism in dairy cows with divergent milk urea concentrations
Possible reference: Prahl, MC. et al. (2022) Hepatic urea, creatinine and uric acid metabolism in dairy cows with divergent milk urea concentrations., Sci Rep, PMID 36266429

PXD033407 Dataset with its publication pending (from PRIDE)
Dataset title: Selective modulation of cell surface proteins during vaccinia infection: a resource for identifying viral immune evasion strategies
Possible reference: Depierreux, DM. et al. (2022) Selective modulation of cell surface proteins during vaccinia infection: A resource for identifying viral immune evasion strategies., PLoS Pathog, PMID 35727847

PXD033403 Dataset with its publication pending (from jPOST)
Dataset title: Time series of E. coli whole proteomic analysis before and after severe heat shock
Possible reference: Shay, JW. et al. (2016) Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015., BMC Genomics, PMID 27454254

PXD033394 Dataset with its publication pending (from PRIDE)
Dataset title: Angel2 phosphatase activity is required for non-canonical mitochondrial RNA processing
Possible reference: Clemente, P. et al. (2022) ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing., Nat Commun, PMID 36180430

PXD033387 Dataset with its publication pending (from PRIDE)
Dataset title: Interactions between paralogous bacterial enhancer binding proteins enable metal-dependent regulation of alternative nitrogenases in Azotobacter vinelandii
Possible reference: Appia-Ayme, C. et al. (2022) Interactions between paralogous bacterial enhancer-binding proteins enable metal-dependent regulation of alternative nitrogenases in Azotobacter vinelandii., Mol Microbiol, PMID 35718936

PXD033375 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of differentially abundant proteins in sugarcane during red rot infection
Possible reference: Ashwin, NMR. et al. (2017) Comparative secretome analysis of Colletotrichum falcatum identifies a cerato-platanin protein (EPL1) as a potential pathogen-associated molecular pattern (PAMP) inducing systemic resistance in sugarcane., J Proteomics, PMID 28546091

PXD033362 Dataset with its publication pending (from jPOST)
Dataset title: Bioenergetic phenotyping of DEN-induced hepatocellular carcinoma reveals a link between adenylate kinase isoform expression and reduced complex I-supported respiration.
Possible reference: McLaughlin, KL. et al. (2022) Bioenergetic Phenotyping of DEN-Induced Hepatocellular Carcinoma Reveals a Link Between Adenylate Kinase Isoform Expression and Reduced Complex I-Supported Respiration., Front Oncol, PMID 35756609

PXD033356 Dataset with its publication pending (from PRIDE)
Dataset title: NCOA4-mediated ferritinophagy is a pancreatic cancer dependency via maintenance of iron bioavailability for iron-sulfur cluster proteins
Possible reference: Santana-Codina, N. et al. (2022) NCOA4-Mediated Ferritinophagy Is a Pancreatic Cancer Dependency via Maintenance of Iron Bioavailability for Iron-Sulfur Cluster Proteins., Cancer Discov, PMID 35771492

PXD033353 Dataset with its publication pending (from PRIDE)
Dataset title: UHMK1 is a novel splicing regulatory kinase
Possible reference: Arfelli, VC. et al. (2023) UHMK1 is a novel splicing regulatory kinase., J Biol Chem, PMID 36803961

PXD033351 Dataset with its publication pending (from PRIDE)
Dataset title: Pan-cancer tumor-specific antigens and membrane targets from transposable elements
Possible reference: Shah, NM. et al. (2023) Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements., Nat Genet, PMID 36973455

PXD033348 Dataset with its publication pending (from PRIDE)
Dataset title: A toolbox for systematic discovery of stable and transient protein interactors in baker’s yeast
Possible reference: Fenech, EJ. et al. (2023) A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast., Mol Syst Biol, PMID 36651308

PXD033341 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of lysine succinylome and acetylome in vancomycin-intermediate Staphylococcus aureus XN108
Possible reference: Tan, L. et al. (2022) Identification of Lysine Succinylome and Acetylome in the Vancomycin-Intermediate Staphylococcus aureus XN108., Microbiol Spectr, PMID 36374118

PXD033334 Dataset with its publication pending (from PRIDE)
Dataset title: Human RNase 4 Improves mRNA Sequence Characterization by LC-MS/MS.
Possible reference: Wolf, EJ. et al. (2022) Human RNase 4 improves mRNA sequence characterization by LC-MS/MS., Nucleic Acids Res, PMID 35871301

PXD033277 Dataset with its publication pending (from jPOST)
Dataset title: Antibiotic-like Activity of Atomic Layer Boron Nitride for Combating Resistant Bacteria
Possible reference: Pan, Y. et al. (2022) Antibiotic-Like Activity of Atomic Layer Boron Nitride for Combating Resistant Bacteria., ACS Nano, PMID 35511445

PXD033257 Dataset with its publication pending (from PRIDE)
Dataset title: Unveiling the mechanism of action of nature-inspired anti-cancer compounds using a multi-Omics approach
Possible reference: Soares, NC. et al. (2022) Unveiling the mechanism of action of nature-inspired anti-cancer compounds using a multi-omics approach., J Proteomics, PMID 35728772

PXD033250 Dataset with its publication pending (from PRIDE)
Dataset title: Virulence induction in Pseudomonas aeruginosa under inorganic phosphate limitation: a proteomics perspective
Possible reference: Matilla, MA. et al. (2022) Virulence Induction in Pseudomonas aeruginosa under Inorganic Phosphate Limitation: a Proteomics Perspective., Microbiol Spectr, PMID 36354317

PXD033249 Dataset with its publication pending (from PRIDE)
Dataset title: Silent recognition by Toll-like receptor 5 of flagellins from human gut commensal bacteria
Possible reference: Clasen, SJ. et al. (2023) Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5., Sci Immunol, PMID 36608151

PXD033230 Dataset with its publication pending (from PRIDE)
Dataset title: Glycosaminoglycan linkage region of urinary bikunin as a potentially useful biomarker for Î²3GalT6-deficient spondylodysplastic Ehlers-Danlos syndrome
Possible reference: Nikpour, M. et al. (2022) Glycosaminoglycan linkage region of urinary bikunin as a potentially useful biomarker for β3GalT6-deficient spondylodysplastic Ehlers-Danlos syndrome., JIMD Rep, PMID 36101818

PXD033226 Dataset with its publication pending (from PRIDE)
Dataset title: Enrichment and Fragmentation Approaches for Enhanced Detection and Characterization of Endogenous Glycosylated Neuropeptides
Possible reference: Phetsanthad, A. et al. (2023) Enrichment and fragmentation approaches for enhanced detection and characterization of endogenous glycosylated neuropeptides., Proteomics, PMID 35906894

PXD033218 Dataset with its publication pending (from iProX)
Dataset title: Data-Independent Acquisition-Based Mass Spectrometry (DIA-MS) for Quantitative Analysis of Human Intestinal Ischemia/reperfusion
Possible reference: Huang, A. et al. (2022) Data-Independent Acquisition-Based Mass Spectrometry (DIA-MS) for Quantitative Analysis of Human Intestinal Ischemia/Reperfusion., Appl Biochem Biotechnol, PMID 35666382

PXD033157 Dataset with its publication pending (from PRIDE)
Dataset title: Evidence for a widespread third system for bacterial polysaccharide export across the outer membrane comprising a composite OPX/Î²-barrel translocon
Possible reference: Schwabe, J. et al. (2022) Evidence for a Widespread Third System for Bacterial Polysaccharide Export across the Outer Membrane Comprising a Composite OPX/β-Barrel Translocon., mBio, PMID 35972145

PXD033155 no publication (from MassIVE)
Dataset title: Proteomic insight into the interaction of Paenibacillus larvae with honey bee larvae before capping collected from an American foulbrood outbreak
Possible reference: Erban, T. et al. (2023) Proteomic insight into the interaction of Paenibacillus larvae with honey bee larvae before capping collected from an American foulbrood outbreak: Pathogen proteins within the host, lysis signatures and interaction markers., Proteomics, PMID 35946602

PXD033125 Dataset with its publication pending (from PRIDE)
Dataset title: GRAMD1C regulates autophagy initiation and mitochondrial bioenergetics
Possible reference: Ng, MYW. et al. (2022) The cholesterol transport protein GRAMD1C regulates autophagy initiation and mitochondrial bioenergetics., Nat Commun, PMID 36270994

PXD033120 Dataset with its publication pending (from PRIDE)
Dataset title: The protein phosphatase 2A holoenzyme is a key regulator of starch metabolism and bradyzoite differentiation in Toxoplasma gondii
Possible reference: Wang, JL. et al. (2022) The protein phosphatase 2A holoenzyme is a key regulator of starch metabolism and bradyzoite differentiation in Toxoplasma gondii., Nat Commun, PMID 36476594

PXD033117 Dataset with its publication pending (from PRIDE)
Dataset title: Effect of Sample Transportation on the Proteome of Human Circulating Blood Extracellular Vesicles
Possible reference: Uldry, AC. et al. (2022) Effect of Sample Transportation on the Proteome of Human Circulating Blood Extracellular Vesicles., Int J Mol Sci, PMID 35562906

PXD033106 no publication (from MassIVE)
Dataset title: HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery
Possible reference: Stražar, M. et al. (2023) HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery., Immunity, PMID 37301199

PXD033102 Dataset with its publication pending (from PRIDE)
Dataset title: Light Quality Modulates Plant Cold Response and Freezing Tolerance
Possible reference: Kinmonth-Schultz, HA. et al. (2013) Circadian clock-regulated physiological outputs: dynamic responses in nature., Semin Cell Dev Biol, PMID 23435352

PXD033071 Dataset with its publication pending (from PRIDE)
Dataset title: E. coli toxin YjjJ (HipH) is a Ser/Thr protein kinase that impacts cell division, carbon metabolism and ribosome assembly
Possible reference: Gratani, FL. et al. (2023) E. coli Toxin YjjJ (HipH) Is a Ser/Thr Protein Kinase That Impacts Cell Division, Carbon Metabolism, and Ribosome Assembly., mSystems, PMID 36537800

PXD033068 Dataset with its publication pending (from PRIDE)
Dataset title: The chromatin-regulating CoREST complex is animal specific and essential for development in the cnidarian Nematostella vectensis
Possible reference: Gahan, JM. et al. (2022) A developmental role for the chromatin-regulating CoREST complex in the cnidarian Nematostella vectensis., BMC Biol, PMID 35999597

PXD033067 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping subcellular localizations of unannotated microproteins with MicroID
Possible reference: Na, Z. et al. (2022) Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID., Mol Cell, PMID 35905735

PXD033064 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondria regulate intracellular coenzyme Q transport and ferroptotic resistance via STARD7
Possible reference: Deshwal, S. et al. (2023) Mitochondria regulate intracellular coenzyme Q transport and ferroptotic resistance via STARD7., Nat Cell Biol, PMID 36658222

PXD033059 Dataset with its publication pending (from PRIDE)
Dataset title: SDR enzymes oxidize specific lipidic alkynylcarbinols into cytotoxic protein-reactive species
Possible reference: Demange, P. et al. (2022) SDR enzymes oxidize specific lipidic alkynylcarbinols into cytotoxic protein-reactive species., Elife, PMID 35535493

PXD033053 Dataset with its publication pending (from PRIDE)
Dataset title: Fish hydrolysate supplementation prevents stress-induced dysregulation of hippocampal proteins relative to mitochondrial metabolism and neuronal network in mice
Possible reference: Le Faouder, J. et al. (2022) Fish Hydrolysate Supplementation Prevents Stress-Induced Dysregulation of Hippocampal Proteins Relative to Mitochondrial Metabolism and the Neuronal Network in Mice., Foods, PMID 35681342

PXD033045 Dataset with its publication pending (from PRIDE)
Dataset title: Nucleoporins facilitate ORC loading onto chromatin
Possible reference: Richards, L. et al. (2022) Nucleoporins facilitate ORC loading onto chromatin., Cell Rep, PMID 36351393

PXD033042 Dataset with its publication pending (from PRIDE)
Dataset title: p166 links membrane and intramitochondrial modules of the trypanosomal tripartite attachment complex
Possible reference: Schimanski, B. et al. (2022) p166 links membrane and intramitochondrial modules of the trypanosomal tripartite attachment complex., PLoS Pathog, PMID 35709300

PXD033036 Dataset with its publication pending (from PRIDE)
Dataset title: Photo-ANA enables profiling of host–bacteria protein interactions during infection
Possible reference: Li, XM. et al. (2023) Photo-ANA enables profiling of host-bacteria protein interactions during infection., Nat Chem Biol, PMID 36702958

PXD033029 Dataset with its publication pending (from PRIDE)
Dataset title: Mouse PolG Mutant Liver Proteome
Possible reference: Trease, AJ. et al. (2024) Mitochondrial DNA Instability Supersedes Parkin Mutations in Driving Mitochondrial Proteomic Alterations and Functional Deficits in Polg Mutator Mice., Int J Mol Sci, PMID 38928146

PXD033022 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping glucose uptake, transport and metabolism in the bovine lens
Possible reference: Zahraei, A. et al. (2021) Mapping glucose metabolites in the normal bovine lens: Evaluation and optimisation of a matrix-assisted laser desorption/ionisation imaging mass spectrometry method., J Mass Spectrom, PMID 33089566

PXD033012 Dataset with its publication pending (from PRIDE)
Dataset title: Regionally defined proteomic profiles of human cerebral tissue and organoids reveal conserved molecular modules of neurodevelopment
Possible reference: Melliou, S. et al. (2022) Regionally defined proteomic profiles of human cerebral tissue and organoids reveal conserved molecular modules of neurodevelopment., Cell Rep, PMID 35613588

PXD033010 Dataset with its publication pending (from PRIDE)
Dataset title: Lung macrophages utilize unique cathepsin K-dependent phagosomal machinery to degrade intracellular collagen
Possible reference: Fabrik, I. et al. (2023) Lung macrophages utilize unique cathepsin K-dependent phagosomal machinery to degrade intracellular collagen., Life Sci Alliance, PMID 36697252

PXD033006 Dataset with its publication pending (from PRIDE)
Dataset title: Placental macrophage (Hofbauer cell) response to viral and bacterial ligands is influenced by fetal sex
Possible reference: Pantazi, P. et al. (2022) Placental macrophage responses to viral and bacterial ligands and the influence of fetal sex., iScience, PMID 36505933

PXD033000 Dataset with its publication pending (from PRIDE)
Dataset title: Neuropeptidome of Zophobas atratus
Possible reference: Marciniak, P. et al. (2022) Neuropeptidomes of Tenebrio molitor L. and Zophobas atratus Fab. (Coleoptera, Polyphaga: Tenebrionidae)., J Proteome Res, PMID 36107737

PXD032975 Dataset with its publication pending (from PRIDE)
Dataset title: dCas9 targeted chromatin and histone enrichment for mass spectrometry (Catchet-MS) identifies IKZF1 as a novel target for HIV-1 latency reversal
Possible reference: Ne, E. et al. (2022) Catchet-MS identifies IKZF1-targeting thalidomide analogues as novel HIV-1 latency reversal agents., Nucleic Acids Res, PMID 35640596

PXD032956 Dataset with its publication pending (from PRIDE)
Dataset title: SUMOylation controls the rapid transcriptional reprogramming induced by chemotherapies in Acute Myeloid Leukemias
Possible reference: Boulanger, M. et al. (2023) DeSUMOylation of chromatin-bound proteins limits the rapid transcriptional reprogramming induced by daunorubicin in acute myeloid leukemias., Nucleic Acids Res, PMID 37462077

PXD032954 Dataset with its publication pending (from PRIDE)
Dataset title: mCherry contains a fluorescent protein isoform that interferes with its reporter function
Possible reference: Fages-Lartaud, M. et al. (2022) mCherry contains a fluorescent protein isoform that interferes with its reporter function., Front Bioeng Biotechnol, PMID 36017355

PXD032947 Dataset with its publication pending (from PRIDE)
Dataset title: Neuropeptidome of Tenebrio molitor
Possible reference: Marciniak, P. et al. (2022) Neuropeptidomes of Tenebrio molitor L. and Zophobas atratus Fab. (Coleoptera, Polyphaga: Tenebrionidae)., J Proteome Res, PMID 36107737

PXD032925 Dataset with its publication pending (from PRIDE)
Dataset title: Distinct roles of the two Elongator subcomplexes during neurodevelopment
Possible reference: Gaik, M. et al. (2023) Elongator and the role of its subcomplexes in human diseases., EMBO Mol Med, PMID 36448458

PXD032924 Dataset with its publication pending (from PRIDE)
Dataset title: Simple and Fast Maximally Deuterated Control (maxD) preparation for HDX MS Experiments
Possible reference: Peterle, D. et al. (2022) Simple and Fast Maximally Deuterated Control (maxD) Preparation for Hydrogen-Deuterium Exchange Mass Spectrometry Experiments., Anal Chem, PMID 35796687

PXD032913 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance
Possible reference: Fazakerley, DJ. et al. (2023) Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance., Nat Commun, PMID 36808134

PXD032877 Josiah Hardesty, Le Day, Jeffrey Warner, Dennis Warner, Marina Gritsenko, Aliya Asghar, Andrew Stolz, Timothy Morgan, Craig McClain, Jon Jacobs, Irina Kirpich. Hepatic Protein and Phosphoprotein Signatures of Alcohol-Associated Cirrhosis and Hepatitis. Am (from MassIVE)
Dataset title: Hepatic protein and phosphoprotein signatures of alcohol-associated cirrhosis and hepatitis
Possible reference: Hardesty, J. et al. (2022) Hepatic Protein and Phosphoprotein Signatures of Alcohol-Associated Cirrhosis and Hepatitis., Am J Pathol, PMID 35490715

PXD032867 Dataset with its publication pending (from jPOST)
Dataset title: Proteome-wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves
Possible reference: Tilak, P. et al. (2023) Proteome-wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves., Plant J, PMID 36961081

PXD032858 Dataset with its publication pending (from iProX)
Dataset title: Metaproteomics on the Beishiku Sandstone Temple in Northwest China
Possible reference: Wu, F. et al. (2023) Metagenomic and metaproteomic insights into the microbiome and the key geobiochemical potentials on the sandstone of rock-hewn Beishiku Temple in Northwest China., Sci Total Environ, PMID 37285993

PXD032840 no publication (from MassIVE)
Dataset title: Interaction of Bartonella henselae with fibronectin represents the molecular basis for adhesion to host cells
Possible reference: Vaca, DJ. et al. (2022) Interaction of Bartonella henselae with Fibronectin Represents the Molecular Basis for Adhesion to Host Cells., Microbiol Spectr, PMID 35435766

PXD032836 Dataset with its publication pending (from PRIDE)
Dataset title: Distinct proteostasis states drive pharmacologic chaperone susceptibility for Cystic Fibrosis Transmembrane Conductance Regulator misfolding mutants
Possible reference: McDonald, EF. et al. (2022) Distinct proteostasis states drive pharmacologic chaperone susceptibility for cystic fibrosis transmembrane conductance regulator misfolding mutants., Mol Biol Cell, PMID 35389766

PXD032824 Dataset with its publication pending (from PRIDE)
Dataset title: Sphingomyelin phodiesterase acid-like 3A promotes hepatocellular carcinoma growth through the enhancer of rudimentary homologSphingomyelin phodiesterase acid-like 3A promotes hepatocellular carcinoma growth through the enhancer of rudimentary homolog
Possible reference: Zhang, Y. et al. (2022) Sphingomyelin Phodiesterase Acid-Like 3A Promotes Hepatocellular Carcinoma Growth Through the Enhancer of Rudimentary Homolog., Front Oncol, PMID 35686107

PXD032794 Dataset with its publication pending (from PRIDE)
Dataset title: Antimicrobial potential of a ponericin-like peptide isolated from Bombyx mori L. hemolymph in response to Pseudomonas aeruginosa infection
Possible reference: Nesa, J. et al. (2022) Antimicrobial potential of a ponericin-like peptide isolated from Bombyx mori L. hemolymph in response to Pseudomonas aeruginosa infection., Sci Rep, PMID 36109567

PXD032792 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated Multi-Omics Reveal Polycomb Repressive Complex 2 Restricts Human Trophoblast Induction
Possible reference: Zijlmans, DW. et al. (2022) Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction., Nat Cell Biol, PMID 35697783

PXD032787 Dataset with its publication pending (from PRIDE)
Dataset title: Rhodnius prolixus hemolymph proteome
Possible reference: Ouali, R. et al. (2022) Rhodnius prolixus Hemolymph Immuno-Physiology: Deciphering the Systemic Immune Response Triggered by Trypanosoma cruzi Establishment in the Vector Using Quantitative Proteomics., Cells, PMID 35563760

PXD032786 Dataset with its publication pending (from PRIDE)
Dataset title: Sequence Coverage Visualizer: A web application for protein sequence coverage 3D visualization
Possible reference: Shao, X. et al. (2023) Sequence Coverage Visualizer: A Web Application for Protein Sequence Coverage 3D Visualization., J Proteome Res, PMID 36511722

PXD032762 Dataset with its publication pending (from PRIDE)
Dataset title: Sideroflexin 4 is a Complex I assembly factor that interacts with the MCIA complex and is required for the assembly of the ND2 module
Possible reference: Jackson, TD. et al. (2022) Sideroflexin 4 is a complex I assembly factor that interacts with the MCIA complex and is required for the assembly of the ND2 module., Proc Natl Acad Sci U S A, PMID 35333655

PXD032708 no publication (from MassIVE)
Dataset title: Multi-omic profiling of the leukemic microenvironment shows bone marrow interstitial fluid is distinct from peripheral blood
Possible reference: Nierves, L. et al. (2022) Multi-omic profiling of the leukemic microenvironment shows bone marrow interstitial fluid is distinct from peripheral blood plasma., Exp Hematol Oncol, PMID 36109804

PXD032703 Dataset with its publication pending (from jPOST)
Dataset title: Characterization of oligopeptides in Solanum lycopersicum xylem exudates
Possible reference: Okamoto, S. et al. (2022) Characterization of Oligopeptides in Solanum lycopersicum Xylem Exudates., Life (Basel), PMID 35455083

PXD032693 no publication (from MassIVE)
Dataset title: Targeting LIPA Independent of its Lipase Activity is a Therapeutic Strategy in Solid Tumors via Induction of Endoplasmic Reticulum Stress
Possible reference: Liu, X. et al. (2022) Targeting LIPA independent of its lipase activity is a therapeutic strategy in solid tumors via induction of endoplasmic reticulum stress., Nat Cancer, PMID 35654861

PXD032688 Dataset with its publication pending (from PRIDE)
Dataset title: Mechano-redox control of Mac-1 de-adhesion from ICAM-1 by protein disulfide isomerase promotes directional movement under flow
Possible reference: Dupuy, A. et al. (2023) Mechano-Redox Control of Mac-1 De-Adhesion by PDI Promotes Directional Movement Under Flow., Circ Res, PMID 37021588

PXD032389 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics of tau and AÎ² amyloid in detergent insoluble fractions from Alzheimerâs disease brains
Possible reference: Thygesen, C. et al. (2018) Age-Dependent Changes in the Sarkosyl-Insoluble Proteome of APPSWE/PS1ΔE9 Transgenic Mice Implicate Dysfunctional Mitochondria in the Pathogenesis of Alzheimer's Disease., J Alzheimers Dis, PMID 29991132

PXD032379 Dataset with its publication pending (from jPOST)
Dataset title: Analysis of Viral Spike Protein N-glycosylation using Ultraviolet Photodissociation Mass Spectrometry
Possible reference: Escobar, EE. et al. (2022) Analysis of Viral Spike Protein N-Glycosylation Using Ultraviolet Photodissociation Mass Spectrometry., Anal Chem, PMID 35388686

PXD032378 Dataset with its publication pending (from PRIDE)
Dataset title: A palmitoyl transferase chemical genetic system to map ZDHHC-specific S-acylation
Possible reference: Ocasio, CA. et al. (2024) A palmitoyl transferase chemical-genetic system to map ZDHHC-specific S-acylation., Nat Biotechnol, PMID 38191663

PXD032374 Dataset with its publication pending (from PRIDE)
Dataset title: Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons
Possible reference: Macdonald, L. et al. (2022) Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons., Elife, PMID 35736539

PXD032373 Dataset with its publication pending (from PRIDE)
Dataset title: A palmitoyl transferase chemical genetic system to map ZDHHC-specific S-acylation
Possible reference: Ocasio, CA. et al. (2024) A palmitoyl transferase chemical-genetic system to map ZDHHC-specific S-acylation., Nat Biotechnol, PMID 38191663

PXD032372 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics of tau and AÎ² amyloid in detergent insoluble fractions from Alzheimerâs disease brains
Possible reference: Thygesen, C. et al. (2018) Age-Dependent Changes in the Sarkosyl-Insoluble Proteome of APPSWE/PS1ΔE9 Transgenic Mice Implicate Dysfunctional Mitochondria in the Pathogenesis of Alzheimer's Disease., J Alzheimers Dis, PMID 29991132

PXD032365 Dataset with its publication pending (from PRIDE)
Dataset title: The diverse susceptibilities and responses of human and rodent cells to orthohantavirus infection reveal different levels of cellular restriction
Possible reference: Gallo, G. et al. (2022) Diverse susceptibilities and responses of human and rodent cells to orthohantavirus infection reveal different levels of cellular restriction., PLoS Negl Trop Dis, PMID 36223391

PXD032358 Dataset with its publication pending (from PRIDE)
Dataset title: Genetic and chemical validation of Plasmodium falciparum aminopeptidase PfA-M17 as a drug target in the hemoglobin digestion pathway
Possible reference: Edgar, RCS. et al. (2022) Genetic and chemical validation of Plasmodium falciparum aminopeptidase PfA-M17 as a drug target in the hemoglobin digestion pathway., Elife, PMID 36097817

PXD032356 Dataset with its publication pending (from PRIDE)
Dataset title: FLEXIBLE AND DIGESTIBLE WOOD CAUSED BY VIRAL-INDUCED ALTERATION OF CELL WALL COMPOSITION
Possible reference: Allen, H. et al. (2022) Flexible and digestible wood caused by viral-induced alteration of cell wall composition., Curr Biol, PMID 35732179

PXD032328 Dataset with its publication pending (from PRIDE)
Dataset title: TMEM260 is a protein-specific O-mannosyltransferase
Possible reference: Larsen, ISB. et al. (2023) The SHDRA syndrome-associated gene TMEM260 encodes a protein-specific O-mannosyltransferase., Proc Natl Acad Sci U S A, PMID 37186866

PXD032327 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic changes associated with maternal dietary low Ï6:Ï3 ratio in piglets supplemented with seaweed Part I: Serum proteomes
Possible reference: Nguyen, TX. et al. (2023) Proteomic changes associated with maternal dietary low ω6:ω3 ratio in piglets supplemented with seaweed. Part I: Serum proteomes., J Proteomics, PMID 36191802

PXD032322 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic and functional analysis of the effects of quinoxaline derivatives on Entamoeba histolytica
Possible reference: Avila-Bonilla, RG. et al. (2022) Proteomic and Functional Analysis of the Effects of Quinoxaline Derivatives on Entamoeba histolytica., Front Cell Infect Microbiol, PMID 35832378

PXD032320 Dataset with its publication pending (from PRIDE)
Dataset title: Cell autonomous immune dysfunction driven by disrupted autophagy in C9orf72-ALS microglia contributes to neurodegeneration
Possible reference: Banerjee, P. et al. (2023) Cell-autonomous immune dysfunction driven by disrupted autophagy in C9orf72-ALS iPSC-derived microglia contributes to neurodegeneration., Sci Adv, PMID 37083530

PXD032318 Dataset with its publication pending (from PRIDE)
Dataset title: Kaposi’s sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs
Possible reference: Murphy, JC. et al. (2023) Kaposi's sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs., Nat Commun, PMID 36653366

PXD032312 Dataset with its publication pending (from PRIDE)
Dataset title: Temporal Quantitative Proteomic Profiling of Murine Embryonic Heart Development
Possible reference: Edwards, W. et al. (2023) Quantitative proteomic profiling identifies global protein network dynamics in murine embryonic heart development., Dev Cell, PMID 37148880

PXD032270 Dataset with its publication pending (from PRIDE)
Dataset title: The role of testosterone in spermatogenesis: lessons from proteome profiling of human spermatozoa in testosterone deficiency
Possible reference: Grande, G. et al. (2022) The Role of Testosterone in Spermatogenesis: Lessons From Proteome Profiling of Human Spermatozoa in Testosterone Deficiency., Front Endocrinol (Lausanne), PMID 35663320

PXD032249 no publication (from MassIVE)
Dataset title: Octreotide-induced changes in the saliva proteome
Possible reference: Cohen, J. et al. (2023) Octreotide may improve pharyngocutaneous fistula healing through downregulation of cystatins: A pilot study., Laryngoscope Investig Otolaryngol, PMID 36846407

PXD032239 Dataset with its publication pending (from PRIDE)
Dataset title: A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo
Possible reference: Kofink, C. et al. (2022) A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo., Nat Commun, PMID 36216795

PXD032236 Dataset with its publication pending (from PRIDE)
Dataset title: Memory CD8+ T cells upregulate glycolysis and effector functions under limiting oxygen conditions
Possible reference: Beumer-Chuwonpad, A. et al. (2023) Memory CD8+ T cells upregulate glycolysis and effector functions under limiting oxygen conditions., Eur J Immunol, PMID 36482267

PXD032235 Dataset with its publication pending (from PRIDE)
Dataset title: Pitfalls and Solutions in Mass Spectrometry-based Identification of Protein Glycation
Possible reference: Ma, W. et al. (2023) Pitfalls and Solutions in Mass Spectrometry-Based Identification of Protein Glycation., Anal Chem, PMID 36630282

PXD032234 Dataset with its publication pending (from PRIDE)
Dataset title: Cellular and culture medium proteomes from umbilical cord mesenchymal stem cell and human umbilical vein endothelial cells
Possible reference: Vieira de Castro, J. et al. (2017) Impact of mesenchymal stem cells' secretome on glioblastoma pathophysiology., J Transl Med, PMID 28969635

PXD032215 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic analysis of whole protein in three melanoma samples of 92.1, 92.1-A and 92.1-B
Possible reference: Fei, X. et al. (2022) Quantitative proteomic dataset of whole protein in three melanoma samples of 92.1, 92.1-A and 92.1-B., Data Brief, PMID 36164296

PXD032188 Dataset with its publication pending (from PRIDE)
Dataset title: Signalling Inhibition by Ponatinib Disrupts Productive Alternative Lengthening of Telomeres (ALT)
Possible reference: Kusuma, FK. et al. (2023) Signalling inhibition by ponatinib disrupts productive alternative lengthening of telomeres (ALT)., Nat Commun, PMID 37024489

PXD032185 Dataset with its publication pending (from PRIDE)
Dataset title: The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism
Possible reference: van Ruiten, MS. et al. (2022) The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism., Nat Struct Mol Biol, PMID 35710836

PXD032184 Dataset with its publication pending (from PRIDE)
Dataset title: Pramel7-Cul2 axis establishes ground-state gene expression in embryonic stem cells
Possible reference: Yang, SH. et al. (2014) Otx2 and Oct4 drive early enhancer activation during embryonic stem cell transition from naive pluripotency., Cell Rep, PMID 24931607

PXD032166 Dataset with its publication pending (from PRIDE)
Dataset title: Exposure of a bovine rumen microbiome model to glyphosate
Possible reference: Riede, S. et al. (2016) Investigations on the possible impact of a glyphosate-containing herbicide on ruminal metabolism and bacteria in�vitro by means of the 'Rumen Simulation Technique'., J Appl Microbiol, PMID 27230806

PXD032161 Dataset with its publication pending (from PRIDE)
Dataset title: Cell type-specific biotin labeling in vivo resolves regional neuronal and astrocyte proteomic differences in mouse brain
Possible reference: Rayaprolu, S. et al. (2022) Cell type-specific biotin labeling in vivo resolves regional neuronal and astrocyte proteomic differences in mouse brain., Nat Commun, PMID 35614064

PXD032153 Dataset with its publication pending (from PRIDE)
Dataset title: Apoptotic brown adipocytes enhance energy expenditure via SLC29A1-regulated extracellular inosine
Possible reference: Niemann, B. et al. (2022) Apoptotic brown adipocytes enhance energy expenditure via extracellular inosine., Nature, PMID 35790189

PXD032142 Dataset with its publication pending (from jPOST)
Dataset title: Label free quantification of LC-MS analysis of Dental pulp cells
Possible reference: Zainol Abidin, IZ. et al. (2023) Label-free Quantitative Proteomic Analysis of Ascorbic Acid-induced Differentially Expressed Osteoblast-related Proteins in Dental Pulp Stem Cells from Deciduous and Permanent Teeth., Curr Stem Cell Res Ther, PMID 35762553

PXD032141 Dataset with its publication pending (from PRIDE)
Dataset title: Influence of sex, age and diabetes on brain transcriptome and proteome modifications following cerebral ischemia
Possible reference: Ramiro, L. et al. (2023) Influence of sex, age and diabetes on brain transcriptome and proteome modifications following cerebral ischemia., BMC Neurosci, PMID 36707762

PXD032132 Dataset with its publication pending (from PRIDE)
Dataset title: Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology
Possible reference: Zhu, Y. et al. (2024) Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies., Nat Commun, PMID 38632225

PXD032129 Dataset with its publication pending (from iProX)
Dataset title: Circadian rhythm disturbance mediates adipose tissue protein analysis in mice
Possible reference: Barclay, JL. et al. (2013) High-fat diet-induced hyperinsulinemia and tissue-specific insulin resistance in Cry-deficient mice., Am J Physiol Endocrinol Metab, PMID 23531614

PXD032093 Dataset with its publication pending (from iProX)
Dataset title: ILF3 safeguards telomere from aberrant homologous recombination as a telomeric R-loop reader
Possible reference: Wang, C. et al. (2024) ILF3 safeguards telomeres from aberrant homologous recombination as a telomeric R-loop reader., Protein Cell, PMID 37991243

PXD032082 Dataset with its publication pending (from PRIDE)
Dataset title: Metabolomic and Proteomic and Revealed Differences in the Distribution and Synthesis Mechanism of Aroma Precursors in Tobacco Leaf, Stem, and Root at Seedling Stage
Possible reference: Liu, A. et al. (2022) Proteomic and Metabolomic Revealed Differences in the Distribution and Synthesis Mechanism of Aroma Precursors in Yunyan 87 Tobacco Leaf, Stem, and Root at the Seedling Stage., ACS Omega, PMID 36157728

PXD032081 Dataset with its publication pending (from PRIDE)
Dataset title: Peptide of Trichinella spiralis infective larval extract that harnesses growth of human hepatoma cells
Possible reference: Ruenchit, P. et al. (2022) Peptide of Trichinella spiralis Infective Larval Extract That Harnesses Growth of Human Hepatoma Cells., Front Cell Infect Microbiol, PMID 35558100

PXD032072 Dataset with its publication pending (from PRIDE)
Dataset title: The PripA-TbcrA complex-centered Rab GAP cascade facilitates macropinosome maturation in Dictyostelium
Possible reference: Tu, H. et al. (2022) The PripA-TbcrA complex-centered Rab GAP cascade facilitates macropinosome maturation in Dictyostelium., Nat Commun, PMID 35379834

PXD032052 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of substrates of palmitoyl protein thioesterase 1 highlights roles of depalmitoylation in disulfide bond formation and synaptic function
Possible reference: Gorenberg, EL. et al. (2022) Identification of substrates of palmitoyl protein thioesterase 1�highlights roles of depalmitoylation in disulfide bond formation and synaptic function., PLoS Biol, PMID 35358180

PXD032030 Dataset with its publication pending (from PRIDE)
Dataset title: Allosteric HSP70 inhibitors in Proteasome Inhibitor Resistant Multiple Myeloma
Possible reference: Ferguson, ID. et al. (2022) Allosteric HSP70 inhibitors perturb mitochondrial proteostasis and overcome proteasome inhibitor resistance in multiple myeloma., Cell Chem Biol, PMID 35853457

PXD032028 Dataset with its publication pending (from PRIDE)
Dataset title: Requirement of hepatic pyruvate carboxylase during fasting, high fat and ketogenic diet
Possible reference: Selen, ES. et al. (2022) Requirement of hepatic pyruvate carboxylase during fasting, high fat, and ketogenic diet., J Biol Chem, PMID 36441025

PXD032000 no publication (from MassIVE)
Dataset title: A mass spectrometry-based atlas of extracellular matrix proteins across 25 mouse organs
Possible reference: McCabe, MC. et al. (2023) Mass Spectrometry-Based Atlas of Extracellular Matrix Proteins across 25 Mouse Organs., J Proteome Res, PMID 36763087

PXD031989 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic comparison of Biomphalaria glabrata excretory-secretory proteins at different time-points of Schistosoma mansoni infection
Possible reference: Fogarty, CE. et al. (2022) Identification of Schistosoma mansoni miracidia attractant candidates in infected Biomphalaria glabrata using behaviour-guided comparative proteomics., Front Immunol, PMID 36300127

PXD031979 Dataset with its publication pending (from iProX)
Dataset title: Multi-platform omics analysis reveals molecular signatures for pathogenesis and activity of systemic lupus erythematosus
Possible reference: Huang, X. et al. (2022) Multi-Platform Omics Analysis Reveals Molecular Signatures for Pathogenesis and Activity of Systemic Lupus Erythematosus., Front Immunol, PMID 35514958

PXD031974 Dataset with its publication pending (from PRIDE)
Dataset title: Shotgun analysis of serum proteome on Schistosoma mansoni infection
Possible reference: Gon�alves-Silva, G. et al. (2022) Profiling the serum proteome during Schistosoma mansoni infection in the BALB/c mice: A focus on the altered lipid metabolism as a key modulator of host-parasite interactions., Front Immunol, PMID 36119112

PXD031972 Dataset with its publication pending (from PRIDE)
Dataset title: Protection of nascent DNA at stalled replication forks is mediated by phosphorylation of RIF1 intrinsically disordered region
Possible reference: Balasubramanian, S. et al. (2022) Protection of nascent DNA at stalled replication forks is mediated by phosphorylation of RIF1 intrinsically disordered region., Elife, PMID 35416772

PXD031964 Dataset with its publication pending (from PRIDE)
Dataset title: UBQLN2 restrains the domesticated retrotransposon PEG10 to maintain neuronal health in ALS
Possible reference: Black, HH. et al. (2023) UBQLN2 restrains the domesticated retrotransposon PEG10 to maintain neuronal health in ALS., Elife, PMID 36951542

PXD031959 Dataset with its publication pending (from jPOST)
Dataset title: Quantitative proteomics reveals metabolic reprogramming in host cells induced by trophozoites and intermediate subunit of Gal/GalNAc lectins from Entamoeba histolytica
Possible reference: Zhao, Y. et al. (2022) Quantitative Proteomics Reveals Metabolic Reprogramming in Host Cells Induced by Trophozoites and Intermediate Subunit of Gal/GalNAc Lectins from Entamoeba histolytica., mSystems, PMID 35343800

PXD031949 no publication (from MassIVE)
Dataset title: Oncogenic deubiquitination controls tyrosine kinase signaling and therapy response in acute lymphoblastic leukemia
Possible reference: Jin, Q. et al. (2022) Oncogenic deubiquitination controls tyrosine kinase signaling and therapy response in acute lymphoblastic leukemia., Sci Adv, PMID 36490346

PXD031929 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Alterations Associated with Residual Disease in Neoadjuvant Chemotherapy Treated Ovarian Cancer Tissues
Possible reference: Penick, ER. et al. (2022) Proteomic alterations associated with residual disease in neoadjuvant chemotherapy treated ovarian cancer tissues., Clin Proteomics, PMID 36195845

PXD031903 Dataset with its publication pending (from iProX)
Dataset title: A terminal alkyne and disulfide functionalized agarose resin specifically enriches azidohomoalanine labeled nascent proteins
Possible reference: Hou, Z. et al. (2021) A terminal alkyne and disulfide functionalized agarose resin specifically enriches azidohomoalanine labeled nascent proteins., J Chromatogr B Analyt Technol Biomed Life Sci, PMID 33486215

PXD031899 no publication (from MassIVE)
Dataset title: Reversible lysine-targeted probes reveal residence time-based kinase selectivity
Possible reference: Yang, T. et al. (2022) Reversible lysine-targeted probes reveal residence time-based kinase selectivity., Nat Chem Biol, PMID 35590003

PXD031898 no publication (from MassIVE)
Dataset title: Ammonium Sulfate-based Prefractionation Improved Proteome Coverage in Arabidopsis thaliana Leaf Extract
Possible reference: Tola, AJ. et al. (2023) Ammonium sulfate-based prefractionation improved proteome coverage and detection of carbonylated proteins in Arabidopsis thaliana leaf extract., Planta, PMID 36808312

PXD031892 (from jPOST)
Dataset title: Sera Protein Signatures of Endometrial Cancer Lymph Node Metastases
Possible reference: Benbrook, DM. et al. (2022) Sera Protein Signatures of Endometrial Cancer Lymph Node Metastases., Int J Mol Sci, PMID 35328698

PXD031878 Dataset with its publication pending (from PRIDE)
Dataset title: Oxygen and hormone effect on rat oligodrendrocyte progenitor cell line (OLN93)
Possible reference: Sunny, DE. et al. (2022) Fetal Zone Steroids Show Discrete Effects on Hyperoxia-Induced Attenuation of Migration in Cultured Oligodendrocyte Progenitor Cells., Oxid Med Cell Longev, PMID 35585881

PXD031875 Dataset with its publication pending (from PRIDE)
Dataset title: Biomarkers for canine Leptospira vaccine potency
Possible reference: Novak, A. et al. (2022) Transcriptome and proteome analysis of innate immune responses to inactivated Leptospira and bivalent Leptospira vaccines in canine 030-D cells., Sci Rep, PMID 35927283

PXD031874 Dataset with its publication pending (from PRIDE)
Dataset title: Trafficking and interactions upon loss of TECPR2
Possible reference: Bhattacharya, D. et al. (2025) Neuropathy-associated Tecpr2 mutation knock-in mice reveal endolysosomal loss of function phenotypes in neurons and microglia., Cell Death Dis, PMID 41173829

PXD031871 Dataset with its publication pending (from PRIDE)
Dataset title: Physiological and proteomic analyses indicate delayed sowing improves photosynthetic capacity in wheat flag leaves under heat stress
Possible reference: Fei, L. et al. (2022) Physiological and Proteomic Analyses Indicate Delayed Sowing Improves Photosynthetic Capacity in Wheat Flag Leaves Under Heat Stress., Front Plant Sci, PMID 35401629

PXD031867 Dataset with its publication pending (from PRIDE)
Dataset title: In Streptococcus thermophilus, ammonia from urea hydrolysis paradoxically boosts acidification and reveals a new regulatory mechanism of glycolysis
Possible reference: Arioli, S. et al. (2022) In Streptococcus thermophilus, Ammonia from Urea Hydrolysis Paradoxically Boosts Acidification and Reveals a New Regulatory Mechanism of Glycolysis., Microbiol Spectr, PMID 35467410

PXD031866 Dataset with its publication pending (from PRIDE)
Dataset title: Stomatin modulates adipogenesis through ERK pathway and regulates fatty acid uptake and lipid droplet growth
Possible reference: Wu, SC. et al. (2022) Stomatin modulates adipogenesis through the ERK pathway and regulates fatty acid uptake and lipid droplet growth., Nat Commun, PMID 35854007

PXD031862 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles derived from the choroid plexus trigger neural stem cells differentiation
Possible reference: Ditte, Z. et al. (2022) Extracellular vesicles derived from the choroid plexus trigger the differentiation of neural stem cells., J Extracell Vesicles, PMID 36325603

PXD031853 Dataset with its publication pending (from iProX)
Dataset title: CTNNBL1 restricts HIV-1 replication
Possible reference: Liang, G. et al. (2022) CTNNBL1 restricts HIV-1 replication by suppressing viral DNA integration into the cell genome., Cell Rep, PMID 35294870

PXD031850 Dataset with its publication pending (from PanoramaPublic)
Dataset title: IFI16-mediated suppression of HSV-1 protein expression
Possible reference: Liu, D. et al. (2023) IFI16 phase separation via multi-phosphorylation drives innate immune signaling., Nucleic Acids Res, PMID 37283074

PXD031833 Dataset with its publication pending (from PRIDE)
Dataset title: TTYH family members form tetrameric complexes at the cell membrane
Possible reference: Melvin, E. et al. (2022) TTYH family members form tetrameric complexes at the cell membrane., Commun Biol, PMID 36042377

PXD031832 no publication (from MassIVE)
Dataset title: TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies
Possible reference: Basisty, N. et al. (2023) TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies., J Proteome Res, PMID 36165806

PXD031809 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis reveals enzymes for Î²-D-glucan formation and degradation in Levilactobacillus brevis TMW 1.2112
Possible reference: Bockwoldt, JA. et al. (2022) Proteomic Analysis Reveals Enzymes for β-D-Glucan Formation and Degradation in Levilactobacillus brevis TMW 1.2112., Int J Mol Sci, PMID 35328813

PXD031791 Dataset with its publication pending (from PRIDE)
Dataset title: The cell-based control and underlying mechanism for inflammatory bone loss
Possible reference: Kontaki, E. et al. (2017) Aberrant function of myeloid-derived suppressor cells (MDSCs) in experimental colitis and in inflammatory bowel disease (IBD) immune responses., Autoimmunity, PMID 28276713

PXD031790 Dataset with its publication pending (from PRIDE)
Dataset title: Double-stranded RNA viruses are released from Trichomonas vaginalis inside exosomes and modulate the exosomal cargo.
Possible reference: Rada, P. et al. (2022) Double-Stranded RNA Viruses Are Released From Trichomonas vaginalis Inside Small Extracellular Vesicles and Modulate the Exosomal Cargo., Front Microbiol, PMID 35602021

PXD031788 Dataset with its publication pending (from PRIDE)
Dataset title: A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment
Possible reference: Bernard, C. et al. (2022) A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment., Nat Commun, PMID 35835784

PXD031779 Dataset with its publication pending (from PRIDE)
Dataset title: Meiotic DNA breaks activate a streamlined response that largely avoids protein level changes-DDA
Possible reference: Kar, FM. et al. (2022) Meiotic DNA breaks activate a streamlined phospho-signaling response that largely avoids protein-level changes., Life Sci Alliance, PMID 36271494

PXD031776 Dataset with its publication pending (from PRIDE)
Dataset title: In vitro erythropoiesis at different pO2 induces adaptations that are independent of prior systemic exposure to hypoxia
Possible reference: Simionato, G. et al. (2022) In Vitro Erythropoiesis at Different pO2 Induces Adaptations That Are Independent of Prior Systemic Exposure to Hypoxia., Cells, PMID 35406648

PXD031774 Dataset with its publication pending (from PRIDE)
Dataset title: A proteomic landscape of Candida albicans in the stepwise evolution to fluconazole resistance
Possible reference: Song, N. et al. (2022) A Proteomic Landscape of Candida albicans in the Stepwise Evolution to Fluconazole Resistance., Antimicrob Agents Chemother, PMID 35343782

PXD031770 Dataset with its publication pending (from PRIDE)
Dataset title: ISG15 Conjugation to Proteins on Nascent DNA Mitigates DNA Replication Stress
Possible reference: Wardlaw, CP. et al. (2022) ISG15 conjugation to proteins on nascent DNA mitigates DNA replication stress., Nat Commun, PMID 36216822

PXD031765 Dataset with its publication pending (from PRIDE)
Dataset title: Advanced in vitro safety assessment of herbal medicines for the treatment of non-psychotic mental disorders in pregnancy
Possible reference: Spiess, D. et al. (2022) Advanced in Vitro Safety Assessment of Herbal Medicines for the Treatment of Non-Psychotic Mental Disorders in Pregnancy., Front Pharmacol, PMID 35814220

PXD031748 no publication (from MassIVE)
Dataset title: Functional interactomes of the Ebola virus polymerase identified by proximity proteomics in the context of viral replication
Possible reference: Fang, J. et al. (2022) Functional interactomes of the Ebola virus polymerase identified by proximity proteomics in the context of viral replication., Cell Rep, PMID 35320713

PXD031739 Dataset with its publication pending (from PRIDE)
Dataset title: Effects on the lipid metabolism of Atlantic cod (Gadus morhua) after in vivo exposure with Ppar agonists
Possible reference: Eide, M. et al. (2023) Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod., Front Physiol, PMID 37035678

PXD031713 Dataset with its publication pending (from PRIDE)
Dataset title: Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation
Possible reference: Qiao, S. et al. (2022) Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation., Nat Commun, PMID 35650207

PXD031708 Dataset with its publication pending (from PRIDE)
Dataset title: Competitive Profiling of Ligandable Cysteines in Staphylococcus aureus with an Organogold Compound
Possible reference: Schmidt, C. et al. (2022) Competitive profiling of ligandable cysteines in Staphylococcus aureus with an organogold compound., Chem Commun (Camb), PMID 35420608

PXD031706 Dataset with its publication pending (from PRIDE)
Dataset title: Antibacterial Activities and Action Mode of Anti-hyperlipidemic Lomitapide Against Staphylococcus aureus_1
Possible reference: Zhang, Y. et al. (2022) Antibacterial activities and action mode of anti-hyperlipidemic lomitapide against Staphylococcus aureus., BMC Microbiol, PMID 35473561

PXD031701 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis on different tissues of Pteria penguin
Possible reference: Li, H. et al. (2017) Characterization of transcriptome and identification of biomineralization genes in winged pearl oyster (Pteria penguin) mantle tissue., Comp Biochem Physiol Part D Genomics Proteomics, PMID 28103531

PXD031689 Dataset with its publication pending (from jPOST)
Dataset title: ctenophore comb plate whole proteins
Possible reference: Sachkova, MY. et al. (2021) Neuropeptide repertoire and 3D anatomy of the ctenophore nervous system., Curr Biol, PMID 34587474

PXD031677 Dataset with its publication pending (from PRIDE)
Dataset title: 40S hnRNP particles are a novel class of nuclear biomolecular condensates
Possible reference: Domanski, M. et al. (2022) 40S hnRNP particles are a novel class of nuclear biomolecular condensates., Nucleic Acids Res, PMID 35687109

PXD031667 no publication (from MassIVE)
Dataset title: Redox-dependent Structure and Dynamics of Macrophage Migration Inhibitory Factor Reveal Sites of Latent Allostery
Possible reference: Skeens, E. et al. (2022) Redox-dependent structure and dynamics of macrophage migration inhibitory factor reveal sites of latent allostery., Structure, PMID 35381187

PXD031647 Dataset with its publication pending (from PRIDE)
Dataset title: SP3-enabled rapid and high coverage chemoproteomic identification of redox-sensitive cysteines
Possible reference: Desai, HS. et al. (2022) SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State-Dependent Redox-Sensitive Cysteines., Mol Cell Proteomics, PMID 35219905

PXD031634 Dataset with its publication pending (from PRIDE)
Dataset title: Multifactorial remodeling of the cancer immunopeptidome by interferon gamma
Possible reference: Newey, A. et al. (2023) Multifactorial Remodeling of the Cancer Immunopeptidome by IFNγ., Cancer Res Commun, PMID 37991387

PXD031627 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications.
Possible reference: Malinovska, L. et al. (2023) Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications., Nat Protoc, PMID 36526727

PXD031625 Dataset with its publication pending (from PRIDE)
Dataset title: Localization of the priming factors CAPS1 and CAPS2 in mouse sensory neurons is determined by their N-termini
Possible reference: Staudt, A. et al. (2022) Localization of the Priming Factors CAPS1 and CAPS2 in Mouse Sensory Neurons Is Determined by Their N-Termini., Front Mol Neurosci, PMID 35493323

PXD031615 Dataset with its publication pending (from PRIDE)
Dataset title: S-Nitrosylation of the Virulence Regulator AphB Promotes Vibrio cholerae Pathogenesis
Possible reference: Chen, J. et al. (2022) S-Nitrosylation of the virulence regulator AphB promotes Vibrio cholerae pathogenesis., PLoS Pathog, PMID 35714156

PXD031611 Dataset with its publication pending (from PRIDE)
Dataset title: Depletion of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication
Possible reference: Moll, T. et al. (2022) Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication., bioRxiv, PMID 35291294

PXD031593 Dataset with its publication pending (from PRIDE)
Dataset title: EGF promotes PKM2 O-GlcNAcylation by stimulating O-GlcNAc transferase phosphorylation at Y976 and their subsequent association
Possible reference: Wang, Y. et al. (2022) EGF promotes PKM2 O-GlcNAcylation by stimulating O-GlcNAc transferase phosphorylation at Y976 and their subsequent association., J Biol Chem, PMID 35931120

PXD031586 Dataset with its publication pending (from PRIDE)
Dataset title: Differential trafficking and expression of PIR proteins in acute and chronic Plasmodium infections
Possible reference: Giorgalli, M. et al. (2022) Differential Trafficking and Expression of PIR Proteins in Acute and Chronic Plasmodium Infections., Front Cell Infect Microbiol, PMID 35782145

PXD031582 Dataset with its publication pending (from PRIDE)
Dataset title: LOSS OF THE BATTEN DISEASE PROTEIN CLN3 LEADS TO MIS-TRAFFICKING OF M6PR AND DEFECTIVE AUTOPHAGIC-LYSOSOMAL REFORMATION
Possible reference: Calcagni', A. et al. (2023) Loss of the batten disease protein CLN3 leads to mis-trafficking of M6PR and defective autophagic-lysosomal reformation., Nat Commun, PMID 37400440

PXD031577 Dataset with its publication pending (from PRIDE)
Dataset title: Grad-seq Enterococcus faecalis and faecium
Possible reference: Michaux, C. et al. (2023) Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens., Microlife, PMID 37223738

PXD031575 Dataset with its publication pending (from PRIDE)
Dataset title: iTRAq and TMTPro datasets Rescored with Prosit
Possible reference: Gabriel, W. et al. (2022) Predicting fragment intensities and retention time of iTRAQ- and TMTPro-labeled peptides with Prosit-TMT., Proteomics, PMID 35578405

PXD031566 no publication (from MassIVE)
Dataset title: Functional protein composition in femoral glands of sand lizards (Lacerta agilis)
Possible reference: Ib��ez, A. et al. (2022) Functional Protein Composition in Femoral Glands of Sand Lizards (Lacerta agilis)., Molecules, PMID 35408771

PXD031537 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of hexadecane utilization by Tsukamurella tyrosinosolvens PS2
Possible reference: Romanova, V. et al. (2022) Significance of both alkB and P450 alkane-degrading systems in Tsukamurella tyrosinosolvens: proteomic evidence., Appl Microbiol Biotechnol, PMID 35396956

PXD031533 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomics of CTS effect on human lung cancer H1975
Possible reference: Cai, P. et al. (2022) Comparative Proteomics Analysis Reveals the Reversal Effect of Cryptotanshinone on Gefitinib-Resistant Cells in Epidermal Growth Factor Receptor-Mutant Lung Cancer., Front Pharmacol, PMID 35370706

PXD031531 Dataset with its publication pending (from PRIDE)
Dataset title: The PAF1 complex promotes 3‘ processing of pervasive transcripts
Possible reference: Liu, X. et al. (2022) The PAF1 complex promotes 3' processing of pervasive transcripts., Cell Rep, PMID 35294889

PXD031529 Dataset with its publication pending (from PRIDE)
Dataset title: Large-scale protein and phosphoprotein profiling to explore potato resistance mechanisms to Spongospora subterranea infection
Possible reference: Balotf, S. et al. (2022) Large-Scale Protein and Phosphoprotein Profiling to Explore Potato Resistance Mechanisms to Spongospora subterranea Infection., Front Plant Sci, PMID 35498715

PXD031522 Dataset with its publication pending (from PRIDE)
Dataset title: Widespread consumption of the common food additive xanthan gum by the human gut microbiota
Possible reference: Ostrowski, MP. et al. (2022) Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota., Nat Microbiol, PMID 35365790

PXD031510 Dataset with its publication pending (from PRIDE)
Dataset title: SimPLIT: Simplified sample preparation for large-scale isobaric tagging proteomics
Possible reference: Sialana, FJ. et al. (2022) SimPLIT: Simplified Sample Preparation for Large-Scale Isobaric Tagging Proteomics., J Proteome Res, PMID 35848491

PXD031500 no publication (from PanoramaPublic)
Dataset title: An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia
Possible reference: Provez, L. et al. (2022) An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia., Sci Data, PMID 36243775

PXD031490 Dataset with its publication pending (from PRIDE)
Dataset title: Cyclodepsipeptides, solonamides, influence motility in the native producer Photobacterium galatheae S2753
Possible reference: Zhang, SD. et al. (2022) Solonamides, a Group of Cyclodepsipeptides, Influence Motility in the Native Producer Photobacterium galatheae S2753., Appl Environ Microbiol, PMID 36000852

PXD031477 no publication (from MassIVE)
Dataset title: Proteomics analysis of FFPE AIS thrombi
Possible reference: Rossi, R. et al. (2022) Potential Biomarkers of Acute Ischemic Stroke Etiology Revealed by Mass Spectrometry-Based Proteomic Characterization of Formalin-Fixed Paraffin-Embedded Blood Clots., Front Neurol, PMID 35518205

PXD031456 Dataset with its publication pending (from PRIDE)
Dataset title: Translational reprogramming in response to accumulating stressors ensures critical threshold levels of Hsp90 for mammalian life
Possible reference: Bhattacharya, K. et al. (2022) Translational reprogramming in response to accumulating stressors ensures critical threshold levels of Hsp90 for mammalian life., Nat Commun, PMID 36270993

PXD031443 Dataset with its publication pending (from PRIDE)
Dataset title: Multiple cis acting polypyrimidine tract elements regulate a cooperative mechanism for Triticum mosaic virus internal ribosomal entry site activity=]
Possible reference: Jaramillo-Mesa, H. et al. (2022) Multiple Cis-acting Polypyrimidine Tract Elements Regulate a Cooperative Mechanism for Triticum Mosaic Virus Internal Ribosomal Entry Site Activity., Front Plant Sci, PMID 35498652

PXD031431 no publication (from MassIVE)
Dataset title: Lysine acetylation of E. coli aconitase isozymes
Possible reference: Araujo, J. et al. (2022) Studying Acetylation of Aconitase Isozymes by Genetic Code Expansion., Front Chem, PMID 35402385

PXD031412 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome dynamics during transition from exponential to stationary phase in yeast
Possible reference: Ridder, MD. et al. (2023) Proteome Dynamics During Transition From Exponential to Stationary Phase Under Aerobic and Anaerobic Conditions in Yeast., Mol Cell Proteomics, PMID 37076048

PXD031408 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular endosulfatase Sulf-2 harbors a chondroitin/dermatan sulfate chain that modulates its enzyme activity
Possible reference: El Masri, R. et al. (2022) Extracellular endosulfatase Sulf-2 harbors a chondroitin/dermatan sulfate chain that modulates its enzyme activity., Cell Rep, PMID 35294879

PXD031400 no publication (from MassIVE)
Dataset title: Carry-over effects of dry period heat stress on mammary gland proteome and phosphoproteome in the subsequent lactation of dairy cows
Possible reference: Skibiel, AL. et al. (2022) Carry-over effects of dry period heat stress on the mammary gland proteome and phosphoproteome in the subsequent lactation of dairy cows., Sci Rep, PMID 35459770

PXD031392 Cruz-Morales, Pablo, et al. "Biosynthesis of polycyclopropanated high energy biofuels." Joule 6.7 (2022): 1590-1605. (from PanoramaPublic)
Dataset title: Biosynthesis of polycyclopropanated high energy biofuels
Possible reference: Yin, K. et al. (2026) Polyketide synthase-based controlled synthesis of polycyclopropanated fuel molecules., Nat Commun, PMID 42204148

PXD031388 Dataset with its publication pending (from PRIDE)
Dataset title: Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis
Possible reference: Sun, Y. et al. (2022) Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis., Sci Adv, PMID 36383657

PXD031379 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted proteoform mapping uncovers specific Neurexin-3 variants required for dendritic inhibition
Possible reference: Hauser, D. et al. (2022) Targeted proteoform mapping uncovers specific Neurexin-3 variants required for dendritic inhibition., Neuron, PMID 35550065

PXD031356 no publication (from MassIVE)
Dataset title: The Proteomic Characteristics of Rainbow Trout Blood with Severe, Moderate and Asymptomatic course of Vibrio anguillarum infection
Possible reference: Kurpe, SR. et al. (2022) Physiological and Biochemical Characteristics of Rainbow Trout with Severe, Moderate and Asymptomatic Course of Vibrio anguillarum Infection., Animals (Basel), PMID 36230384

PXD031355 Dataset with its publication pending (from PRIDE)
Dataset title: A Bacterial Mannose Binding Lectin as a Tool for the Enrichment of C-and O- Mannosylated Peptides
Possible reference: H�tte, HJ. et al. (2022) A Bacterial Mannose Binding Lectin as a Tool for the Enrichment of C- and O-Mannosylated Peptides., Anal Chem, PMID 35549177

PXD031351 Dataset with its publication pending (from PRIDE)
Dataset title: Control of variant surface glycoprotein expression by CFB2 in African trypanosomes and quantitative proteomic connections to translation and cytokinesis initiation
Possible reference: Bravo Ruiz, G. et al. (2022) Control of Variant Surface Glycoprotein Expression by CFB2 in Trypanosoma brucei and Quantitative Proteomic Connections to Translation and Cytokinesis., mSphere, PMID 35306877

PXD031343 Dataset with its publication pending (from PRIDE)
Dataset title: Impact of modified atmospheres on growth and metabolism of meat-spoilage relevant Photobacterium spp. as predicted by comparative proteomics
Possible reference: Fuertes-Perez, S. et al. (2022) Impact of Modified Atmospheres on Growth and Metabolism of Meat-Spoilage Relevant Photobacterium spp. as Predicted by Comparative Proteomics., Front Microbiol, PMID 35722325

PXD031337 Dataset with its publication pending (from PRIDE)
Dataset title: Formation of toxic oligomers of polyQ-expanded Huntingtin by prion-mediated cross-seeding
Possible reference: Gropp, MHM. et al. (2022) Formation of toxic oligomers of polyQ-expanded Huntingtin by prion-mediated cross-seeding., Mol Cell, PMID 36272412

PXD031335 Dataset with its publication pending (from PRIDE)
Dataset title: Paramecium Polycomb Repressive Complex 2 physically interacts with the small RNA binding PIWI protein to repress transposable elements
Possible reference: Mir�-Pina, C. et al. (2022) Paramecium Polycomb repressive complex 2 physically interacts with the small RNA-binding PIWI protein to repress transposable elements., Dev Cell, PMID 35429435

PXD031331 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of differential anther development from sterile/fertile lines in Capsicum annuum L.
Possible reference: Pei, H. et al. (2022) Proteomic analysis of differential anther development from sterile/fertile lines in Capsicum annuum L., PeerJ, PMID 35651745

PXD031322 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic analysis of oxaliplatin induced peripheral neurotoxicity
Possible reference: Yang, L. et al. (2022) Quantitative proteomic analysis of oxaliplatin induced peripheral neurotoxicity., J Proteomics, PMID 35830924

PXD031319 Dataset with its publication pending (from PRIDE)
Dataset title: Novel assays monitoring direct GR protein activity exhibit high predictive power for ligand activity on endogenous GR gene targets
Possible reference: Van Moortel, L. et al. (2022) Novel assays monitoring direct glucocorticoid receptor protein activity exhibit high predictive power for ligand activity on endogenous gene targets., Biomed Pharmacother, PMID 35709653

PXD031318 Dataset with its publication pending (from PRIDE)
Dataset title: Changes in saliva associated to COVID-19: a proteomic study
Possible reference: Mu�oz-Prieto, A. et al. (2022) Saliva changes in composition associated to COVID-19: a preliminary study., Sci Rep, PMID 35760827

PXD031315 Dataset with its publication pending (from PRIDE)
Dataset title: The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer
Possible reference: Saleh, A. et al. (2022) The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer., Nat Commun, PMID 35614055

PXD031311 Dataset with its publication pending (from PRIDE)
Dataset title: RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity
Possible reference: Feng, S. et al. (2022) RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity., Nat Commun, PMID 35177609

PXD031290 Dataset with its publication pending (from iProX)
Dataset title: Serum Proteome profiling of Cryoglobulinemia
Possible reference: Wang, JJ. et al. (2018) Molecular Profiling and Clonal Tracking of Secreted Rheumatoid Factors in Primary Sj�gren's Syndrome., Arthritis Rheumatol, PMID 29697211

PXD031287 Dataset with its publication pending (from iProX)
Dataset title: Serum proteomics unveil characteristic protein diagnostic biomarkers and signaling pathways in patients with esophageal squamous cell carcinoma
Possible reference: Liu, W. et al. (2022) Serum proteomics unveil characteristic protein diagnostic biomarkers and signaling pathways in patients with esophageal squamous cell carcinoma., Clin Proteomics, PMID 35610567

PXD031278 Dataset with its publication pending (from PRIDE)
Dataset title: Thrombo-Inflammation in Preeclampsia and Pregnancy Induced Hypertension: Proteomics And Metabolomics Profiling of Platelets and Plasma Mediators
Possible reference: de Almeida, LGN. et al. (2022) Proteomics and Metabolomics Profiling of Platelets and Plasma Mediators of Thrombo-Inflammation in Gestational Hypertension and Preeclampsia., Cells, PMID 35455936

PXD031277 Dataset with its publication pending (from PRIDE)
Dataset title: Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing
Possible reference: Koenig, C. et al. (2022) Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing., Proteomics, PMID 35713889

PXD031229 Dataset with its publication pending (from PRIDE)
Dataset title: Knockdown of DHRS7 in LNCaP cells
Possible reference: Seibert, JK. et al. (2015) A role for the dehydrogenase DHRS7 (SDR34C1) in prostate cancer., Cancer Med, PMID 26311046

PXD031225 Dataset with its publication pending (from PRIDE)
Dataset title: Structure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences
Possible reference: Shon, DJ. et al. (2022) Structure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences., J Biol Chem, PMID 35405095

PXD031224 Dataset with its publication pending (from PRIDE)
Dataset title: RIPK3 is released into Extracellular Vesicles during Necroptosis through a Rab27 independent mechanism
Possible reference: Gupta, K. et al. (2022) Necroptosis is associated with Rab27-independent expulsion of extracellular vesicles containing RIPK3 and MLKL., J Extracell Vesicles, PMID 36063142

PXD031222 Dataset with its publication pending (from PRIDE)
Dataset title: Augmented enterocyte damage during Candida albicans and Proteus mirabilis coinfection
Possible reference: Niemiec, MJ. et al. (2022) Augmented Enterocyte Damage During Candida albicans and Proteus mirabilis Coinfection., Front Cell Infect Microbiol, PMID 35651758

PXD031216 Dataset with its publication pending (from PRIDE)
Dataset title: Effects of non-thermal methods (High-Pressure Processing, UV-C irradiation and thermoultrasonication) on donor human milk safety and functionality
Possible reference: Kontopodi, E. et al. (2022) Effects of High-Pressure Processing, UV-C Irradiation and Thermoultrasonication on Donor Human Milk Safety and Quality., Front Pediatr, PMID 35386262

PXD031199 Dataset with its publication pending (from PRIDE)
Dataset title: A phylogenomic approach to explore the Aspergillus fumigatus conidia surforme and its role in pathogenesis
Possible reference: Valero, C. et al. (2023) A phylogenetic approach to explore the Aspergillus fumigatus conidial surface-associated proteome and its role in pathogenesis., bioRxiv, PMID 37662192

PXD031193 Dataset with its publication pending (from PRIDE)
Dataset title: Chronic stress causes striatal disinhibition mediated by SOM-interneurons
Possible reference: Rodrigues, D. et al. (2022) Chronic stress causes striatal disinhibition mediated by SOM-interneurons in male mice., Nat Commun, PMID 36446783

PXD031184 Dataset with its publication pending (from iProX)
Dataset title: Protein glycosylation changes during systemic acquired resistance in Arabidopsis thaliana
Possible reference: Holmes, EC. et al. (2021) Arabidopsis UGT76B1 glycosylates N-hydroxy-pipecolic acid and inactivates systemic acquired resistance in tomato., Plant Cell, PMID 33955491

PXD031174 Dataset with its publication pending (from PRIDE)
Dataset title: Aging-Associated Changes in CSF Protein Abundances and Structures Revealed by a Modified LiP-MS Screen
Possible reference: Shuken, SR. et al. (2022) Limited Proteolysis-Mass Spectrometry Reveals Aging-Associated Changes in Cerebrospinal Fluid Protein Abundances and Structures., Nat Aging, PMID 36741774

PXD031173 Dataset with its publication pending (from PRIDE)
Dataset title: Bacterial necromass is rapidly metabolized by heterotrophic bacteria and supports multiple trophic levels of the groundwater microbiome
Possible reference: Geesink, P. et al. (2022) Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome., Microbiol Spectr, PMID 35699474

PXD031170 Dataset with its publication pending (from PRIDE)
Dataset title: Replisome composition of stalled, terminating replication forks
Possible reference: Priego Moreno, S. et al. (2019) Mitotic replisome disassembly depends on TRAIP ubiquitin ligase activity., Life Sci Alliance, PMID 30979826

PXD031169 Dataset with its publication pending (from PRIDE)
Dataset title: Engineering and exploiting synthetic allostery of NanoLuc luciferase
Possible reference: Guo, Z. et al. (2022) Engineering and exploiting synthetic allostery of NanoLuc luciferase., Nat Commun, PMID 35145068

PXD031147 Dataset with its publication pending (from PRIDE)
Dataset title: Comparing two acetification profiles from natural raw materials: a quantitative approach in Komagataeibacter europaeus
Possible reference: Rom�n-Camacho, JJ. et al. (2022) Unraveling the Role of Acetic Acid Bacteria Comparing Two Acetification Profiles From Natural Raw Materials: A Quantitative Approach in Komagataeibacter europaeus., Front Microbiol, PMID 35572698

PXD031144 Dataset with its publication pending (from PRIDE)
Dataset title: Regulators of proteostasis are translationally repressed in fibroblasts from sporadic and LRRK2-G2019S Parkinson’s patients
Possible reference: Flinkman, D. et al. (2023) Regulators of proteostasis are translationally repressed in fibroblasts from patients with sporadic and LRRK2-G2019S Parkinson's disease., NPJ Parkinsons Dis, PMID 36746972

PXD031139 no publication (from MassIVE)
Dataset title: How do Protein Contaminants Influence DDA and DIA Proteomics?
Possible reference: Frankenfield, AM. et al. (2022) Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics., J Proteome Res, PMID 35793413

PXD031136 Dataset with its publication pending (from PRIDE)
Dataset title: Decoupling astrocytes in adult mice impairs synaptic plasticity and spatial learning
Possible reference: H�sli, L. et al. (2022) Decoupling astrocytes in adult mice impairs synaptic plasticity and spatial learning., Cell Rep, PMID 35263595

PXD031128 Dataset with its publication pending (from jPOST)
Dataset title: Selective removal of unhydrolyzed monolinked peptides from enriched crosslinked peptides to improve the coverage of protein complexes analysis
Possible reference: An, Y. et al. (2022) Selective Removal of Unhydrolyzed Monolinked Peptides from Enriched Crosslinked Peptides To Improve the Coverage of Protein Complex Analysis., Anal Chem, PMID 35191685

PXD031124 Dataset with its publication pending (from PRIDE)
Dataset title: Genotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1
Possible reference: Fan, L. et al. (2022) Genotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1., Nat Commun, PMID 35277499

PXD031123 Dataset with its publication pending (from PRIDE)
Dataset title: A seed-like proteome in oil-rich tubers
Possible reference: Niemeyer, PW. et al. (2022) A seed-like proteome in oil-rich tubers., Plant J, PMID 36050843

PXD031115 Dataset with its publication pending (from PRIDE)
Dataset title: Prenylcysteine oxidase 1 like protein is required for neutrophil bactericidal activities
Possible reference: Petenkova, A. et al. (2023) Prenylcysteine oxidase 1 like protein is required for neutrophil bactericidal activities., Nat Commun, PMID 37179332

PXD031114 Dataset with its publication pending (from PRIDE)
Dataset title: Optimized TMT-based quantitative cross-linking mass spectrometry strategy for large-scale interactomic studies
Possible reference: Ruwolt, M. et al. (2022) Optimized TMT-Based Quantitative Cross-Linking Mass Spectrometry Strategy for Large-Scale Interactomic Studies., Anal Chem, PMID 35290030

PXD031109 Dataset with its publication pending (from PRIDE)
Dataset title: comparative mass spectrometry analysis of the PARP1 and PAR-PARP1 interactomes
Possible reference: Pavan, IC. et al. (2016) Different interactomes for p70-S6K1 and p54-S6K2 revealed by proteomic analysis., Proteomics, PMID 27493124

PXD031103 Dataset with its publication pending (from jPOST)
Dataset title: Proteome-wide deconvolution of drug targets and binding sites by lysine reactivity profiling
Possible reference: Ruan, C. et al. (2022) Proteome-Wide Deconvolution of Drug Targets and Binding Sites by Lysine Reactivity Profiling., Anal Chem, PMID 35147412

PXD031102 no publication (from MassIVE)
Dataset title: Proteomic identification of phosphorylation dependent Septin 7 interactors that drive dendritic spine formation
Possible reference: Byeon, S. et al. (2022) Proteomic Identification of Phosphorylation-Dependent Septin 7 Interactors that Drive Dendritic Spine Formation., Front Cell Dev Biol, PMID 35602601

PXD031083 Dataset with its publication pending (from PRIDE)
Dataset title: Gel-like inclusions of C-terminal fragments of TDP-43 sequester stalled proteasomes in neurons
Possible reference: Riemenschneider, H. et al. (2022) Gel-like inclusions of C-terminal fragments of TDP-43 sequester stalled proteasomes in neurons., EMBO Rep, PMID 35438230

PXD031078 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Investigation of Evolved Daptomycin-Tolerant MRSA due to Mutation in YycH
Possible reference: Sulaiman, JE. et al. (2022) Mutation in the Two-Component System Regulator YycH Leads to Daptomycin Tolerance in Methicillin-Resistant Staphylococcus aureus upon Evolution with a Population Bottleneck., Microbiol Spectr, PMID 35913149

PXD031063 Dataset with its publication pending (from PRIDE)
Dataset title: ABP1-TMK auxin perception mediates rapid phosphorylation for regeneration and auxin canalization
Possible reference: Friml, J. et al. (2022) ABP1-TMK auxin perception for global phosphorylation and auxin canalization., Nature, PMID 36071161

PXD031059 Maven et al., The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5, Stem Cell Reports (2023), https://doi.org/10.1016/j.stemcr.2023.09.014 (from PanoramaPublic)
Dataset title: The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5
Possible reference: Maven, BEJ. et al. (2023) The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5., Stem Cell Reports, PMID 37863045

PXD031054 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics and in-cell cross-linking reveal cellular reorganisation during early neuronal differentiation of SH-SY5Y cells
Possible reference: Barth, M. et al. (2022) Quantitative proteomics and in-cell cross-linking reveal cellular reorganisation during early neuronal differentiation of SH-SY5Y cells., Commun Biol, PMID 35672350

PXD031048 Dataset with its publication pending (from PRIDE)
Dataset title: An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease
Possible reference: Palanski, BA. et al. (2022) An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease., Nat Commun, PMID 35173144

PXD031046 Dataset with its publication pending (from PRIDE)
Dataset title: Tgfbr2 in dental pulp cells guides neurite outgrowth in developing teeth
Possible reference: Stanwick, M. et al. (2022) Tgfbr2 in Dental Pulp Cells Guides Neurite Outgrowth in Developing Teeth., Front Cell Dev Biol, PMID 35265620

PXD031025 Dataset with its publication pending (from PRIDE)
Dataset title: Human serum glycoproteome - Glyco-Decipher
Possible reference: Liu, L. et al. (2026) A Protein-Centric Strategy Coupled with Match-Between-Run Glycoproteomics Enables Discovery of Robust Site-Specific Glycan Biomarkers for Hepatocellular Carcinoma., Adv Sci (Weinh), PMID 41674345

PXD031021 Dataset with its publication pending (from iProX)
Dataset title: Glycyrrhetinic acid restricts mitochondrial energy metabolism through targeting SHMT2
Possible reference: Jin, X. et al. (2022) Glycyrrhetinic acid restricts mitochondrial energy metabolism by targeting SHMT2., iScience, PMID 35602963

PXD031016 Dataset with its publication pending (from PRIDE)
Dataset title: Isoform-dependent lysosomal degradation and internalization of Apolipoprotein E requires autophagy proteins
Possible reference: Fote, GM. et al. (2022) Isoform-dependent lysosomal degradation and internalization of apolipoprotein E requires autophagy proteins., J Cell Sci, PMID 34982109

PXD030979 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics on pink1 mutant Drosophila melanogaster
Possible reference: Auburger, G. et al. (2019) SerThr-PhosphoProteome of Brain from Aged PINK1-KO+A53T-SNCA Mice Reveals pT1928-MAP1B and pS3781-ANK2 Deficits, as Hub between Autophagy and Synapse Changes., Int J Mol Sci, PMID 31277379

PXD030963 Dataset with its publication pending (from PRIDE)
Dataset title: Off the shelf proximity biotinylation using ProtA-TurboID
Possible reference: Santos-Barriopedro, I. et al. (2023) Off-the-shelf proximity biotinylation using ProtA-TurboID., Nat Protoc, PMID 36224470

PXD030962 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive insights into sepsis-induced cardiac dysfunction through proteomics and metabolomics
Possible reference: Ji, H. et al. (2026) Comprehensive insights into sepsis-induced cardiac dysfunction through proteomics and metabolomics., BMC Res Notes, PMID 41566375

PXD030955 Dataset with its publication pending (from PRIDE)
Dataset title: Characteristics of extracellular vesicles secreted by senescent human vascular smooth muscle cells and its influence on immune cells.
Possible reference: Głuchowska, A. et al. (2022) Unbiased proteomic analysis of extracellular vesicles secreted by senescent human vascular smooth muscle cells reveals their ability to modulate immune cell functions., Geroscience, PMID 35900662

PXD030953 Dataset with its publication pending (from PRIDE)
Dataset title: Spatiotemporal expression of regulatory kinases directs the transition from mitosis to cellular morphogenesis in Drosophila
Possible reference: Yang, S. et al. (2022) Spatiotemporal expression of regulatory kinases directs the transition from mitosis to cellular morphogenesis in Drosophila., Nat Commun, PMID 35140224

PXD030940 Dataset with its publication pending (from PRIDE)
Dataset title: Cell membrane remodeling mediates polymyxin B resistance in Klebsiella pneumoniae: an integrated proteomics and metabolomics study
Possible reference: Chen, X. et al. (2022) Cell Membrane Remodeling Mediates Polymyxin B Resistance in Klebsiella pneumoniae: An Integrated Proteomics and Metabolomics Study., Front Microbiol, PMID 35222333

PXD030936 Dataset with its publication pending (from PRIDE)
Dataset title: Red blood cells protein profile is modified in breast cancer patients
Possible reference: Pereira-Veiga, T. et al. (2022) Red Blood Cells Protein Profile Is Modified in Breast Cancer Patients., Mol Cell Proteomics, PMID 36519745

PXD030925 Dataset with its publication pending (from PRIDE)
Dataset title: Rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought
Possible reference: Venkataraman, K. et al. (2023) Two novel, tightly linked, and rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought., Elife, PMID 36744865

PXD030915 Dataset with its publication pending (from PRIDE)
Dataset title: Spatiotemporal profiling of the bovine oviduct fluid proteome around the time of ovulation
Possible reference: Mah�, C. et al. (2022) Spatiotemporal profiling of the bovine oviduct fluid proteome around the time of ovulation., Sci Rep, PMID 35264682

PXD030889 Dataset with its publication pending (from PRIDE)
Dataset title: Translation rescue by targeting Ppp1r15a upstream open reading frame in vivo
Possible reference: Kidwell, A. et al. (2023) Translation Rescue by Targeting Ppp1r15a through Its Upstream Open Reading Frame in Sepsis-Induced Acute Kidney Injury in a Murine Model., J Am Soc Nephrol, PMID 36283811

PXD030886 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic and functional analyses of the periodic membrane skeleton in neurons
Possible reference: Zhou, R. et al. (2022) Proteomic and functional analyses of the periodic membrane skeleton in neurons., Nat Commun, PMID 35680881

PXD030870 no publication (from MassIVE)
Dataset title: Proteomic screen reveals diverse protein transport between connected neurons in the visual system.
Possible reference: Schiapparelli, LM. et al. (2022) Proteomic screen reveals diverse protein transport between connected neurons in the visual system., Cell Rep, PMID 35081342

PXD030854 Dataset with its publication pending (from iProX)
Dataset title: Proteomic insight into soybean response to flooding stress reveals changes in energy metabolism and cell wall modifications
Possible reference: Khan, MN. et al. (2022) Proteomic insight into soybean response to flooding stress reveals changes in energy metabolism and cell wall modifications., PLoS One, PMID 35511817

PXD030820 Dataset with its publication pending (from PRIDE)
Dataset title: The Inhibitory Receptor Siglec-8 Interacts with FcÎµRI and Globally Inhibits Intracellular Signaling in Primary Mast Cells Upon Activation
Possible reference: Korver, W. et al. (2022) The Inhibitory Receptor Siglec-8 Interacts With FcεRI and Globally Inhibits Intracellular Signaling in Primary Mast Cells Upon Activation., Front Immunol, PMID 35154156

PXD030819 Dataset with its publication pending (from PRIDE)
Dataset title: Protein-based engineering of the initial acquired enamel pellicle in vivo: proteomic evaluation
Possible reference: Ara�jo, TT. et al. (2022) Protein-based engineering of the initial acquired enamel pellicle in vivo: Proteomic evaluation., J Dent, PMID 34798481

PXD030818 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic study reveals differential expression of matricellular proteins between fibrous dysplasia and cemento-ossifying fibroma pathogenesis
Possible reference: Duarte-Andrade, FF. et al. (2022) Quantitative proteomic study reveals differential expression of matricellular proteins between fibrous dysplasia and cemento-ossifying fibroma pathogenesis., J Oral Pathol Med, PMID 35103997

PXD030804 Dataset with its publication pending (from PRIDE)
Dataset title: Precision structural interpretation of site-specific N-glycans in seminal plasma
Possible reference: Xin, M. et al. (2022) Precision Structural Interpretation of Site-Specific N-Glycans in Seminal Plasma., J Proteome Res, PMID 35616904

PXD030798 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in Frankliniella occidentalis
Possible reference: Ding, C. et al. (2022) Proteome-wide analysis of lysine 2-hydroxyisobutyrylation in Frankliniella occidentalis., BMC Genomics, PMID 36038823

PXD030797 Dataset with its publication pending (from PRIDE)
Dataset title: Comparison of SPEED, S-Trap, and In-Solution based sample preparation methods for tandem mass spectrometry
Possible reference: Templeton, EM. et al. (2023) Comparison of SPEED, S-Trap, and In-Solution-Based Sample Preparation Methods for Mass Spectrometry in Kidney Tissue and Plasma., Int J Mol Sci, PMID 37047281

PXD030796 Dataset with its publication pending (from PRIDE)
Dataset title: Comparison of SPEED, S-Trap, and In-Solution based sample preparation methods for tandem mass spectrometry
Possible reference: Templeton, EM. et al. (2023) Comparison of SPEED, S-Trap, and In-Solution-Based Sample Preparation Methods for Mass Spectrometry in Kidney Tissue and Plasma., Int J Mol Sci, PMID 37047281

PXD030785 Dataset with its publication pending (from PRIDE)
Dataset title: Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection
Possible reference: Pekayvaz, K. et al. (2022) Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection., Nat Commun, PMID 35197461

PXD030783 Dataset with its publication pending (from PRIDE)
Dataset title: SARS-CoV-2 Cysteine Disulfide Mapping
Possible reference: Nanda, B. et al. (2026) Conformational Heterogeneity and Redox Switching of the Cysteine Residues in SARS-CoV-2 Main Protease: A Raman Molecular Fingerprint., J Phys Chem B, PMID 41622872

PXD030782 Dataset with its publication pending (from PRIDE)
Dataset title: Peroxisome-derived hydrogen peroxide can modulate the sulfenylation profiles of key redox signaling proteins in Flp-In T-REx 293 cells
Possible reference: Lismont, C. et al. (2022) Peroxisome-Derived Hydrogen Peroxide Modulates the Sulfenylation Profiles of Key Redox Signaling Proteins in Flp-In T-REx 293 Cells., Front Cell Dev Biol, PMID 35557958

PXD030773 Dataset with its publication pending (from PRIDE)
Dataset title: The proto-oncogene TCL1A deregulates mitotic checkpoint transition and genomic stability in CLL
Possible reference: Stachelscheid, J. et al. (2023) The proto-oncogene TCL1A deregulates cell cycle and�genomic stability in CLL., Blood, PMID 36179280

PXD030757 Dataset with its publication pending (from PRIDE)
Dataset title: Integrative metabolomics, proteomics and transcriptomics analysis reveals liver toxicity of mesoporous silica nanoparticles
Possible reference: Li, J. et al. (2022) Integrative Metabolomics, Proteomics and Transcriptomics Analysis Reveals Liver Toxicity of Mesoporous Silica Nanoparticles., Front Pharmacol, PMID 35153799

PXD030754 Dataset with its publication pending (from PRIDE)
Dataset title: Histidine Kinase Inhibitors Impair Shoot Regeneration in Arabidopsis thaliana via Cytokinin Signalling and SAM Patterning Determinants
Possible reference: Lardon, R. et al. (2022) Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants., Front Plant Sci, PMID 36684719

PXD030729 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of CCNF/Cyclin F targets
Possible reference: Zhang, Y. et al. (2021) Identification of hub genes in colorectal cancer based on weighted gene co-expression network analysis and clinical data from The Cancer Genome Atlas., Biosci Rep, PMID 34308980

PXD030725 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated Proteogenomic Characterization of Adenocarcinoma of the esophagogastric junction
Possible reference: Li, S. et al. (2023) Integrative proteomic characterization of adenocarcinoma of esophagogastric junction., Nat Commun, PMID 36774361

PXD030712 Dataset with its publication pending (from PRIDE)
Dataset title: Salivary Hemoglobin Protects against Erosive Tooth Wear in Gastric Reflux Patients
Possible reference: Martini, T. et al. (2020) Salivary Hemoglobin Protects against Erosive Tooth Wear in Gastric Reflux Patients., Caries Res, PMID 33171464

PXD030708 Dataset with its publication pending (from PRIDE)
Dataset title: MetaNovo : an open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets
Possible reference: Potgieter, MG. et al. (2023) MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets., PLoS Comput Biol, PMID 37327214

PXD030673 no publication (from MassIVE)
Dataset title: Proximity Profiling of the CFTR Interaction Landscape In Response to Orkambi
Possible reference: Iazzi, M. et al. (2022) Proximity Profiling of the CFTR Interaction Landscape in Response to Orkambi., Int J Mol Sci, PMID 35269585

PXD030672 Dataset with its publication pending (from PRIDE)
Dataset title: Off-target effects of the lysosomal acid lipase inhibitors Lalistat-1 and Lalistat-2 on neutral lipid hydrolases
Possible reference: Bradić, I. et al. (2022) Off-target effects of the lysosomal acid lipase inhibitors Lalistat-1 and Lalistat-2 on neutral lipid hydrolases., Mol Metab, PMID 35504532

PXD030669 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analyses of excess starch and early senescent leaf mutant lses1 in rice
Possible reference: Chen, Z. et al. (2022) Integration of transcriptomic and proteomic analyses reveals several levels of metabolic regulation in the excess starch and early senescent leaf mutant lses1 in rice., BMC Plant Biol, PMID 35321646

PXD030667 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated Proteogenomic Characterization of Adenocarcinoma of the esophagogastric junction
Possible reference: Li, S. et al. (2023) Integrative proteomic characterization of adenocarcinoma of esophagogastric junction., Nat Commun, PMID 36774361

PXD030666 Dataset with its publication pending (from PRIDE)
Dataset title: Systematic identification of factors involved in the silencing of germline genes in mouse embryonic stem cells
Possible reference: Al Adhami, H. et al. (2023) Systematic identification of factors involved in the silencing of germline genes in mouse embryonic stem cells., Nucleic Acids Res, PMID 36772830

PXD030663 Dataset with its publication pending (from PRIDE)
Dataset title: Cell-type-specific labeling and profiling of glycans in living mice
Possible reference: Fan, X. et al. (2022) Cell-type-specific labeling and profiling of glycans in living mice., Nat Chem Biol, PMID 35513511

PXD030633 Dataset with its publication pending (from PRIDE)
Dataset title: Cellular Protein Client Recovery by Human Hsp40s DNAJB1 and DNAJB8
Possible reference: Montoya, MR. et al. (2024) Factors affecting protein recovery during Hsp40 affinity profiling., Anal Bioanal Chem, PMID 38850318

PXD030631 Dataset with its publication pending (from PRIDE)
Dataset title: OXSR1 inhibits inflammasome activation by limiting potassium efflux during mycobacterial infection
Possible reference: Hortle, E. et al. (2022) OXSR1 inhibits inflammasome activation by limiting potassium efflux during mycobacterial infection., Life Sci Alliance, PMID 35545295

PXD030630 Dataset with its publication pending (from PRIDE)
Dataset title: Patterning of the autotrophic, mixotrophic and heterotrophic proteomes of oxygen evolving cyanobacterium Synechocystis sp. PCC 6803
Possible reference: Muth-Pawlak, D. et al. (2022) Patterning of the Autotrophic, Mixotrophic, and Heterotrophic Proteomes of Oxygen-Evolving Cyanobacterium Synechocystis sp. PCC 6803., Front Microbiol, PMID 35694301

PXD030619 Dataset with its publication pending (from PRIDE)
Dataset title: Mass Spectrometry Uncovers Protein Interactions and Stoichiometry of Intermediates and Sub-complexes for SNARE Complex Assembly
Possible reference: Hesselbarth, J. et al. (2023) Mass spectrometry uncovers intermediates and off-pathway complexes for SNARE complex assembly., Commun Biol, PMID 36806321

PXD030613 Dataset with its publication pending (from PRIDE)
Dataset title: Venomics analysis of Thai Daboia siamensis using integrated omics data
Possible reference: Saethang, T. et al. (2022) Identification of Daboia siamensis venome using integrated multi-omics data., Sci Rep, PMID 35907887

PXD030609 Dataset with its publication pending (from PRIDE)
Dataset title: Two closely related white rot fungi, Obba rivulosa and Gelatoporia subvermispora, produce orthologous plant cell wall degrading enzymes for spruce wood degradation
Possible reference: Marinov�c, M. et al. (2022) Comparative Analysis of Enzyme Production Patterns of Lignocellulose Degradation of Two White Rot Fungi: Obba rivulosa and Gelatoporia subvermispora., Biomolecules, PMID 35892327

PXD030594 Dataset with its publication pending (from PRIDE)
Dataset title: Intercepting IRE1 Kinase-FMRP Signaling Prevents Atherosclerosis Progression
Possible reference: Yildirim, Z. et al. (2022) Intercepting IRE1 kinase-FMRP signaling prevents atherosclerosis progression., EMBO Mol Med, PMID 35191199

PXD030593 Dataset with its publication pending (from PRIDE)
Dataset title: Human cerebrospinal fluid after subarachnoid hemorrhage LC-MSMS
Possible reference: Hopkins, K. et al. (2023) Comparative proteomic analysis of ventricular and cisternal cerebrospinal fluid in haemorrhagic stroke patients., J Clin Neurosci, PMID 36525746

PXD030591 Dataset with its publication pending (from PRIDE)
Dataset title: Promiscuity of peptides presented in HLA-DP molecules from different immunogenicity groups is associated with T-cell cross-reactivity
Possible reference: Laghmouchi, A. et al. (2022) Promiscuity of Peptides Presented in HLA-DP Molecules from Different Immunogenicity Groups Is Associated With T-Cell Cross-Reactivity., Front Immunol, PMID 35251023

PXD030569 Dataset with its publication pending (from PRIDE)
Dataset title: Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF
Possible reference: Gorbovytska, V. et al. (2022) Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF., Nat Commun, PMID 35508485

PXD030555 Dataset with its publication pending (from iProX)
Dataset title: Mass Spectrometry in iMEF cell
Possible reference: Lin, J. et al. (2014) Inhibition of autophagy enhances the anticancer activity of silver nanoparticles., Autophagy, PMID 25484080

PXD030539 Dataset with its publication pending (from PRIDE)
Dataset title: thermal proteome profiling of hypomethylating agents in infant ALL
Possible reference: Cheung, LC. et al. (2023) Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy., Leukemia, PMID 36380143

PXD030535 Dataset with its publication pending (from PRIDE)
Dataset title: Metal removal capability of two cyanobacterial species in autotrophic and mixotrophic mode of nutrition
Possible reference: Ghorbani, E. et al. (2022) Metal removal capability of two cyanobacterial species in autotrophic and mixotrophic mode of nutrition., BMC Microbiol, PMID 35176992

PXD030532 Dataset with its publication pending (from PRIDE)
Dataset title: Cross-linking of the Endolysosomal System Reveals Potential Flotillin Structures and Cargo
Possible reference: Singh, J. et al. (2022) Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo., Nat Commun, PMID 36266287

PXD030530 no publication (from MassIVE)
Dataset title: SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein
Possible reference: Walter, M. et al. (2022) SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein., bioRxiv, PMID 35018374

PXD030529 Dataset with its publication pending (from PRIDE)
Dataset title: Palaeoproteomics identifies beaver fur and fur trade in Danish high-status Viking Age burials
Possible reference: Brandt, L�. et al. (2022) Palaeoproteomics identifies beaver fur in Danish high-status Viking Age burials - direct evidence of fur trade., PLoS One, PMID 35895633

PXD030485 Dataset with its publication pending (from PRIDE)
Dataset title: Mouse inguinal white adipose tissue (iWAT) LC-MS
Possible reference: Jiang, M. et al. (2026) Hilnc-mediated UCP1 translation repression contributes to thermogenesis and energy expenditure., Theranostics, PMID 41608567

PXD030475 no publication (from MassIVE)
Dataset title: Modeling FSHR function with hPSCs
Possible reference: Borutinskaitė, VV. et al. (2026) Reproductive tissue-derived stromal cells rescue fertility by coupling follicular activation with endometrial remodeling., Stem Cells Transl Med, PMID 41888633

PXD030467 Dataset with its publication pending (from PRIDE)
Dataset title: Functional Requirements for a Samd14-Capping Protein Complex in Stress Erythropoiesis
Possible reference: Ray, S. et al. (2022) Functional requirements for a Samd14-capping protein complex in stress erythropoiesis., Elife, PMID 35713400

PXD030466 Dataset with its publication pending (from PRIDE)
Dataset title: Writing and erasing O-GlcNAc on casein kinase 2 alpha alters the phosphoproteome
Possible reference: Schwein, PA. et al. (2022) Writing and Erasing O-GlcNAc on Casein Kinase 2 Alpha Alters the Phosphoproteome., ACS Chem Biol, PMID 35467332

PXD030445 Dataset with its publication pending (from PRIDE)
Dataset title: Phospho-docking protein 14-3-3 regulates microtubule-associated proteins in oocytes including the chromosomal passenger Borealin.
Possible reference: Repton, C. et al. (2022) The phospho-docking protein 14-3-3 regulates microtubule-associated proteins in oocytes including the chromosomal passenger Borealin., PLoS Genet, PMID 35666772

PXD030442 no publication (from MassIVE)
Dataset title: Oligosarcomas, IDH-mutant are distinct and aggressive
Possible reference: Suwala, AK. et al. (2022) Oligosarcomas, IDH-mutant are distinct and aggressive., Acta Neuropathol, PMID 34967922

PXD030434 Dataset with its publication pending (from iProX)
Dataset title: Comprehensive Comparison of Sample Preparation workflow for Large Scaled Proteome Identification
Possible reference: Karayel, O. et al. (2020) DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift., Proc Natl Acad Sci U S A, PMID 33288721

PXD030429 Dataset with its publication pending (from PRIDE)
Dataset title: MiniTurbo-based interactomics of two plasma membrane-localized SNARE proteins in Marchantia polymorpha
Possible reference: Melkonian, K. et al. (2022) miniTurbo-based interactomics of two plasma membrane-localized SNARE proteins in Marchantia polymorpha., New Phytol, PMID 35396742

PXD030424 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteomic analysis of breast cancer-derived extracellular vesicles reveals disease-specific phosphorylated enzymes
Possible reference: Minic, Z. et al. (2022) Phosphoproteomic Analysis of Breast Cancer-Derived Small Extracellular Vesicles Reveals Disease-Specific Phosphorylated Enzymes., Biomedicines, PMID 35203617

PXD030422 Dataset with its publication pending (from PRIDE)
Dataset title: Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer
Possible reference: Nicolas, AM. et al. (2022) Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer., Cancer Cell, PMID 35120600

PXD030409 no publication (from MassIVE)
Dataset title: Development of an experimental approach to achieve spatially resolved plant root-associated metaproteomics using an agar-plate system
Possible reference: Appidi, MR. et al. (2022) Development of an Experimental Approach to Achieve Spatially Resolved Plant Root-Associated Metaproteomics Using an Agar-Plate System., Mol Plant Microbe Interact, PMID 35349304

PXD030407 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics and secretome characterisation of a senescence-like cell state upon CDK4/6 inhibition
Possible reference: Beykou, M. et al. (2022) Proteomic characterisation of triple negative breast cancer cells following CDK4/6 inhibition., Sci Data, PMID 35817775

PXD030393 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense to fermentative and various respiratory metabolisms
Possible reference: Willemin, MS. et al. (2023) Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms., Front Microbiol, PMID 36733918

PXD030390 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Signature for Detection of High Grade Ovarian Cancer in germline BRCA mutation carriers
Possible reference: Bahar-Shany, K. et al. (2023) Proteomic signature for detection of high-grade ovarian cancer in germline BRCA mutation carriers., Int J Cancer, PMID 36214786

PXD030381 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanism-based traps enable protease and hydrolase substrate discovery
Possible reference: Tang, S. et al. (2022) Mechanism-based traps enable protease and hydrolase substrate discovery., Nature, PMID 35173328

PXD030367 Dataset with its publication pending (from PanoramaPublic)
Dataset title: Preserving the phosphoproteome of clinical biopsies using a quick freeze collection device
Possible reference: Kennedy, JJ. et al. (2022) Preserving the Phosphoproteome of Clinical Biopsies Using a Quick-Freeze Collection Device., Biopreserv Biobank, PMID 36301140

PXD030363 Dataset with its publication pending (from PRIDE)
Dataset title: SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression
Possible reference: Casteels, T. et al. (2022) SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression., Cell Rep, PMID 36044849

PXD030362 Dataset with its publication pending (from PRIDE)
Dataset title: SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression
Possible reference: Casteels, T. et al. (2022) SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression., Cell Rep, PMID 36044849

PXD030361 Dataset with its publication pending (from PRIDE)
Dataset title: SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression
Possible reference: Casteels, T. et al. (2022) SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression., Cell Rep, PMID 36044849

PXD030348 Dataset with its publication pending (from PRIDE)
Dataset title: A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimers disease
Possible reference: Boeddrich, A. et al. (2023) A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease., Genome Med, PMID 37468900

PXD030337 Dataset with its publication pending (from PRIDE)
Dataset title: Migration of Acanthamoeba through Legionella biofilms is regulated by bacterial quorum sensing, effectors and the flagellum
Possible reference: Hochstrasser, R. et al. (2022) Migration of Acanthamoeba through Legionella biofilms is regulated by the bacterial Lqs-LvbR network, effector proteins and the flagellum., Environ Microbiol, PMID 35415862

PXD030336 Dataset with its publication pending (from PRIDE)
Dataset title: The nitrobenzoxadiazole derivative NBDHEX behaves as Plasmodium falciparum gametocyte selective inhibitor with malaria parasite transmission blocking activity
Possible reference: Siciliano, G. et al. (2022) The Nitrobenzoxadiazole Derivative NBDHEX Behaves as Plasmodium falciparum Gametocyte Selective Inhibitor with Malaria Parasite Transmission Blocking Activity., Pharmaceuticals (Basel), PMID 35215282

PXD030334 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Analysis of Human Conjunctival Cells and Tears Collected with Schirmer Strips Using TimsTOF Pro
Possible reference: Akkurt Arslan, M. et al. (2021) Proteomic Analysis of Tears and Conjunctival Cells Collected with Schirmer Strips Using timsTOF Pro: Preanalytical Considerations., Metabolites, PMID 35050124

PXD030324 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic response of Neoporphyra haitanensis to dehydration-rehydration cycles
Possible reference: Chen, H. et al. (2022) Insights into the Ancient Adaptation to Intertidal Environments by Red Algae Based on a Genomic and Multiomics Investigation of Neoporphyra haitanensis., Mol Biol Evol, PMID 34730826

PXD030312 Dataset with its publication pending (from PRIDE)
Dataset title: Visualization of early ribosome assembly in action
Possible reference: Qin, B. et al. (2023) Cryo-EM captures early ribosome assembly in action., Nat Commun, PMID 36797249

PXD030301 Dataset with its publication pending (from PRIDE)
Dataset title: Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells
Possible reference: Mehta, S. et al. (2022) Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells., Cell Chem Biol, PMID 35839780

PXD030299 Dataset with its publication pending (from PRIDE)
Dataset title: Integrative structure models of the α-Synuclein dimer conformations
Possible reference: Sluchanko, NN. et al. (2017) Moonlighting chaperone-like activity of the universal regulatory 14-3-3 proteins., FEBS J, PMID 27973707

PXD030287 Dataset with its publication pending (from PRIDE)
Dataset title: Macaca mulatta serum exosomes MS
Possible reference: Vucetic, A. et al. (2023) Extracellular vesicle storm during the course of Ebola virus infection in primates., Front Cell Infect Microbiol, PMID 38035334

PXD030266 Dataset with its publication pending (from PRIDE)
Dataset title: Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies
Possible reference: Molitor, L. et al. (2023) Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies., Nucleic Acids Res, PMID 36651277

PXD030249 Dataset with its publication pending (from PRIDE)
Dataset title: The Plasmodium falciparum Nuclear Protein Phosphatase NIF4 is Required for Efficient Merozoite Invasion and Regulates Artemisinin Sensitivity
Possible reference: Zhu, X. et al. (2022) The Plasmodium falciparum Nuclear Protein Phosphatase NIF4 Is Required for Efficient Merozoite Invasion and Regulates Artemisinin Sensitivity., mBio, PMID 35938722

PXD030246 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial E3 ubiquitin ligase MARCHF5 controls BAK function independently of BH3-only proteins
Possible reference: Huang, AS. et al. (2023) Mitochondrial E3 ubiquitin ligase MARCHF5 controls BAK apoptotic activity independently of BH3-only proteins., Cell Death Differ, PMID 36171332

PXD030242 Dataset with its publication pending (from jPOST)
Dataset title: Phosphorylation of CAD1, PLDdelta, NDT1, RPM1 proteins induced resistance in tomatoes infected by Ralstonia solanacearum
Possible reference: Nounurai, P. et al. (2022) Phosphorylation of CAD1, PLDdelta, NDT1, RPM1 Proteins Induce Resistance in Tomatoes Infected by Ralstonia solanacearum., Plants (Basel), PMID 35336608

PXD030220 Dataset with its publication pending (from iProX)
Dataset title: An Integrative Proteome-Based Pharmacologic Characterization and Therapeutic Strategy Exploration of SAHA in Solid Malignancies
Possible reference: Liu, Q. et al. (2022) An Integrative Proteome-Based Pharmacologic Characterization and Therapeutic Strategy Exploration of SAHA in Solid Malignancies., J Proteome Res, PMID 35172096

PXD030210 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated analysis of early transcriptomic and proteomic alterations in mouse models of ALS/FTD identify early metabolic adaptions with similarities to mitochondrial dysfunction disorders
Possible reference: Matveeva, A. et al. (2024) Integrated analysis of transcriptomic and proteomic alterations in mouse models of ALS/FTD identify early metabolic adaptions with similarities to mitochondrial dysfunction disorders., Amyotroph Lateral Scler Frontotemporal Degener, PMID 37779364

PXD030206 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic response of SK-MEL-2 cells to polymyxin B
Possible reference: Zhang, C. et al. (2022) Proteomic Response Revealed Signaling Pathways Involving in the Mechanism of Polymyxin B-Induced Melanogenesis., Microbiol Spectr, PMID 35377227

PXD030201 no publication (from MassIVE)
Dataset title: Oxidation of whey proteins during thermal treatment characterized by a site-specific LC-MS/MS-based proteomic approach
Possible reference: Li, C. et al. (2022) Oxidation of Whey Proteins during Thermal Treatment Characterized by a Site-Specific LC-MS/MS-Based Proteomic Approach., J Agric Food Chem, PMID 35380828

PXD030190 Dataset with its publication pending (from PRIDE)
Dataset title: Succinylome and acetylome analyses of Staphylococcus aureusSuccinylome and acetylome analyses of Staphylococcus aureus
Possible reference: Tan, L. et al. (2022) Identification of Lysine Succinylome and Acetylome in the Vancomycin-Intermediate Staphylococcus aureus XN108., Microbiol Spectr, PMID 36374118

PXD030188 Stefano Doccini*, Maria Marchese, Federica Morani, Nicola Gammaldi, Serena Mero, Francesco Pezzini, Rabah Soliymani, Melissa Santi, Giovanni Signore, Asahi Ogi, Silvia Rocchiccioli, Katja M. Kanninen, Alessandro Simonati, Maciej M. Lalowski*, Filippo M. S (from MassIVE)
Dataset title: Lysosomal proteomics links disturbances in lipid homeostasis and sphingolipid metabolism to CLN5 disease.
Possible reference: Doccini, S. et al. (2022) Lysosomal Proteomics Links Disturbances in Lipid Homeostasis and Sphingolipid Metabolism to CLN5 Disease., Cells, PMID 35681535

PXD030179 Dataset with its publication pending (from PRIDE)
Dataset title: Cultivation impact on the protein expression profile of Mycobacterium bovis BCG strains Moreau and Pasteur
Possible reference: Corr�a, PR. et al. (2025) Culture conditions impact the protein expression profile of Mycobacterium bovis BCG strains Moreau and Pasteur., BMC Microbiol, PMID 41420210

PXD030176 Dataset with its publication pending (from jPOST)
Dataset title: Shotgun proteomics (label-free quantitation) of Pyrodinium bahamense
Possible reference: Subong, BJJ. et al. (2021) Biochemical Mapping of Pyrodinium bahamense Unveils Molecular Underpinnings behind Organismal Processes., Int J Mol Sci, PMID 34948131

PXD030167 Dataset with its publication pending (from PRIDE)
Dataset title: Surgical trauma in mice modifies the content of circulating extracellular vesicles
Possible reference: Mkrtchian, S. et al. (2021) Surgical Trauma in Mice Modifies the Content of Circulating Extracellular Vesicles., Front Immunol, PMID 35116043

PXD030142 Dataset with its publication pending (from PRIDE)
Dataset title: Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains
Possible reference: Eninger, T. et al. (2022) Signatures of glial activity can be detected in the CSF proteome., Proc Natl Acad Sci U S A, PMID 35666874

PXD030134 Dataset with its publication pending (from PRIDE)
Dataset title: RNase L activating 2′-5′ oligoadenlyates bind ABCF1, -3 and Decr-1
Possible reference: Govande, AA. et al. (2023) RNase L-activating 2'-5' oligoadenylates bind ABCF1, ABCF3 and Decr-1., J Gen Virol, PMID 37676257

PXD030131 Dataset with its publication pending (from PRIDE)
Dataset title: Global analysis of lysine 2-hydroxyisobutyrylation during Fusarium graminearum infection in maize
Possible reference: Zhang, K. et al. (2022) Global analysis of lysine 2-hydroxyisobutyrylation during Fusarium graminearum infection in maize., Front Plant Sci, PMID 36186065

PXD030130 Dataset with its publication pending (from PRIDE)
Dataset title: Age-related differences in structure and function of nasal epithelial cultures from healthy children and elderly people
Possible reference: Bal�zs, A. et al. (2022) Age-Related Differences in Structure and Function of Nasal Epithelial Cultures From Healthy Children and Elderly People., Front Immunol, PMID 35296085

PXD030128 Dataset with its publication pending (from PRIDE)
Dataset title: Label-Free Proteomics-based analysis of peripheral nerve injury induced by Japanese encephalitis virus
Possible reference: Wang, X. et al. (2022) Label-free proteomics-based analysis of peripheral nerve injury induced by Japanese encephalitis virus., J Proteomics, PMID 35605915

PXD030092 Dataset with its publication pending (from PRIDE)
Dataset title: The proteome of irradiated glioma stem cells and of their extracellular vesicles
Possible reference: Pan, J. et al. (2022) Extracellular vesicles derived from glioblastoma promote proliferation and migration of neural progenitor cells via PI3K-Akt pathway., Cell Commun Signal, PMID 35022057

PXD030076 Dataset with its publication pending (from PRIDE)
Dataset title: Distinct ribosome states trigger diverse mRNA quality control pathways
Possible reference: Saito, K. et al. (2015) Inhibiting K63 polyubiquitination abolishes no-go type stalled translation surveillance in Saccharomyces cerevisiae., PLoS Genet, PMID 25909477

PXD030072 Dataset with its publication pending (from PRIDE)
Dataset title: Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR
Possible reference: Perez Verdaguer, M. et al. (2022) Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR., Cell Rep, PMID 35705039

PXD030061 Dataset with its publication pending (from PRIDE)
Dataset title: AP-BNPAGE YAP1 complexes separation
Possible reference: Uliana, F. et al. (2023) Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration., Mol Syst Biol, PMID 36896621

PXD030057 Dataset with its publication pending (from PRIDE)
Dataset title: A positive feedback loop mediates crosstalk between calcium, cyclic nucleotide and lipid signaling in Toxoplasma gondii.
Possible reference: Nofal, SD. et al. (2022) A positive feedback loop mediates crosstalk between calcium, cyclic nucleotide and lipid signalling in calcium-induced Toxoplasma gondii egress., PLoS Pathog, PMID 36265000

PXD030056 Dataset with its publication pending (from PRIDE)
Dataset title: Polymer type specific microplastic effects on Dreissena bugensis’ proteome, antioxidant activity and behavior
Possible reference: Brehm, J. et al. (2022) In-depth characterization revealed polymer type and chemical content specific effects of microplastic on Dreissena bugensis., J Hazard Mater, PMID 35728319

PXD030053 no publication (from MassIVE)
Dataset title: Deciphering the Physiological Response of Escherichia coli Under High ATP Demand
Possible reference: Boecker, S. et al. (2021) Deciphering the physiological response of Escherichia coli under high ATP demand., Mol Syst Biol, PMID 34928538

PXD030049 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis on the protective effect of eriodictyol on benzo(a)pyrene-induced Caco-2 cytotoxicity
Possible reference: Wang, C. et al. (2022) Proteomic Analysis of the Protective Effect of Eriodictyol on Benzo(a)pyrene-Induced Caco-2 Cytotoxicity., Front Nutr, PMID 35308267

PXD030044 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of BRCA1-associated protein 1 (BAP1)-associated proteins
Possible reference: Murali, R. et al. (2013) Tumours associated with BAP1 mutations., Pathology, PMID 23277170

PXD030030 Dataset with its publication pending (from iProX)
Dataset title: Mass spectrometry experiments to detect mettl3 related proteins and modifications
Possible reference: Liu, K. et al. (2023) Short-chain fatty acid-butyric acid ameliorates granulosa cells inflammation through regulating METTL3-mediated N6-methyladenosine modification of FOSL2 in polycystic ovarian syndrome., Clin Epigenetics, PMID 37179374

PXD029994 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative Phenotypic, Proteomic, and Phosphoproteomic Analysis Reveals Different Roles of Serine/Threonine Phosphatase and Kinase in the Growth, Cell Division, and Pathogenicity of Streptococcus suis
Possible reference: Hu, Q. et al. (2021) Comparative Phenotypic, Proteomic, and Phosphoproteomic Analysis Reveals Different Roles of Serine/Threonine Phosphatase and Kinase in the Growth, Cell Division, and Pathogenicity of Streptococcus suis., Microorganisms, PMID 34946045

PXD029988 Dataset with its publication pending (from PRIDE)
Dataset title: Subcellular proteomics of murine presomitic mesoderm
Possible reference: M�ller, J. et al. (2014) O-fucosylation of the notch ligand mDLL1 by POFUT1 is dispensable for ligand function., PLoS One, PMID 24533113

PXD029942 Dataset with its publication pending (from PRIDE)
Dataset title: Von Willebrand factor A1 domain affinity for GPIbÎ± and stability are differentially regulated by its O-glycosylated N-linker and C-linker
Possible reference: Bonazza, K. et al. (2022) Von Willebrand factor A1 domain stability and affinity for GPIbα are differentially regulated by its O-glycosylated N- and C-linker., Elife, PMID 35532124

PXD029940 Dataset with its publication pending (from PRIDE)
Dataset title: Sumoylation regulates protein cargo in Astrocyte-derived small extracellular vesicles
Possible reference: Fernandez, A. et al. (2024) Sumoylation in astrocytes induces changes in the proteome of the derived small extracellular vesicles which change protein synthesis and dendrite morphology in target neurons., Brain Res, PMID 37972846

PXD029902 Dataset with its publication pending (from PRIDE)
Dataset title: A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline
Possible reference: Reilly, L. et al. (2023) A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline., Cell Rep Methods, PMID 37729920

PXD029882 Dataset with its publication pending (from PRIDE)
Dataset title: The oncogenic fusion protein DNAJB1-PRKACA can be specifically targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma
Possible reference: Bauer, J. et al. (2022) The oncogenic fusion protein DNAJB1-PRKACA can be specifically targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma., Nat Commun, PMID 36302754

PXD029870 no publication (from MassIVE)
Dataset title: Spatial Venomics - Cobra Venom System Reveals Spatial Distinction of Snake Toxins by Mass Spectrometry Imaging
Possible reference: Nachtigall, PG. et al. (2025) The gene regulatory mechanisms shaping the heterogeneity of venom production in the Cape coral snake., Genome Biol, PMID 40390047

PXD029866 Dataset with its publication pending (from PRIDE)
Dataset title: A Global Phosphorylation Atlas of Proteins within Pathological Site of Rotator Cuff Tendinopathy
Possible reference: Wang, Y. et al. (2021) A Global Phosphorylation Atlas of Proteins Within Pathological Site of Rotator Cuff Tendinopathy., Front Mol Biosci, PMID 35242811

PXD029857 Dataset with its publication pending (from iProX)
Dataset title: Immunoglobulin-Associated Proteome (IgAP) in Patients of Acute Myocardial Infarction and Chronic Coronary Syndromes
Possible reference: Tan, M. et al. (2022) Quantitative proteomics reveals differential immunoglobulin-associated proteome (IgAP) in patients of acute myocardial infarction and chronic coronary syndromes., J Proteomics, PMID 34890869

PXD029856 Dataset with its publication pending (from iProX)
Dataset title: Discovery of Metal-binding Proteins by METAL-TPP with TPEN
Possible reference: Zeng, X. et al. (2024) Discovery of metal-binding proteins by thermal proteome profiling., Nat Chem Biol, PMID 38409364

PXD029844 Dataset with its publication pending (from PRIDE)
Dataset title: Preserving the phosphoproteome of clinical biopsies using a quick freeze collection device
Possible reference: Kennedy, JJ. et al. (2022) Preserving the Phosphoproteome of Clinical Biopsies Using a Quick-Freeze Collection Device., Biopreserv Biobank, PMID 36301140

PXD029824 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic consequences of TDA1 deficiency in Saccharomyces cerevisiae
Possible reference: M�ller, H. et al. (2022) Proteomic consequences of TDA1 deficiency in Saccharomyces cerevisiae: Protein kinase Tda1 is essential for Hxk1 and Hxk2 serine 15 phosphorylation., Sci Rep, PMID 36302925

PXD029806 Dataset with its publication pending (from PRIDE)
Dataset title: Effects of neck-arm restraint suspension of beef carcasses on meat quality and proteome of different muscles during post-mortem aging
Possible reference: Cai, W. et al. (2021) Effects of Neck-Arm Restraint Suspension of Beef Carcasses on Meat Quality and Proteome of Different Muscles During Post-mortem Aging., Front Nutr, PMID 34993220

PXD029780 Dataset with its publication pending (from PRIDE)
Dataset title: A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies
Possible reference: Lombard-Banek, C. et al. (2022) A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies., J Proteome Res, PMID 35404046

PXD029772 Dataset with its publication pending (from iProX)
Dataset title: Iodoacetyl tandem mass tag (iodoTMT)-based redox proteomics of Arabidopsis thaliana
Possible reference: Nietzel, T. et al. (2020) Redox-mediated kick-start of mitochondrial energy metabolism drives resource-efficient seed germination., Proc Natl Acad Sci U S A, PMID 31871212

PXD029757 no publication (from MassIVE)
Dataset title: Proteomic changes associated with predator induced morphological defenses in Olympia oysters
Possible reference: Evans, TG. et al. (2022) Proteomic changes associated with predator-induced morphological defences in oysters., Mol Ecol, PMID 35754098

PXD029728 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of biofilm associated protein (Bap) in Staphylococcus xylosus
Possible reference: Schiffer, C. et al. (2019) Bap and Cell Surface Hydrophobicity Are Important Factors in Staphylococcus xylosus Biofilm Formation., Front Microbiol, PMID 31293539

PXD029725 Dataset with its publication pending (from PRIDE)
Dataset title: Oncogenic Mutations of KRAS Modulate Its Turnover by the CUL3/LZTR1 E3 ligase Complex
Possible reference: Damianou, A. et al. (2024) Oncogenic mutations of KRAS modulate its turnover by the CUL3/LZTR1 E3 ligase complex., Life Sci Alliance, PMID 38453365

PXD029691 Dataset with its publication pending (from PRIDE)
Dataset title: Reprogramming of sorghum proteome in response to sugarcane aphid infestation
Possible reference: Grover, S. et al. (2022) Reprogramming of sorghum proteome in response to sugarcane aphid infestation., Plant Sci, PMID 35643611

PXD029689 Dataset with its publication pending (from PRIDE)
Dataset title: Amyloid-like aggregating proteins cause lysosomal defects in neurons via gain-of-function toxicity
Possible reference: Riera-Tur, I. et al. (2022) Amyloid-like aggregating proteins cause lysosomal defects in neurons via gain-of-function toxicity., Life Sci Alliance, PMID 34933920

PXD029683 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome dataset of peripheral blood mononuclear cells in postpartum dairy cows supplemented with different sources of omega-3 fatty acids
Possible reference: Kra, G. et al. (2022) Proteome dataset of peripheral blood mononuclear cells in postpartum dairy cows supplemented with different sources of omega-3 fatty acids., Data Brief, PMID 35036486

PXD029682 Dataset with its publication pending (from PRIDE)
Dataset title: CDC-like Kinase 4 Deficiency Contributes to Pathological Cardiac Hypertrophy by Modulating NEXN Phosphorylation
Possible reference: Huang, J. et al. (2022) CDC-like kinase 4 deficiency contributes to pathological cardiac hypertrophy by modulating NEXN phosphorylation., Nat Commun, PMID 35907876

PXD029653 Dataset with its publication pending (from PRIDE)
Dataset title: A Co-culture System Reveals a Cross-talk between Alveolar Epithelium and Pulmonary Microvascular Endothelium during SARS-CoV-2 Infection
Possible reference: Wang, P. et al. (2020) A cross-talk between epithelium and endothelium mediates human alveolar-capillary injury during SARS-CoV-2 infection., Cell Death Dis, PMID 33293527

PXD029635 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics investigations of potential protein biomarkers in sera of rabbits infected with Schistosoma japonicum
Possible reference: Bi, NN. et al. (2021) Proteomics Investigations of Potential Protein Biomarkers in Sera of Rabbits Infected With Schistosoma japonicum., Front Cell Infect Microbiol, PMID 35004354

PXD029620 Dataset with its publication pending (from PRIDE)
Dataset title: Colon cancer, cell line, overexpressed CCDC12
Possible reference: Du, F. et al. (2022) CCDC12 promotes tumor development and invasion through the Snail pathway in colon adenocarcinoma., Cell Death Dis, PMID 35217636

PXD029616 Dataset with its publication pending (from PRIDE)
Dataset title: N-Acetylation of secreted proteins is widespread in Apicomplexa and independent of acetyl-CoA transporter AT1
Possible reference: Nyonda, MA. et al. (2022) N-acetylation of secreted proteins in Apicomplexa is widespread and is independent of the ER acetyl-CoA transporter AT1., J Cell Sci, PMID 35621049

PXD029596 Dataset with its publication pending (from PRIDE)
Dataset title: Thymine DNA glycosylase (TDG) regulates cell cycle–driven p53 transcriptional control in pluripotent cells
Possible reference: Aranda, S. et al. (2023) Thymine DNA glycosylase regulates cell-cycle-driven p53 transcriptional control in pluripotent cells., Mol Cell, PMID 37506700

PXD029580 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy
Possible reference: Krause, GJ. et al. (2023) Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy., Cell Rep, PMID 38060380

PXD029566 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Analysis Suggests Altered Mitochondrial Metabolic Profile Associated with Diabetic Cardiomyopathy
Possible reference: Gomes, KP. et al. (2022) Proteomic Analysis Suggests Altered Mitochondrial Metabolic Profile Associated With Diabetic Cardiomyopathy., Front Cardiovasc Med, PMID 35310970

PXD029557 Dataset with its publication pending (from jPOST)
Dataset title: Dietary germinated paddy rice and stocking density affect egg performance, serum biochemical properties, and proteomic and transcriptomic response of laying hens exposed to chronic heat stress
Possible reference: Incharoen, T. et al. (2021) Dietary Germinated Paddy Rice and Stocking Density Affect Egg Performance, Serum Biochemical Properties, and Proteomic and Transcriptomic Response of Laying Hens Exposed to Chronic Heat Stress., Proteomes, PMID 34941813

PXD029538 Dataset with its publication pending (from PRIDE)
Dataset title: Neuralized-like protein 4 (Neurl4) mediates ADP-ribosylation of mitochondrial proteins
Possible reference: Cardamone, MD. et al. (2022) Neuralized-like protein 4 (NEURL4) mediates ADP-ribosylation of mitochondrial proteins., J Cell Biol, PMID 35157000

PXD029518 Dataset with its publication pending (from PRIDE)
Dataset title: Crosstalk between Mutant p53 and p62/SQSTM1 Augments Cancer Cell Migration by Promoting the Degradation of Cell Adhesion Proteins
Possible reference: Mukherjee, S. et al. (2022) Cross-talk between mutant p53 and p62/SQSTM1 augments cancer cell migration by promoting the degradation of cell adhesion proteins., Proc Natl Acad Sci U S A, PMID 35439056

PXD029501 Dataset with its publication pending (from PRIDE)
Dataset title: Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration.
Possible reference: Senabouth, A. et al. (2022) Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration., Nat Commun, PMID 35882847

PXD029489 Dataset with its publication pending (from PRIDE)
Dataset title: RNF31 inhibition sensitizes tumors to bystander killing by innate and adaptive immune cells
Possible reference: Zhang, Z. et al. (2022) RNF31 inhibition sensitizes tumors to bystander killing by innate and adaptive immune cells., Cell Rep Med, PMID 35688159

PXD029480 Dataset with its publication pending (from PRIDE)
Dataset title: Site-specific protein modification by 3-n-butylphthalide in primary hepatocytes: covalent protein adducts diminished by glutathione and N-acetylcysteine
Possible reference: Xue, Y. et al. (2021) Site-specific protein modification by 3-n-butylphthalide in primary hepatocytes: Covalent protein adducts diminished by glutathione and N-acetylcysteine., Life Sci, PMID 34762904

PXD029396 Dataset with its publication pending (from PRIDE)
Dataset title: Actinobacillus pleuropneumoniae serotype 2 exoproteome LF-LC-MS/MS
Possible reference: Stancheva, SG. et al. (2022) Proteomic and immunoproteomic insights into the exoproteome of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia., Microb Pathog, PMID 36087692

PXD029374 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling and alteration in Tuta absoluta upon infection with entomopathogenic fungi, Beauveria bassiana and Purpureocillium lilacinum
Possible reference: Bali, GK. et al. (2022) An insight in proteome profiling of Tuta absoluta larvae after entomopathogenic fungal infection., Sci Data, PMID 35986033

PXD029368 Dataset with its publication pending (from PRIDE)
Dataset title: Rat parathyroid glands LC-MS/MS
Possible reference: Şenkal-Turhan, S. et al. (2024) Induced Pluripotent Stem Cell-Derived Parathyroid Organoids Resemble Parathyroid Morphology and Function., Adv Sci (Weinh), PMID 39331961

PXD029343 Dataset with its publication pending (from PRIDE)
Dataset title: Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock
Possible reference: Schmal, C. et al. (2023) Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock., PLoS Biol, PMID 37379316

PXD029319 Dataset with its publication pending (from PRIDE)
Dataset title: Putative methylomirabilis lanthanidiphila surface layer protein
Possible reference: Gambelli, L. et al. (2021) The Polygonal Cell Shape and Surface Protein Layer of Anaerobic Methane-Oxidizing Methylomirabilis lanthanidiphila Bacteria., Front Microbiol, PMID 34925275

PXD029303 Dataset with its publication pending (from jPOST)
Dataset title: eIF4A1-bound 48S complex in HEK293T cells
Possible reference: Babaylova, E. et al. (2019) Tetrapeptide 60-63 of human ribosomal protein uS3 is crucial for translation initiation., Biochim Biophys Acta Gene Regul Mech, PMID 31356988

PXD029302 Dataset with its publication pending (from jPOST)
Dataset title: eIF4A1-bound 48S complex in HEK293T cells
Possible reference: Babaylova, E. et al. (2019) Tetrapeptide 60-63 of human ribosomal protein uS3 is crucial for translation initiation., Biochim Biophys Acta Gene Regul Mech, PMID 31356988

PXD029301 Dataset with its publication pending (from jPOST)
Dataset title: eIF4A1-bound 48S complex in HEK293T cells
Possible reference: Babaylova, E. et al. (2019) Tetrapeptide 60-63 of human ribosomal protein uS3 is crucial for translation initiation., Biochim Biophys Acta Gene Regul Mech, PMID 31356988

PXD029291 Dataset with its publication pending (from PRIDE)
Dataset title: N1-methylpseudouridine found within COVID-19 mRNA vaccines produces faithful protein products
Possible reference: Kim, KQ. et al. (2022) N1-methylpseudouridine found within COVID-19 mRNA vaccines produces faithful protein products., Cell Rep, PMID 35988540

PXD029278 Andrew Frando, Vishant Boradia, Marina Gritsenko, Michael-Claude Beltejar, Le Day, David R. Sherman, Shuyi Ma, Jon M. Jacobs, Christoph Grundner. The Mycobacterium tuberculosis protein O-phosphorylation landscape. bioRxiv. Epub 2022 Feb 17. doi: https://d (from MassIVE)
Dataset title: The Mycobacterium tuberculosis O-phosphorylation landscape
Possible reference: Frando, A. et al. (2023) The Mycobacterium tuberculosis protein O-phosphorylation landscape., Nat Microbiol, PMID 36690861

PXD029270 Dataset with its publication pending (from PRIDE)
Dataset title: Cysteine 253 of UCP1 regulates energy expenditure and adipose tissue inflammation
Possible reference: Mills, EL. et al. (2022) Cysteine 253 of UCP1 regulates energy expenditure and sex-dependent adipose tissue inflammation., Cell Metab, PMID 34861155

PXD029269 Dataset with its publication pending (from PRIDE)
Dataset title: Boost-DiLeu: Enhanced Isobaric N,N-Dimethyl Leucine Tagging Strategy for Comprehensive Quantitative Glycoproteomic Analysis
Possible reference: Wang, D. et al. (2022) Boost-DiLeu: Enhanced Isobaric N,N-Dimethyl Leucine Tagging Strategy for a Comprehensive Quantitative Glycoproteomic Analysis., Anal Chem, PMID 35960654

PXD029267 Dataset with its publication pending (from PRIDE)
Dataset title: The spread of herds and horses into the Altai
Possible reference: Ventresca Miller, AR. et al. (2022) The spread of herds and horses into the Altai: How livestock and dairying drove social complexity in Mongolia., PLoS One, PMID 35544454

PXD029241 Dataset with its publication pending (from PRIDE)
Dataset title: Changes in the proteome and secretome of rat liver sinusoidal endothelial cells during early primary culture and effects of dexamethasone
Possible reference: Li, R. et al. (2022) Changes in the proteome and secretome of rat liver sinusoidal endothelial cells during early primary culture and effects of dexamethasone., PLoS One, PMID 36054185

PXD029226 Dataset with its publication pending (from PRIDE)
Dataset title: Liver mitochondria-associated ER membrane proteomics for studying the effects of ZiBuPiYin recipe on Zucker diabetic fatty rats after chronic psychological stress
Possible reference: Xu, H. et al. (2022) Liver mitochondria-associated endoplasmic reticulum membrane proteomics for studying the effects of ZiBuPiYin recipe on Zucker diabetic fatty rats after chronic psychological stress., Front Cell Dev Biol, PMID 36407109

PXD029205 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic dataset of the moss Physcomitrium patens SMG1 KO mutant line
Possible reference: Mamaeva, A. et al. (2022) Quantitative proteomic dataset of the moss Physcomitrium patens SMG1 KO mutant line., Data Brief, PMID 34977295

PXD029202 Dataset with its publication pending (from PRIDE)
Dataset title: Using Quantitative Proteomic Assessments and their Association with Long Term Healing Outcomes
Possible reference: Chen, J. et al. (2022) Complement factor D as a predictor of Achilles tendon healing and long-term patient outcomes., FASEB J, PMID 35596679

PXD029195 Dataset with its publication pending (from PRIDE)
Dataset title: Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer’s disease
Possible reference: Yu, M. et al. (2023) Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer's disease., Cell Rep, PMID 37925638

PXD029193 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of antimicrobial peptides isolated from the skin mucus of African Catfish, Clarias gariepinus (Burchell, 1822)
Possible reference: Okella, H. et al. (2021) Identification of Antimicrobial Peptides Isolated From the Skin Mucus of African Catfish, Clarias gariepinus (Burchell, 1822)., Front Microbiol, PMID 34987491

PXD029187 Dataset with its publication pending (from PRIDE)
Dataset title: TMT-based quantitative proteomic analysis reveals the physiological regulatory networks of embryo dehydration protection in lotus (Nelumbo nucifera)
Possible reference: Zhang, D. et al. (2021) TMT-Based Quantitative Proteomic Analysis Reveals the Physiological Regulatory Networks of Embryo Dehydration Protection in Lotus (Nelumbo nucifera)., Front Plant Sci, PMID 34975978

PXD029170 no publication (from MassIVE)
Dataset title: Site-specific characterization of heat-induced disulfide rearrangement in beta-lactoglobulin by liquid chromatography-mass spectrometry
Possible reference: Li, C. et al. (2022) Site-Specific Characterization of Heat-Induced Disulfide Rearrangement in Beta-Lactoglobulin by Liquid Chromatography-Mass Spectrometry., J Agric Food Chem, PMID 35025507

PXD029169 Dataset with its publication pending (from jPOST)
Dataset title: Reversible flower opening regulated by CPK16-dependent phosphorylation and activation of aquaporin PIP2;2 in Gentiana
Possible reference: Nemoto, K. et al. (2022) Calcium-dependent protein kinase 16 phosphorylates and activates the aquaporin PIP2;2 to regulate reversible flower opening in Gentiana scabra., Plant Cell, PMID 35441691

PXD029163 Dataset with its publication pending (from PRIDE)
Dataset title: SPHINGOSINE 1-PHOSPHATE MEDIATES ADIPONECTIN RECEPTOR SIGNALING ESSENTIAL FOR LIPID HOMEOSTASIS AND EMBRYOGENESIS
Possible reference: Ruiz, M. et al. (2022) Sphingosine 1-phosphate mediates adiponectin receptor signaling essential for lipid homeostasis and embryogenesis., Nat Commun, PMID 36418331

PXD029156 Dataset with its publication pending (from PRIDE)
Dataset title: CLUH controls astrin-1 expression to couple mitochondrial metabolism to cell cycle progression
Possible reference: Schatton, D. et al. (2022) CLUH controls astrin-1 expression to couple mitochondrial metabolism to cell cycle progression., Elife, PMID 35559794

PXD029152 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of Trichomonas vaginalis phagolysosomes, lysosomal targeting, and unconventional secretion of cysteine peptidases
Possible reference: Zimmann, N. et al. (2022) Proteomic Analysis of Trichomonas vaginalis Phagolysosome, Lysosomal Targeting, and Unconventional Secretion of Cysteine Peptidases., Mol Cell Proteomics, PMID 34763061

PXD029145 Dataset with its publication pending (from PRIDE)
Dataset title: CLUH controls astrin-1 expression to couple mitochondrial metabolism to cell cycle progression
Possible reference: Schatton, D. et al. (2022) CLUH controls astrin-1 expression to couple mitochondrial metabolism to cell cycle progression., Elife, PMID 35559794

PXD029144 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics and immunoproteomics of Anoplocephala perfoliata
Possible reference: Hautala, K. et al. (2022) Label-free quantitative proteomics and immunoblotting identifies immunoreactive and other excretory-secretory (E/S) proteins of Anoplocephala perfoliata., Front Immunol, PMID 36466892

PXD029143 Dataset with its publication pending (from PRIDE)
Dataset title: Noninvasive Nasopharyngeal Proteomics Identify Coagulation Abnormalities in SARS-CoV-2
Possible reference: Ayass, MA. et al. (2022) Noninvasive nasopharyngeal proteomics of COVID-19 patient identify abnormalities related to complement and coagulation cascade and mucosal immune system., PLoS One, PMID 36094909

PXD029142 Dataset with its publication pending (from PRIDE)
Dataset title: CLUH controls astrin-1 expression to couple mitochondrial metabolism to cell cycle progression
Possible reference: Schatton, D. et al. (2022) CLUH controls astrin-1 expression to couple mitochondrial metabolism to cell cycle progression., Elife, PMID 35559794

PXD029136 Dataset with its publication pending (from PRIDE)
Dataset title: Role of the E3 Ubiquitin-ligase Hakai in intestinal inflammation and cancer bowel disease
Possible reference: Roca-Lema, D. et al. (2022) Role of the E3 ubiquitin-ligase Hakai in intestinal inflammation and cancer bowel disease., Sci Rep, PMID 36266428

PXD029130 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic analysis for revealing the advantage mechanisms of Salt-tolerant tomato (Solanum lycopersicum)
Possible reference: Wang, Q. et al. (2022) Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium)., PeerJ, PMID 35251781

PXD029124 no publication (from MassIVE)
Dataset title: Dietary relevant concentrations of BDE-47, -99, -209 and their mixture differently affect HepG2 transcriptomic and proteomic profiles.
Possible reference: Casella, M. et al. (2022) BDE-47, -99, -209 and Their Ternary Mixture Disrupt Glucose and Lipid Metabolism of Hepg2 Cells at Dietary Relevant Concentrations: Mechanistic Insight through Integrated Transcriptomics and Proteomics Analysis., Int J Mol Sci, PMID 36430946

PXD029122 Dataset with its publication pending (from PRIDE)
Dataset title: Modular bottom-up proteomic sample preparation for high-throughput applications
Possible reference: Toby, TK. et al. (2019) A comprehensive pipeline for translational top-down proteomics from a single blood draw., Nat Protoc, PMID 30518910

PXD029120 Dataset with its publication pending (from PRIDE)
Dataset title: G3BP1 inhibits Cul3SPOP to amplify AR signaling and promote prostate cancer
Possible reference: Mukhopadhyay, C. et al. (2021) G3BP1 inhibits Cul3SPOP to amplify AR signaling and promote prostate cancer., Nat Commun, PMID 34795264

PXD029080 Dataset with its publication pending (from PRIDE)
Dataset title: Eggshell-matrix protein proteome for squamates
Possible reference: Xie, HX. et al. (2022) The eggshell-matrix protein gene OC-17 is functionally lost in the viviparous Chinese crocodile lizard., J Evol Biol, PMID 36129910

PXD029068 Dataset with its publication pending (from iProX)
Dataset title: Epicatechin rescues memory deficits by inducing autophagy in tauopathy
Possible reference: Wu, Y. et al. (2025) (-)-Epicatechin Rescues Memory Deficits by Activation of Autophagy in a Mouse Model of Tauopathies., MedComm (2020), PMID 40135197

PXD029048 Dataset with its publication pending (from PRIDE)
Dataset title: Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium
Possible reference: Romeu, MJ. et al. (2022) Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium., NPJ Biofilms Microbiomes, PMID 36253388

PXD029029 Dataset with its publication pending (from PRIDE)
Dataset title: Citrullinated epitopes identified on tumor MHC class II by peptide elution stimulate both regulatory and Th1 responses and require careful selection for optimal tumor therapy
Possible reference: Symonds, P. et al. (2021) Citrullinated Epitopes Identified on Tumour MHC Class II by Peptide Elution Stimulate Both Regulatory and Th1 Responses and Require Careful Selection for Optimal Anti-Tumour Responses., Front Immunol, PMID 34858415

PXD029025 Xiaowei Gao ,Bhagyashree N. Swarge, Henk L. Dekker, Winfried Roseboom, Stanley Brul, and Gertjan Kramer. The Membrane Proteome of Spores and Vegetative Cells of the Food-Borne Pathogen Bacillus cereus. Int. J. Mol. Sci. 2021, 22(22), 12475. (from MassIVE)
Dataset title: The membrane proteome of spores and vegetative cells of the food-borne pathogen Bacillus cereus.
Possible reference: Gao, X. et al. (2021) The Membrane Proteome of Spores and Vegetative Cells of the Food-Borne Pathogen Bacillus cereus., Int J Mol Sci, PMID 34830357

PXD029008 Dataset with its publication pending (from PRIDE)
Dataset title: C. elegans TFIIH subunit GTF-2H5/TTDA is a non-essential transcription factor indispensable for DNA repairC. elegans TFIIH subunit GTF-2H5/TTDA is a non-essential transcription factor indispensable for DNA repair.
Possible reference: Thijssen, KL. et al. (2021) C. elegans TFIIH subunit GTF-2H5/TTDA is a non-essential transcription factor indispensable for DNA repair., Commun Biol, PMID 34824371

PXD029002 no publication (from MassIVE)
Dataset title: Cowen_Myers_Chemogenomics_2021
Possible reference: Fu, C. et al. (2021) Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets., Nat Commun, PMID 34764269

PXD028995 no publication (from MassIVE)
Dataset title: Expanding the biological role of lipo-chitooligosaccharides and chitooligosaccharides in Laccaria bicolor growth and development
Possible reference: Villalobos Solis, MI. et al. (2022) Expanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and Development., Front Fungal Biol, PMID 37746234

PXD028987 Dataset with its publication pending (from PRIDE)
Dataset title: Hypoxia-induced aquaporins and regulation of redox homeostasis by a trans-plasma membrane electron transport system in maize roots
Possible reference: Hofmann, A. et al. (2022) Hypoxia-Induced Aquaporins and Regulation of Redox Homeostasis by a Trans-Plasma Membrane Electron Transport System in Maize Roots., Antioxidants (Basel), PMID 35624700

PXD028974 Dataset with its publication pending (from PRIDE)
Dataset title: A longer isoform of Stim1 is a negative SOCE regulator but increases cAMP modulated NFAT signaling
Possible reference: Knapp, ML. et al. (2022) A longer isoform of Stim1 is a negative SOCE regulator but increases cAMP-modulated NFAT signaling., EMBO Rep, PMID 34942054

PXD028973 no publication (from MassIVE)
Dataset title: The F-box protein Bard (CG14317) targets the Smaug RNA-binding protein for destruction during the Drosophila maternal-to-zygotic transition
Possible reference: Cao, WX. et al. (2022) The F-box protein Bard (CG14317) targets the Smaug RNA-binding protein for destruction during the Drosophila maternal-to-zygotic transition., Genetics, PMID 34757425

PXD028940 Dataset with its publication pending (from PRIDE)
Dataset title: Connections between exoproteome heterogeneity and virulence in the oral pathogen Aggregatibacter actinomycetemcomitans
Possible reference: Fu, Y. et al. (2022) Connections between Exoproteome Heterogeneity and Virulence in the Oral Pathogen Aggregatibacter actinomycetemcomitans., mSystems, PMID 35695491

PXD028937 Dataset with its publication pending (from PRIDE)
Dataset title: Pfcerli2, a duplicated gene in the malaria parasite Plasmodium falciparum essential for invasion of erythrocytes as revealed by phylogenetic and cell biological analysis.
Possible reference: Liffner, B. et al. (2022) Cell biological analysis reveals an essential role for Pfcerli2 in erythrocyte invasion by malaria parasites., Commun Biol, PMID 35140336

PXD028933 Dataset with its publication pending (from PRIDE)
Dataset title: Competitive binding of E3 ligases TRIM26 and WWP2 controls SOX2 in glioblastoma
Possible reference: Mahlokozera, T. et al. (2021) Competitive binding of E3 ligases TRIM26 and WWP2 controls SOX2 in glioblastoma., Nat Commun, PMID 34732716

PXD028907 Dataset with its publication pending (from PRIDE)
Dataset title: Î²-1,3-glucan recognition by Acanthamoeba castellanii as a putative mechanism of amoeba-fungal interactions
Possible reference: Ferreira, MdS. et al. (2024) β-1,3-Glucan recognition by Acanthamoeba castellanii as a putative mechanism of amoeba-fungal interactions., Appl Environ Microbiol, PMID 38259076

PXD028904 Dataset with its publication pending (from PRIDE)
Dataset title: New molecular insights into atrial fibrillation due to obscurin Ig58/59 deletion
Possible reference: Grogan, A. et al. (2023) Alterations in cytoskeletal and Ca2+ cycling regulators in atria lacking the obscurin Ig58/59 module., Front Cardiovasc Med, PMID 37304957

PXD028901 Dataset with its publication pending (from PRIDE)
Dataset title: MSLibrarian: Optimized predicted spectral libraries for DIA proteomics
Possible reference: Isaksson, M. et al. (2022) MSLibrarian: Optimized Predicted Spectral Libraries for Data-Independent Acquisition Proteomics., J Proteome Res, PMID 35042333

PXD028886 Dataset with its publication pending (from PRIDE)
Dataset title: Paeonia lactiflora extract increase the muscle function via downregulation of high mobility group box 1 and NF-kB signaling in mdx mice, an animal model of Duchenne muscular dystrophy
Possible reference: Sim, I. et al. (2022) Paeonia lactiflora extract improves the muscle function of mdx mice, an animal model of Duchenne muscular dystrophy, via downregulating the high mobility group box 1 protein., J Ethnopharmacol, PMID 35149132

PXD028880 Dataset with its publication pending (from PRIDE)
Dataset title: Extending the range of SLIM-labeling applications: from human cell lines in culture to Caenorhabditis elegans whole-organism labeling
Possible reference: Lignieres, L. et al. (2023) Extending the Range of SLIM-Labeling Applications: From Human Cell Lines in Culture to Caenorhabditis elegans Whole-Organism Labeling., J Proteome Res, PMID 36748112

PXD028879 Dataset with its publication pending (from PRIDE)
Dataset title: Split-TurboID with Bre5 and Rps2 in Saccharomyces cerevisiae
Possible reference: Schmitt, K. et al. (2021) A Multi-Perspective Proximity View on the Dynamic Head Region of the Ribosomal 40S Subunit., Int J Mol Sci, PMID 34769086

PXD028853 Dataset with its publication pending (from PRIDE)
Dataset title: Enhancing Cysteine Chemoproteomic Coverage Through Systematic Assessment of Click Chemistry Product Fragmentation
Possible reference: Yan, T. et al. (2022) Enhancing Cysteine Chemoproteomic Coverage through Systematic Assessment of Click Chemistry Product Fragmentation., Anal Chem, PMID 35195394

PXD028849 Dataset with its publication pending (from PRIDE)
Dataset title: Shotgun proteomic profiling of dormant, 'non-culturable' Mycobacterium tuberculosis
Possible reference: Nikitushkin, V. et al. (2022) Shotgun proteomic profiling of dormant, 'non-culturable' Mycobacterium tuberculosis., PLoS One, PMID 35944020

PXD028846 Dataset with its publication pending (from PRIDE)
Dataset title: Shared and specific functions of Arfs 1-5 at the golgi revealed by systematic knockouts
Possible reference: Pennauer, M. et al. (2022) Shared and specific functions of Arfs 1-5 at the Golgi revealed by systematic knockouts., J Cell Biol, PMID 34749397

PXD028833 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of the wood decay fungus Fomitopsis pinicola is altered by substrate
Possible reference: Sabat, G. et al. (2022) Proteome of the Wood Decay Fungus Fomitopsis pinicola Is Altered by Substrate., Microbiol Resour Announc, PMID 35969048

PXD028787 Dataset with its publication pending (from PRIDE)
Dataset title: A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening THP-1 cells]
Possible reference: Ren, Y. et al. (2021) A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation., Genome Biol, PMID 34649616

PXD028736 Dataset with its publication pending (from PRIDE)
Dataset title: Solvent Precipitation SP3 (SP4) enhances recovery for proteomics sample preparation without magnetic beads
Possible reference: Johnston, HE. et al. (2022) Solvent Precipitation SP3 (SP4) Enhances Recovery for Proteomics Sample Preparation without Magnetic Beads., Anal Chem, PMID 35848328

PXD028713 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic and phosphoproteomic of C2C12 myogenesis and MAPK inhibition
Possible reference: Lee, H. et al. (2017) A Phosphoproteomic Screen Identifies a Guanine Nucleotide Exchange Factor for Rab3A Protein as a Mitogen-activated Protein (MAP) Kinase Phosphatase-5-regulated MAP Kinase Target in Interleukin 6 (IL-6) Secretion and Myogenesis., J Biol Chem, PMID 28096466

PXD028704 Dataset with its publication pending (from PRIDE)
Dataset title: Master mitotic kinases regulate viral genome delivery during papillomavirus cell entry
Possible reference: Rizzato, M. et al. (2023) Master mitotic kinases regulate viral genome delivery during papillomavirus cell entry., Nat Commun, PMID 36683055

PXD028701 Dataset with its publication pending (from PRIDE)
Dataset title: The nucleoporin Nup50 activates the Ran guanyl-nucleotide exchange factor RCC1 to promote NPC assembly at the end of mitosis
Possible reference: Holzer, G. et al. (2021) The nucleoporin Nup50 activates the Ran guanine nucleotide exchange factor RCC1 to promote NPC assembly at the end of mitosis., EMBO J, PMID 34725842

PXD028680 Dataset with its publication pending (from PRIDE)
Dataset title: A20 and ABIN-1 cooperate in balancing CBM complex-triggered NF-kB signaling in activated T cells
Possible reference: Yin, H. et al. (2022) A20 and ABIN-1 cooperate in balancing CBM complex-triggered NF-κB signaling in activated T cells., Cell Mol Life Sci, PMID 35099607

PXD028668 Dataset with its publication pending (from PRIDE)
Dataset title: A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening K562 cells]
Possible reference: Ren, Y. et al. (2021) A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation., Genome Biol, PMID 34649616

PXD028666 Dataset with its publication pending (from PRIDE)
Dataset title: Elucidation of the translation initiation factor interaction network of Haloferax volcanii reveals coupling of transcription and translation in haloarchaea
Possible reference: Schramm, F. et al. (2021) Elucidation of the Translation Initiation Factor Interaction Network of Haloferax volcanii Reveals Coupling of Transcription and Translation in Haloarchaea., Front Microbiol, PMID 34764944

PXD028665 Dataset with its publication pending (from PRIDE)
Dataset title: FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer
Possible reference: Guneri-Sozeri, PY. et al. (2023) FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer., Commun Biol, PMID 36805539

PXD028656 Dataset with its publication pending (from PRIDE)
Dataset title: Mutant glucocerebrosidase impairs ï¡-synuclein degradation by blockade of chaperone-mediated autophagy
Possible reference: Kuo, SH. et al. (2022) Mutant glucocerebrosidase impairs α-synuclein degradation by blockade of chaperone-mediated autophagy., Sci Adv, PMID 35138901

PXD028640 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive Phosphoproteomic Analysis of Nostoc flagelliforme in Response to Dehydration Provides Insights into Plant ROS Signaling Transduction
Possible reference: Liang, W. et al. (2021) Comprehensive Phosphoproteomic Analysis of Nostoc flagelliforme in Response to Dehydration Provides Insights into Plant ROS Signaling Transduction., ACS Omega, PMID 34095650

PXD028629 no publication (from MassIVE)
Dataset title: Northern elephant seal skeletal muscle, blubber, and plasma proteome responses to prolonged fasting
Possible reference: Khudyakov, JI. et al. (2022) Changes in apolipoprotein abundance dominate proteome responses to prolonged fasting in elephant seals., J Exp Biol, PMID 35188212

PXD028621 Dataset with its publication pending (from jPOST)
Dataset title: Protein lactylation induced by neural excitation
Possible reference: Hagihara, H. et al. (2021) Protein lactylation induced by neural excitation., Cell Rep, PMID 34644564

PXD028618 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic analysis of HPV(+) oropharyngeal squamous cell carcinoma recurrence
Possible reference: Ho, AS. et al. (2022) Comparative Proteomic Analysis of HPV(+) Oropharyngeal Squamous Cell Carcinoma Recurrence., J Proteome Res, PMID 34846153

PXD028609 Dataset with its publication pending (from iProX)
Dataset title: DRAK2 aggravates nonalcoholic fatty liver disease progression through SRSF6-associated RNA alternative splicing
Possible reference: Li, Y. et al. (2021) DRAK2 aggravates nonalcoholic fatty liver disease progression through SRSF6-associated RNA alternative splicing., Cell Metab, PMID 34614409

PXD028607 Dataset with its publication pending (from PRIDE)
Dataset title: Campylobacter hepaticus glycoproteome analysis
Possible reference: McDonald, JB. et al. (2023) Characterisation of N-linked protein glycosylation in the bacterial pathogen�Campylobacter hepaticus., Sci Rep, PMID 36604449

PXD028590 Dataset with its publication pending (from PRIDE)
Dataset title: Amphiregulin mediates non-cell-autonomous effect of senescence on reprogramming
Possible reference: von Joest, M. et al. (2022) Amphiregulin mediates non-cell-autonomous effect of senescence on reprogramming., Cell Rep, PMID 35830812

PXD028583 Dataset with its publication pending (from PRIDE)
Dataset title: Frequency of change determines effectiveness of microbial response strategies in sulfidic stream microbiomes
Possible reference: Li, S. et al. (2023) Frequency of change determines effectiveness of microbial response strategies., ISME J, PMID 37723339

PXD028579 Dataset with its publication pending (from PRIDE)
Dataset title: Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation
Possible reference: Qiao, S. et al. (2022) Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation., Nat Commun, PMID 35650207

PXD028576 Dataset with its publication pending (from PRIDE)
Dataset title: The Arabidopsis mature endosperm promotes seedling cuticle formation via release of sulfated peptides
Possible reference: De Giorgi, J. et al. (2021) The Arabidopsis mature endosperm promotes seedling cuticle formation via release of sulfated peptides., Dev Cell, PMID 34706263

PXD028561 Dataset with its publication pending (from PRIDE)
Dataset title: Glucose dissociates DDX21 dimers to regulate mRNA splicing and promote epidermal differentiation
Possible reference: Miao, W. et al. (2023) Glucose dissociates DDX21 dimers to regulate mRNA splicing and tissue differentiation., Cell, PMID 36608661

PXD028550 Dataset with its publication pending (from PRIDE)
Dataset title: ProMetIS: deep phenotyping of mouse models by proteomics and metabolomics
Possible reference: Imbert, A. et al. (2021) ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis., Sci Data, PMID 34862403

PXD028543 Dataset with its publication pending (from PRIDE)
Dataset title: Chlamydia trachomatis effector Dre1 interacts with dynactin to reposition host organelles during infection.
Possible reference: Sherry, J. et al. (2025) The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection., Cell Rep, PMID 40186871

PXD028530 Dataset with its publication pending (from PRIDE)
Dataset title: Light-triggered and phosphorylation-dependent 14-3-3 association with NON-PHOTOTROPIC HYPOCOTYL 3 is required for hypocotyl phototropism
Possible reference: Reuter, L. et al. (2021) Light-triggered and phosphorylation-dependent 14-3-3 association with NON-PHOTOTROPIC HYPOCOTYL 3 is required for hypocotyl phototropism., Nat Commun, PMID 34675219

PXD028526 Dataset with its publication pending (from PRIDE)
Dataset title: Metabolic Remodeling during Nitrogen Fixation in Zymomonas
Possible reference: Martien, JI. et al. (2021) Metabolic Remodeling during Nitrogen Fixation in Zymomonas mobilis., mSystems, PMID 34783580

PXD028524 Dataset with its publication pending (from PRIDE)
Dataset title: Drosophila female reproductive glands contribute to mating plug composition and the timing of sperm ejection
Possible reference: McDonough-Goldstein, CE. et al. (2022) Drosophila female reproductive glands contribute to mating plug composition and the timing of sperm ejection., Proc Biol Sci, PMID 35105240

PXD028523 Dataset with its publication pending (from PRIDE)
Dataset title: Cell-surface tethered promiscuous biotinylators enable comparative small-scale surface proteomic analysis of human extracellular vesicles and cells
Possible reference: Kirkemo, LL. et al. (2022) Cell-surface tethered promiscuous biotinylators enable comparative small-scale surface proteomic analysis of human extracellular vesicles and cells., Elife, PMID 35257663

PXD028522 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular architecture of the antiophidic protein DM64 and its binding specificity to myotoxin II from Bothrops asper venom
Possible reference: Soares, BS. et al. (2021) Molecular Architecture of the Antiophidic Protein DM64 and its Binding Specificity to Myotoxin II From Bothrops asper Venom., Front Mol Biosci, PMID 35155563

PXD028516 Dataset with its publication pending (from PRIDE)
Dataset title: importance of MTFP1 for mitochondrial function in the heart
Possible reference: Wang, K. et al. (2017) Circular RNA mediates cardiomyocyte death via miRNA-dependent upregulation of MTP18 expression., Cell Death Differ, PMID 28498369

PXD028506 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation of Bacillus velezensis Kos for the control of Lecanicillium fungicola
Possible reference: Clarke, J. et al. (2025) The control of mushroom pathogen Lecanicillium fungicola with fungicides and Bacillus-based biocontrol treatments during crop trial studies., BMC Microbiol, PMID 41261405

PXD028502 Dataset with its publication pending (from PRIDE)
Dataset title: Correlative proteomics identify the key roles of stress tolerance strategies in Acinetobacter baumannii in response to polymyxin and macrophages
Possible reference: Kho, ZY. et al. (2022) Correlative proteomics identify the key roles of stress tolerance strategies in Acinetobacter baumannii in response to polymyxin and human macrophages., PLoS Pathog, PMID 35231068

PXD028484 Dataset with its publication pending (from PRIDE)
Dataset title: Drosophila nicotinic acetylcholine receptor subunits and their native interactions with insecticidal peptide toxins
Possible reference: Korona, D. et al. (2022) Drosophila nicotinic acetylcholine receptor subunits and their native interactions with insecticidal peptide toxins., Elife, PMID 35575460

PXD028458 Dataset with its publication pending (from jPOST)
Dataset title: Brain-synthetized IGF-1 sexual dimorphism and proteostasis
Possible reference: Terry, GA. et al. (2026) Agomelatine drives sex-specific neuroprotection and reduced pathology in rat and human Alzheimer's models., bioRxiv, PMID 41648350

PXD028429 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of serum samples from COVID-19 ARDS and bacterial ARDS patients
Possible reference: Kewalramani, N. et al. (2025) Heme-induced lung injury in human precision cut lung slices: a new model for acute lung injury., Respir Res, PMID 40176049

PXD028421 Dataset with its publication pending (from PRIDE)
Dataset title: “Identifying the SLC25A46 interactome in transgenic mice: cerebrum”
Possible reference: Perivolidi, VI. et al. (2022) Proteomic Identification of the SLC25A46 Interactome in Transgenic Mice Expressing SLC25A46-FLAG., J Proteome Res, PMID 34983179

PXD028416 Dataset with its publication pending (from PRIDE)
Dataset title: ProMetIS: deep phenotyping of mouse models by proteomics and metabolomics.
Possible reference: Imbert, A. et al. (2021) ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis., Sci Data, PMID 34862403

PXD028396 Dataset with its publication pending (from PRIDE)
Dataset title: Klebsiella pneumoniae x546,ATCC15380, TMT
Possible reference: Wang, X. et al. (2021) Rational Proteomic Analysis of a New Domesticated Klebsiella pneumoniae x546 Producing 1,3-Propanediol., Front Microbiol, PMID 34899654

PXD028358 Dataset with its publication pending (from PRIDE)
Dataset title: Proteotoxicity caused by perturbed protein complexes underlies hybrid incompatibility
Possible reference: Swamy, KBS. et al. (2022) Proteotoxicity caused by perturbed protein complexes underlies hybrid incompatibility in yeast., Nat Commun, PMID 35906261

PXD028351 Dataset with its publication pending (from PRIDE)
Dataset title: The Hsp90 cochaperone TTT promotes cotranslational maturation of PIKK kinases prior to complex assembly
Possible reference: Toullec, D. et al. (2021) The Hsp90 cochaperone TTT promotes cotranslational maturation of PIKKs prior to complex assembly., Cell Rep, PMID 34686329

PXD028339 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of proteome-size scaling by integrative omics reveals mechanisms of proliferation control in cancer
Possible reference: Jones, I. et al. (2023) Characterization of proteome-size scaling by integrative omics reveals mechanisms of proliferation control in cancer., Sci Adv, PMID 36696495

PXD028326 Dataset with its publication pending (from PRIDE)
Dataset title: Short poly(A) tails are protected from deadenylation by the LARP1-PABP complex
Possible reference: Park, J. et al. (2023) Short poly(A) tails are protected from deadenylation by the LARP1-PABP complex., Nat Struct Mol Biol, PMID 36849640

PXD028324 Dataset with its publication pending (from PRIDE)
Dataset title: Arginine methylation and ubiquitylation crosstalk controls DNA end-resection and homologous recombination repair
Possible reference: Sanchez-Bailon, MP. et al. (2021) Arginine methylation and ubiquitylation crosstalk controls DNA end-resection and homologous recombination repair., Nat Commun, PMID 34728620

PXD028312 Dataset with its publication pending (from PRIDE)
Dataset title: Fox serum proteomics analysis suggests host-specific responses to Angiostrongylus vasorum infection
Possible reference: Gillis-Germitsch, N. et al. (2021) Fox Serum Proteomics Analysis Suggests Host-Specific Responses to Angiostrongylus�vasorum Infection in Canids., Pathogens, PMID 34832667

PXD028276 Dataset with its publication pending (from PRIDE)
Dataset title: The interferon-inducible antiviral GTPase MxB promotes capsid disassembly and genome release of herpesviruses
Possible reference: Serrero, MC. et al. (2022) The interferon-inducible GTPase MxB promotes capsid disassembly and genome release of herpesviruses., Elife, PMID 35475759

PXD028247 Dataset with its publication pending (from PRIDE)
Dataset title: AK2 promotes the migration and invasion of lung adenocarcinoma by activating TGF-Î²/Smad pathway in vitro and in vivo
Possible reference: Cai, F. et al. (2021) AK2 Promotes the Migration and Invasion of Lung Adenocarcinoma by Activating TGF-β/Smad Pathway In vitro and In vivo., Front Pharmacol, PMID 34630090

PXD028245 Dataset with its publication pending (from PRIDE)
Dataset title: Global phosphoproteomics in SCF stimulated human skin mast cells
Possible reference: Franke, K. et al. (2022) The SCF/KIT axis in human mast cells: Capicua acts as potent KIT repressor and ERK predominates PI3K., Allergy, PMID 35652819

PXD028241 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of sulfur-respiring haloarchaea from hypersaline lakes
Possible reference: Sorokin, DY. et al. (2017) Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats., ISME J, PMID 28106880

PXD028240 Dataset with its publication pending (from PRIDE)
Dataset title: Regulatory Mechanisms between Pattern- and Effector-Triggered Immunity in Tomato Leaves Revealed by Integrative Proteomic and Phosphoproteomic Analyses
Possible reference: Yu, J. et al. (2021) Integrative Proteomic and Phosphoproteomic Analyses of Pattern- and Effector-Triggered Immunity in Tomato., Front Plant Sci, PMID 34925416

PXD028235 Dataset with its publication pending (from iProX)
Dataset title: The acetylated lysine residues of Pta
Possible reference: Kuczyńska-Wiśnik, D. et al. (2016) The effect of protein acetylation on the formation and processing of inclusion bodies and endogenous protein aggregates in Escherichia coli cells., Microb Cell Fact, PMID 27832787

PXD028206 Dataset with its publication pending (from jPOST)
Dataset title: Enhanced antibacterial effect of a novel Friunavirus phage vWU2001 in combination with colistin against carbapenem-resistant Acinetobacter baumannii
Possible reference: Wintachai, P. et al. (2022) Enhanced antibacterial effect of a novel Friunavirus phage vWU2001 in combination with colistin against carbapenem-resistant Acinetobacter baumannii., Sci Rep, PMID 35173237

PXD028204 no publication (from MassIVE)
Dataset title: Defining the dynamic regulation of O-GlcNAc proteome in the mouse cortex -- The O-GlcNAcylation of synaptic and trafficking proteins related to neurodegenerative diseases
Possible reference: Huynh, VN. et al. (2021) Defining the Dynamic Regulation of O-GlcNAc Proteome in the Mouse Cortex---the O-GlcNAcylation of Synaptic and Trafficking Proteins Related to Neurodegenerative Diseases., Front Aging, PMID 35822049

PXD028184 no publication (from MassIVE)
Dataset title: Pah1 phosphorylation by Rim11
Possible reference: Khondker, S. et al. (2022) Glycogen synthase kinase homolog Rim11 regulates lipid synthesis through the phosphorylation of Pah1 phosphatidate phosphatase in yeast., J Biol Chem, PMID 35780834

PXD028162 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated Multi-Omics Reveal Polycomb Repressive Complex 2 Restricts Human Trophoblast Induction
Possible reference: Zijlmans, DW. et al. (2022) Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction., Nat Cell Biol, PMID 35697783

PXD028160 Dataset with its publication pending (from PRIDE)
Dataset title: RNA-binding proteins hnRNPM and ELAVL1 promote type-I interferon induction downstream of the nucleic acid sensors cGAS and RIG-I
Possible reference: Kirchhoff, A. et al. (2025) RNA-binding proteins hnRNPM and ELAVL1 promote type-I interferon induction downstream of the nucleic acid sensors cGAS and RIG-I., EMBO J, PMID 39707025

PXD028150 Dataset with its publication pending (from PRIDE)
Dataset title: Interrogating kinase-substrate relationships with proximity labeling and phosphorylation enrichment
Possible reference: Zhang, T. et al. (2022) Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment., J Proteome Res, PMID 35044772

PXD028136 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation of disposable-trap column nanoLC-FAIMS-MS/MS for the proteomic analysis of FFPE tissue
Possible reference: Eckert, S. et al. (2021) Evaluation of Disposable Trap Column nanoLC-FAIMS-MS/MS for the Proteomic Analysis of FFPE Tissue., J Proteome Res, PMID 34735149

PXD028128 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome characterization of mitochondria, ER, and mitochondrial-associated membrane from BAT and liver
Possible reference: Klionsky, DJ. et al. (2016) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)., Autophagy, PMID 26799652

PXD028117 Dataset with its publication pending (from PRIDE)
Dataset title: Low cell number proteomic analysis using in-cell protease digests reveals a robust signature for cell cycle state classification
Possible reference: Kelly, V. et al. (2022) Low Cell Number Proteomic Analysis Using In-Cell Protease Digests Reveals a Robust Signature for Cell Cycle State Classification., Mol Cell Proteomics, PMID 34742921

PXD028111 Dataset with its publication pending (from PRIDE)
Dataset title: Polycomb Repressive Complex 2 Restricts Human Naive Pluripotent Stem Cell to Trophoblast Fate Induction
Possible reference: Zijlmans, DW. et al. (2022) Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction., Nat Cell Biol, PMID 35697783

PXD028082 Dataset with its publication pending (from PRIDE)
Dataset title: Bioinformatics and mass spectrometry-based proteomics reveal alcohol dehydrogenase 1B as a blood biomarker candidate to monitor acetaminophen-induced liver injury
Possible reference: Pailleux, F. et al. (2021) Mass Spectrometry-Based Proteomics Reveal Alcohol Dehydrogenase 1B as a Blood Biomarker Candidate to Monitor Acetaminophen-Induced Liver Injury., Int J Mol Sci, PMID 34681731

PXD028063 Dataset with its publication pending (from PRIDE)
Dataset title: Defining proximity proteomics of Histone modifications by antibody-mediated protein A-APEX2 labeling
Possible reference: Li, X. et al. (2022) Defining Proximity Proteome of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling., Genomics Proteomics Bioinformatics, PMID 34555496

PXD028055 no publication (from MassIVE)
Dataset title: A Multi-omics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem Cell-derived Cardiomyocytes
Possible reference: Bayne, EF. et al. (2021) Multiomics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem-Cell-Derived Cardiomyocytes., J Proteome Res, PMID 34499502

PXD028049 Dataset with its publication pending (from PRIDE)
Dataset title: Unravelling the layering of microbial community, proteins and chemical structure in aerobic granules
Possible reference: Cydzik-Kwiatkowska, A. et al. (2022) Unravelling gradient layers of microbial communities, proteins, and chemical structure in aerobic granules., Sci Total Environ, PMID 35276168

PXD028040 Dataset with its publication pending (from PRIDE)
Dataset title: Patch-Clamp Proteomics of Single Neurons in Tissue Using Electrophysiology and Subcellular Capillary Electrophoresis Mass Spectrometry
Possible reference: Choi, SB. et al. (2022) Patch-Clamp Proteomics of Single Neurons in Tissue Using Electrophysiology and Subcellular Capillary Electrophoresis Mass Spectrometry., Anal Chem, PMID 34964611

PXD028037 Dataset with its publication pending (from PRIDE)
Dataset title: A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumors
Possible reference: Cui, C. et al. (2021) A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumours., Nat Nanotechnol, PMID 34764452

PXD028030 no publication (from MassIVE)
Dataset title: Characterization of covalent bonding of 4-methylcatechol to beta-lactoglobulin and the effect on in vitro protein digestibility
Possible reference: Waqar, K. et al. (2022) Covalent bonding of 4-methylcatechol to β-lactoglobulin results in the release of cysteine-4-methylcatechol adducts after in vitro digestion., Food Chem, PMID 35917780

PXD028002 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping protein interactions in the active TOM-TIM23 supercomplex
Possible reference: Gomkale, R. et al. (2021) Mapping protein interactions in the active TOM-TIM23 supercomplex., Nat Commun, PMID 34588454

PXD027956 no publication (from MassIVE)
Dataset title: Peroxynitrite in tumor microenvironment change the profile of peptide epitopes on tumor cells allowing their escape from cancer immunotherapy
Possible reference: Tcyganov, EN. et al. (2022) Peroxynitrite in the tumor microenvironment changes the profile of antigens allowing escape from cancer immunotherapy., Cancer Cell, PMID 36220073

PXD027946 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of ubiquitin binding protein using TurboID analysis
Possible reference: Schmitt, K. et al. (2021) A Multi-Perspective Proximity View on the Dynamic Head Region of the Ribosomal 40S Subunit., Int J Mol Sci, PMID 34769086

PXD027940 Dataset with its publication pending (from PRIDE)
Dataset title: Tomato trifoliate mutant proteome
Possible reference: Tyagi, K. et al. (2022) Seeing the unseen: a trifoliate (MYB117) mutant allele fortifies folate and carotenoids in tomato fruits., Plant J, PMID 35899408

PXD027935 Dataset with its publication pending (from PRIDE)
Dataset title: A nuclear role for the Argonaute protein AGO2 in mammalian gametogenesis
Possible reference: Griffin, KN. et al. (2022) Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction., Genome Res, PMID 36109149

PXD027927 no publication (from MassIVE)
Dataset title: Proteomics of high density lipoprotein subfractions in type 1 diabetes mellitus and controls
Possible reference: Toyoshima, MTK. et al. (2023) Proteomics of high-density lipoprotein subfractions and subclinical atherosclerosis in type 1 diabetes mellitus: a case-control study., Diabetol Metab Syndr, PMID 36899434

PXD027917 Dataset with its publication pending (from PRIDE)
Dataset title: A proximity interactome map of the VAC14-FIG4 complex using BioID
Possible reference: Qiu, S. et al. (2021) Proximity Interactome Map of the Vac14-Fig4 Complex Using BioID., J Proteome Res, PMID 34554760

PXD027891 Dataset with its publication pending (from PRIDE)
Dataset title: pH dependence of succinimide ester-based protein cross-linking for structural mass spectrometry applications
Possible reference: Trabjerg, E. et al. (2022) pH Dependence of Succinimide-Ester-Based Protein Cross-Linking for Structural Mass Spectrometry Applications., ACS Meas Sci Au, PMID 36785722

PXD027853 no publication (from MassIVE)
Dataset title: Triazine pyridine Chemistry for Protein Labelling on Tyrosine.
Possible reference: Jiang, H. et al. (2022) Triazine-pyridine chemistry for protein labelling on tyrosine., Chem Commun (Camb), PMID 35648412

PXD027847 Dataset with its publication pending (from PRIDE)
Dataset title: Lentil and fava bean with contrasting germination kinetics: a focus on digestion of proteins and bioactivity of resistant peptides
Possible reference: Bautista-Exp�sito, S. et al. (2021) Lentil and Fava Bean With Contrasting Germination Kinetics: A Focus on Digestion of Proteins and Bioactivity of Resistant Peptides., Front Plant Sci, PMID 34759946

PXD027842 Dataset with its publication pending (from iProX)
Dataset title: Platelets Derived Transthyretin Participate in The Development of Sepsis Associated Acute Kidney
Possible reference: Lv, D. et al. (2022) Platelets Derived Transthyretin Participate in The Development of Sepsis Associated Acute Kidney Injury by Inducing Oxidative Stress and Apoptosis of Renal Tubular Epithelial Cells., Shock, PMID 35081075

PXD027835 Dataset with its publication pending (from PRIDE)
Dataset title: Growth Rate Dependent and Nutrient-specific Gene Expression Resource Allocation in Fission Yeast
Possible reference: Kleijn, IT. et al. (2022) Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast., Life Sci Alliance, PMID 35228260

PXD027825 Dataset with its publication pending (from PRIDE)
Dataset title: HA-MOP knockin mice express the canonical �-opioid receptor but lack detectable splice variants
Possible reference: Fritzwanker, S. et al. (2021) HA-MOP knockin mice express the canonical �-opioid receptor but lack detectable splice variants., Commun Biol, PMID 34522000

PXD027821 Dataset with its publication pending (from PRIDE)
Dataset title: Interval-based secretomics unravels the time-dependent acute phase response in hepatocyte model systems
Possible reference: Knecht, S. et al. (2022) Interval-Based Secretomics Unravels Acute-Phase Response in Hepatocyte Model Systems., Mol Cell Proteomics, PMID 35525403

PXD027815 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics analysis based upon TNBS-induced UC model rats
Possible reference: Rong, Y. et al. (2021) Photodynamic Therapy of Novel Photosensitizer Ameliorates TNBS-Induced Ulcerative Colitis via Inhibition of AOC1., Front Pharmacol, PMID 34744725

PXD027812 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome landscape of schizophrenia in patient-derived cerebral organoids
Possible reference: Notaras, M. et al. (2021) The proteomic architecture of schizophrenia iPSC-derived cerebral organoids reveals alterations in GWAS and neuronal development factors., Transl Psychiatry, PMID 34667143

PXD027798 Dataset with its publication pending (from iProX)
Dataset title: Rack1 is Essential for Corticogenesis by Preventing P21-Dependent Senescence in Neural Stem Cells
Possible reference: Zhu, Q. et al. (2021) Rack1 is essential for corticogenesis by preventing p21-dependent senescence in neural stem cells., Cell Rep, PMID 34469723

PXD027796 Dataset with its publication pending (from PRIDE)
Dataset title: Diel proteomes of field Trichodesmium populations
Possible reference: Held, NA. et al. (2022) Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium., Nat Microbiol, PMID 35013592

PXD027780 Dataset with its publication pending (from PRIDE)
Dataset title: Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer
Possible reference: Busso-Lopes, AF. et al. (2022) Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer., Nat Commun, PMID 36344512

PXD027757 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in failing murine heart
Possible reference: Caudal, A. et al. (2022) Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart., Nat Cardiovasc Res, PMID 36405497

PXD027749 Dataset with its publication pending (from PRIDE)
Dataset title: Peripheral blood CD4+CCR6+ compartment differentiate HIV-1 positive elite controllers from long-term successfully treated individuals
Possible reference: Svensson Akusj�rvi, S. et al. (2022) Peripheral blood CD4+CCR6+ compartment differentiates HIV-1 infected or seropositive elite controllers from long-term successfully treated individuals., Commun Biol, PMID 35418589

PXD027738 Dataset with its publication pending (from PRIDE)
Dataset title: Neprilysins regulate muscle contraction and heart function via cleavage of SERCA-inhibitory micropeptides
Possible reference: Schiemann, R. et al. (2022) Neprilysins regulate muscle contraction and heart function via cleavage of SERCA-inhibitory micropeptides., Nat Commun, PMID 35906206

PXD027720 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of residues from experimental ceramics
Possible reference: Rafalska, KT. et al. (2024) A Comparison of White and Yellow Seminal Plasma Phosphoproteomes Obtained from Turkey (Meleagris gallopavo) Semen., Int J Mol Sci, PMID 39337428

PXD027715 Dataset with its publication pending (from PRIDE)
Dataset title: Myeloid-derived suppressor cells and tolerogenic dendritic cells are distinctively induced by PI3K and Wnt signaling pathways
Possible reference: van Wigcheren, GF. et al. (2023) Myeloid-derived suppressor cells and tolerogenic dendritic cells are distinctively induced by PI3K and Wnt signaling pathways., J Biol Chem, PMID 37739035

PXD027713 Dataset with its publication pending (from PRIDE)
Dataset title: Ancient proteins resolve controversy over the identity of Genyornis eggshell
Possible reference: Demarchi, B. et al. (2022) Ancient proteins resolve controversy over the identity of Genyornis eggshell., Proc Natl Acad Sci U S A, PMID 35609205

PXD027688 no publication (from MassIVE)
Dataset title: Thiol-Based Functional Mimicry of Phosphorylation of the Two-Component System Response Regulator ArcA Promotes Pathogenesis in Enteric Pathogens
Possible reference: Zhou, Y. et al. (2021) Thiol-based functional mimicry of phosphorylation of the two-component system response regulator ArcA promotes pathogenesis in enteric pathogens., Cell Rep, PMID 34936880

PXD027687 Dataset with its publication pending (from jPOST)
Dataset title: ITS2 sequencing and targeted meta-proteomics of infant gut mycobiome reveal the functional role of Rhodotorula sp. during atopic dermatitis manifestation
Possible reference: Mok, K. et al. (2021) ITS2 Sequencing and Targeted Meta-Proteomics of Infant Gut Mycobiome Reveal the Functional Role of Rhodotorula sp. during Atopic Dermatitis Manifestation., J Fungi (Basel), PMID 34575786

PXD027656 Dataset with its publication pending (from PRIDE)
Dataset title: Intratumoral magnetic hyperthermia in combination with 5-fluorouracil induces thrombogenic collagen fibers, cellular stress, and immune responses in heterotopic human colon cancer in mice
Possible reference: Dabaghi, M. et al. (2021) Iron Oxide Nanoparticles Carrying 5-Fluorouracil in Combination with Magnetic Hyperthermia Induce Thrombogenic Collagen Fibers, Cellular Stress, and Immune Responses in Heterotopic Human Colon Cancer in Mice., Pharmaceutics, PMID 34683917

PXD027622 Dataset with its publication pending (from PRIDE)
Dataset title: “Identifying the SLC25A46 interactome in transgenic mice: Heart"
Possible reference: Perivolidi, VI. et al. (2022) Proteomic Identification of the SLC25A46 Interactome in Transgenic Mice Expressing SLC25A46-FLAG., J Proteome Res, PMID 34983179

PXD027621 Dataset with its publication pending (from PRIDE)
Dataset title: Protective effect and mechanism of kinsenoside on alcoholic liver injury
Possible reference: Gao, L. et al. (2021) Kinsenoside Alleviates Alcoholic Liver Injury by Reducing Oxidative Stress, Inhibiting Endoplasmic Reticulum Stress, and Regulating AMPK-Dependent Autophagy., Front Pharmacol, PMID 35115920

PXD027614 Dataset with its publication pending (from PRIDE)
Dataset title: Global ubiquitylation analysis of mitochondria in primary neurons identifies endogenous Parkin targets following activation of PINK1
Possible reference: Antico, O. et al. (2021) Global ubiquitylation analysis of mitochondria in primary neurons identifies endogenous Parkin targets following activation of PINK1., Sci Adv, PMID 34767452

PXD027613 Dataset with its publication pending (from PRIDE)
Dataset title: Paleofeces Analysis from Iron Age Hallstatt Salt Miners
Possible reference: Maixner, F. et al. (2021) Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period., Curr Biol, PMID 34648730

PXD027599 Dataset with its publication pending (from PRIDE)
Dataset title: “Identifying the SLC25A46 interactome in transgenic mice: cerebellum”
Possible reference: Perivolidi, VI. et al. (2022) Proteomic Identification of the SLC25A46 Interactome in Transgenic Mice Expressing SLC25A46-FLAG., J Proteome Res, PMID 34983179

PXD027594 Dataset with its publication pending (from PRIDE)
Dataset title: Functional multi-omics reveals genetic and pharmacologic regulation of surface CD38 in multiple myeloma
Possible reference: Choudhry, P. et al. (2024) Functional multiomics reveals genetic and pharmacologic regulation of surface CD38 in multiple myeloma., Blood Neoplasia, PMID 40453054

PXD027588 Dataset with its publication pending (from PRIDE)
Dataset title: Deciphering the major metabolic pathways associated with aluminum tolerance in popcorn roots using label-free quantitative proteomics
Possible reference: Pinto, VB. et al. (2021) Deciphering the major metabolic pathways associated with aluminum tolerance in popcorn roots using label-free quantitative proteomics., Planta, PMID 34821986

PXD027586 Dataset with its publication pending (from PRIDE)
Dataset title: Temporal Analysis of Protein Ubiquitylation and Phosphorylation During Parkin-dependent Mitophagy
Possible reference: Zittlau, KI. et al. (2022) Temporal Analysis of Protein Ubiquitylation and Phosphorylation During Parkin-Dependent Mitophagy., Mol Cell Proteomics, PMID 34974192

PXD027549 Dataset with its publication pending (from PRIDE)
Dataset title: O-GlcNAcylation of fatty acid synthase under nutritional stress as a pro-survival mechanism in cancer cells
Possible reference: Wong, YK. et al. (2022) O-GlcNAcylation promotes fatty acid synthase activity under nutritional stress as a pro-survival mechanism in cancer cells., Proteomics, PMID 35083852

PXD027543 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Analysis of Oil-Roasted Cashew Using a Customized Database
Possible reference: Chen, S. et al. (2022) Proteomic Analysis of Oil-Roasted Cashews Using a Customized Allergen-Focused Protein Database., J Proteome Res, PMID 35658452

PXD027538 Dataset with its publication pending (from PRIDE)
Dataset title: TMT proteomic analysis of thyroid cancer tissue sample
Possible reference: Li, J. et al. (2023) Identification of potential diagnostic and prognostic biomarkers for papillary thyroid microcarcinoma (PTMC) based on TMT-labeled LC-MS/MS and machine learning., J Endocrinol Invest, PMID 36418670

PXD027534 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of mouse striatal dopamine synaptosomes purified by fluorescence sorting
Possible reference: Paget-Blanc, V. et al. (2022) A synaptomic analysis reveals dopamine hub synapses in the mouse striatum., Nat Commun, PMID 35660742

PXD027525 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling to predict therapeutic response to anti-PD1 therapy in advanced melanoma
Possible reference: Trilla-Fuertes, L. et al. (2026) Protein content of extracellular vesicles from patients with advanced melanoma changes upon progression to anti-PD1 therapy., Sci Rep, PMID 41565745

PXD027520 Dataset with its publication pending (from PRIDE)
Dataset title: The Angiostrongylus vasorum excretory/secretory proteome contains putative modulators of the host coagulation
Possible reference: Gillis-Germitsch, N. et al. (2021) The Angiostrongylus vasorum Excretory/Secretory and Surface Proteome Contains Putative Modulators of the Host Coagulation., Front Cell Infect Microbiol, PMID 34796127

PXD027502 Dataset with its publication pending (from PRIDE)
Dataset title: : GRAMD1C regulates autophagy initiation and mitochondrial bioenergetics through ER-Mitochondria cholesterol transport
Possible reference: Ng, MYW. et al. (2022) The cholesterol transport protein GRAMD1C regulates autophagy initiation and mitochondrial bioenergetics., Nat Commun, PMID 36270994

PXD027489 Dataset with its publication pending (from PRIDE)
Dataset title: Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs
Possible reference: Sun, YH. et al. (2021) Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs., Nat Commun, PMID 34645830

PXD027481 Dataset with its publication pending (from PRIDE)
Dataset title: Coccolith Vesicle Proteins from Emiliania huxleyi
Possible reference: Nam, O. et al. (2019) De novo transcriptome profile of coccolithophorid alga Emiliania huxleyi CCMP371 at different calcium concentrations with proteome analysis., PLoS One, PMID 31465514

PXD027452 Dataset with its publication pending (from PRIDE)
Dataset title: Annexin A1 is a polarity cue that directs planar mitotic spindle orientation during mammalian epithelial morphogenesis
Possible reference: Fankhaenel, M. et al. (2023) Annexin A1 is a polarity cue that directs mitotic spindle orientation during mammalian epithelial morphogenesis., Nat Commun, PMID 36631478

PXD027448 Dataset with its publication pending (from iProX)
Dataset title: Plasma exosome proteomics analysis of adolescent idiopathic scoliosis patients
Possible reference: Wang, Q. et al. (2025) Plasma exosome proteomics reveals upregulation of CILP-1 in concave side of paraspinal muscle in adolescent idiopathic scoliosis., Clin Proteomics, PMID 40461962

PXD027425 Dataset with its publication pending (from PRIDE)
Dataset title: Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein
Possible reference: Chang, D. et al. (2021) Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein., Anal Bioanal Chem, PMID 34635934

PXD027417 Dataset with its publication pending (from PRIDE)
Dataset title: Global identification and systematic analysis of lysine malonylation in maize (Zea mays L.
Possible reference: Xu, M. et al. (2021) Global Identification and Systematic Analysis of Lysine Malonylation in Maize (Zea mays L.)., Front Plant Sci, PMID 34490025

PXD027388 Dataset with its publication pending (from PRIDE)
Dataset title: Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in maintenance and expression of embryogenic competence in sugarcane callus
Possible reference: Xavier, LR. et al. (2022) Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in the maintenance and expression of embryogenic competence in sugarcane callus., J Plant Physiol, PMID 34906795

PXD027377 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of the aggregated proteins from LONP1 knockdown HeLa cells
Possible reference: Pollecker, K. et al. (2021) Proteomic analysis demonstrates the role of the quality control protease LONP1 in mitochondrial protein aggregation., J Biol Chem, PMID 34461102

PXD027373 no publication (from MassIVE)
Dataset title: Mammalian hybrid pre-autophagosomal structure HyPAS generates autophagosomes
Possible reference: Kumar, S. et al. (2021) Mammalian hybrid pre-autophagosomal structure HyPAS generates autophagosomes., Cell, PMID 34741801

PXD027372 Dataset with its publication pending (from PanoramaPublic)
Dataset title: Loss of DNAJC3 impairs cholesterol metabolism and mitochondrial function
Possible reference: Jennings, MJ. et al. (2021) Intracellular Lipid Accumulation and Mitochondrial Dysfunction Accompanies Endoplasmic Reticulum Stress Caused by Loss of the Co-chaperone DNAJC3., Front Cell Dev Biol, PMID 34692675

PXD027366 Dataset with its publication pending (from PRIDE)
Dataset title: Myxopyronin B inhibits growth of a Fidaxomicin-resistant Clostridioides difficile isolate and interferes with toxin synthesis
Possible reference: Brauer, M. et al. (2022) Myxopyronin�B inhibits growth of a Fidaxomicin-resistant Clostridioides�difficile isolate and interferes with toxin synthesis., Gut Pathog, PMID 34991700

PXD027360 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of Nrf2 knocked down in HT29
Possible reference: Cheraghi, O. et al. (2022) The effect of Nrf2 deletion on the proteomic signature in a human colorectal cancer cell line., BMC Cancer, PMID 36100939

PXD027358 Dataset with its publication pending (from PRIDE)
Dataset title: A streamlined data analysis pipeline for the identification of sites of citrullination
Possible reference: Maurais, AJ. et al. (2021) A Streamlined Data Analysis Pipeline for the Identification of Sites of Citrullination., Biochemistry, PMID 34491035

PXD027318 Dataset with its publication pending (from PRIDE)
Dataset title: Senescence Biomarker Discovery by LC-MS-based Proteomics
Possible reference: Lynn, KS. et al. (2019) Vegetable Signatures Derived from Human Urinary Metabolomic Data in Controlled Feeding Studies., J Proteome Res, PMID 30517004

PXD027312 no publication (from MassIVE)
Dataset title: ZNF768 links oncogenic RAS to cellular senescence
Possible reference: Villot, R. et al. (2021) ZNF768 links oncogenic RAS to cellular senescence., Nat Commun, PMID 34404770

PXD027301 Dataset with its publication pending (from PRIDE)
Dataset title: A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum-infected red blood cell proteome
Possible reference: Siddiqui, G. et al. (2022) A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum-infected red blood cell proteome., Gigascience, PMID 35254426

PXD027283 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of molecular machinery mediating ER to lipid droplet protein targeting
Possible reference: Song, J. et al. (2022) Identification of two pathways mediating protein targeting from ER to lipid droplets., Nat Cell Biol, PMID 36050470

PXD027278 Dataset with its publication pending (from PRIDE)
Dataset title: Candida albicans CUG codon translation, comparison with other yeasts
Possible reference: Zhou, XL. et al. (2013) Aminoacylation and translational quality control strategy employed by leucyl-tRNA synthetase from a human pathogen with genetic code ambiguity., Nucleic Acids Res, PMID 23969415

PXD027265 Dataset with its publication pending (from PRIDE)
Dataset title: A universal peptide matrix interactomics approach to disclose motif dependent protein binding
Possible reference: Ramberger, E. et al. (2021) A Universal Peptide Matrix Interactomics Approach to Disclose Motif-Dependent Protein Binding., Mol Cell Proteomics, PMID 34391889

PXD027250 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of potential of new therapeutic approaches for JAK2 V617F mutant patients
Possible reference: Pearson, S. et al. (2023) Identification of curaxin as a potential new therapeutic for JAK2 V617F mutant patients., PLoS One, PMID 37253035

PXD027229 Dataset with its publication pending (from PRIDE)
Dataset title: Characterisation of the free and membrane-associated fractions of the thylakoid lumen proteome in Arabidopsis thaliana
Possible reference: Gollan, PJ. et al. (2021) Characterization of the Free and Membrane-Associated Fractions of the Thylakoid Lumen Proteome in Arabidopsis thaliana., Int J Mol Sci, PMID 34360890

PXD027205 Dataset with its publication pending (from PRIDE)
Dataset title: lysine acetylation and succinylation in Streptomyces coelicolor
Possible reference: Zhang, H. et al. (2019) ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor., Mol Cell Proteomics, PMID 31337674

PXD027195 Dataset with its publication pending (from PRIDE)
Dataset title: Conserved exchange of paralog proteins during neuronal differentiation
Possible reference: Schmidt, S. et al. (2014) Function and regulation of the Rho guanine nucleotide exchange factor Trio., Small GTPases, PMID 24987837

PXD027156 Dataset with its publication pending (from PRIDE)
Dataset title: Cysteamine inhibits glycine utilisation and disrupts virulence in Pseudomonas aeruginosa
Possible reference: Fraser-Pitt, DJ. et al. (2021) Cysteamine Inhibits Glycine Utilisation and Disrupts Virulence in Pseudomonas aeruginosa., Front Cell Infect Microbiol, PMID 34631600

PXD027148 Dataset with its publication pending (from PRIDE)
Dataset title: Impacts of Ser/Thr protein kinase Stk1 on proteome, twitching motility and competitive advantage in Pseudomonas aeruginosaImpacts of Ser/Thr protein kinase Stk1 on proteome, twitching motility and competitive advantage in Pseudomonas aeruginosa
Possible reference: Zhu, X. et al. (2021) Impacts of Ser/Thr Protein Kinase Stk1 on the Proteome, Twitching Motility, and Competitive Advantage in Pseudomonas aeruginosa., Front Microbiol, PMID 34733256

PXD027134 Dataset with its publication pending (from PanoramaPublic)
Dataset title: The addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor Biopsies
Possible reference: Sweet, S. et al. (2022) The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies., Sci Rep, PMID 35974054

PXD027121 Dataset with its publication pending (from PRIDE)
Dataset title: In vivo structure-function analysis and redox interactomes of Leishmania tarentolae Erv
Possible reference: Turra, GL. et al. (2021) In Vivo Structure-Function Analysis and Redox Interactomes of Leishmania tarentolae Erv., Microbiol Spectr, PMID 34585988

PXD027107 no publication (from MassIVE)
Dataset title: Bone collagen from Australian marsupials for ZooMS peptide markers
Possible reference: Peters, C. et al. (2021) Species identification of Australian marsupials using collagen fingerprinting., R Soc Open Sci, PMID 34729210

PXD027105 Dataset with its publication pending (from PRIDE)
Dataset title: Evidence of immune modulators in the secretome of the equine tapeworm Anoplocephala perfoliata
Possible reference: Wititkornkul, B. et al. (2021) Evidence of Immune Modulators in the Secretome of the Equine Tapeworm Anoplocephala perfoliata., Pathogens, PMID 34358062

PXD027080 no publication (from MassIVE)
Dataset title: Protein kinase signalling at the Leishmania kinetochore captured by XL-BioID
Possible reference: Geoghegan, V. et al. (2022) CLK1/CLK2-driven signalling at the Leishmania kinetochore is captured by spatially referenced proximity phosphoproteomics., Commun Biol, PMID 36437406

PXD027060 no publication (from MassIVE)
Dataset title: Long-lived mitochondrial cristae proteins in mouse heart and brain
Possible reference: Bomba-Warczak, E. et al. (2021) Long-lived mitochondrial cristae proteins in mouse heart and brain., J Cell Biol, PMID 34259807

PXD027057 Dataset with its publication pending (from jPOST)
Dataset title: Phosphoproteomics of Vicia GCPs treated with ABA
Possible reference: Hayashi, Y. et al. (2021) Identification of Abscisic Acid-Dependent Phosphorylated Basic Helix-Loop-Helix Transcription Factors in Guard Cells of Vicia faba by Mass Spectrometry., Front Plant Sci, PMID 34987530

PXD027055 Dataset with its publication pending (from PRIDE)
Dataset title: Early and late processes driving NET formation, and the autocrine/paracrine role of endogenous RAGE ligands
Possible reference: Tatsiy, O. et al. (2021) Early and Late Processes Driving NET Formation, and the Autocrine/Paracrine Role of Endogenous RAGE Ligands., Front Immunol, PMID 34616390

PXD027049 Dataset with its publication pending (from PRIDE)
Dataset title: GM-CSF nitration is a new driver of myeloid suppressor cell activity in tumors
Possible reference: Cal�, B. et al. (2021) GM-CSF Nitration Is a New Driver of Myeloid Suppressor Cell Activity in Tumors., Front Immunol, PMID 34675917

PXD027038 Dataset with its publication pending (from PRIDE)
Dataset title: Colobanthus quitensis differential proteomics
Possible reference: Bertini, L. et al. (2021) What Antarctic Plants Can Tell Us about Climate Changes: Temperature as a Driver for Metabolic Reprogramming., Biomolecules, PMID 34439761

PXD027030 Dataset with its publication pending (from PRIDE)
Dataset title: Time-series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations
Possible reference: Jim�nez, A. et al. (2022) Time-series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations., Mol Syst Biol, PMID 35285572

PXD027026 Dataset with its publication pending (from PRIDE)
Dataset title: Two related coactivator complexes SAGA and ATAC control embryonic stem cell self-renewal through two different acetyltransferase-independent mechanisms
Possible reference: Fischer, V. et al. (2021) The related coactivator complexes SAGA and ATAC control embryonic stem cell self-renewal through acetyltransferase-independent mechanisms., Cell Rep, PMID 34433046

PXD027007 Dataset with its publication pending (from PRIDE)
Dataset title: Crotonylation of GAPDH regulates human embryonic stem cell endodermal lineage differentiation and metabolic switch
Possible reference: Zhang, J. et al. (2023) Crotonylation of GAPDH regulates human embryonic stem cell endodermal lineage differentiation and metabolic switch., Stem Cell Res Ther, PMID 37013624

PXD026998 Dataset with its publication pending (from PRIDE)
Dataset title: Pro-inflammatory Beta Cell Small Extracellular Vesicles Induce Beta Cell Failure Through Activation of the CXCL10/CXCR3 Axis in Diabetes
Possible reference: Javeed, N. et al. (2021) Pro-inflammatory β cell small extracellular vesicles induce β cell failure through activation of the CXCL10/CXCR3 axis in diabetes., Cell Rep, PMID 34433033

PXD026991 Dataset with its publication pending (from PRIDE)
Dataset title: SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells
Possible reference: Fischer, V. et al. (2022) SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells., Nucleic Acids Res, PMID 35871303

PXD026978 Dataset with its publication pending (from PRIDE)
Dataset title: Sex-specific social behavior and amygdala proteomic deficits in Foxp2+/- mutant mice
Possible reference: Herrero, MJ. et al. (2021) Sex-Specific Social Behavior and Amygdala Proteomic Deficits in Foxp2 +/- Mutant Mice., Front Behav Neurosci, PMID 34421555

PXD026950 Dataset with its publication pending (from PRIDE)
Dataset title: iTRAQ-based quantitative serum proteomic analysis in ischemic stroke patients
Possible reference: Sharma, R. et al. (2015) Proteomic Signature of Endothelial Dysfunction Identified in the Serum of Acute Ischemic Stroke Patients by the iTRAQ-Based LC-MS Approach., J Proteome Res, PMID 25807139

PXD026930 Dataset with its publication pending (from PRIDE)
Dataset title: Impact of Alanyl-tRNA Synthetase Editing Deficiency in Yeast
Possible reference: Zhang, H. et al. (2021) Impact of alanyl-tRNA synthetase editing deficiency in yeast., Nucleic Acids Res, PMID 34500470

PXD026917 no publication (from MassIVE)
Dataset title: Fused in sarcoma regulates DNA replication timing and progression
Possible reference: Jia, W. et al. (2021) Fused in sarcoma regulates DNA replication timing and kinetics., J Biol Chem, PMID 34375640

PXD026893 Dataset with its publication pending (from PRIDE)
Dataset title: p53 forms redox-dependent protein-protein interactions through cysteine 277
Possible reference: Shi, T. et al. (2021) p53 Forms Redox-Dependent Protein-Protein Interactions through Cysteine 277., Antioxidants (Basel), PMID 34679713

PXD026889 Dataset with its publication pending (from PRIDE)
Dataset title: The bZIP transcription factor HapX is post-translationally regulated to control iron homeostasis in Aspergillus fumigatus
Possible reference: L�pez-Berges, MS. et al. (2021) The bZIP Transcription Factor HapX Is Post-Translationally Regulated to Control Iron Homeostasis in Aspergillus fumigatus., Int J Mol Sci, PMID 34299357

PXD026872 Dataset with its publication pending (from PRIDE)
Dataset title: A YAP/TAZ-TEAD signaling module links endothelial nutrient acquisition to angiogenic growth
Possible reference: Ong, YT. et al. (2022) A YAP/TAZ-TEAD signalling module links endothelial nutrient acquisition to angiogenic growth., Nat Metab, PMID 35726026

PXD026859 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of filaggrin insufficient keratinocytes and secreted exosomes.
Possible reference: Kobiela, A. et al. (2024) Keratinocyte-derived small extracellular vesicles supply antigens for CD1a-resticted T cells and promote their type 2 bias in the context of filaggrin insufficiency., Front Immunol, PMID 38585273

PXD026846 Dataset with its publication pending (from iProX)
Dataset title: N-terminomic Analysis of Mycobacterium tuberculosis H37Rv
Possible reference: Shi, J. et al. (2022) Deep N-terminomics of Mycobacterium tuberculosis H37Rv extensively correct annotated encoding genes., Genomics, PMID 34915127

PXD026843 Dataset with its publication pending (from PRIDE)
Dataset title: The E3 ubiquitin ligase RNF115 regulates phagosome maturation and host response to infection
Possible reference: Bilkei-Gorzo, O. et al. (2022) The E3 ubiquitin ligase RNF115 regulates phagosome maturation and host response to bacterial infection., EMBO J, PMID 36281581

PXD026821 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated liver and plasma proteomics in obese mice reveals complex metabolic and immune regulation
Possible reference: Stocks, B. et al. (2022) Integrated Liver and Plasma Proteomics in Obese Mice Reveals Complex Metabolic Regulation., Mol Cell Proteomics, PMID 35093608

PXD026812 no publication (from MassIVE)
Dataset title: Proteomic analysis of bacteriophage fD1 infecting Yersinia pestis
Possible reference: Skurnik, M. et al. (2021) Bacteriophages fEV-1 and fD1 Infect Yersinia pestis., Viruses, PMID 34372590

PXD026811 no publication (from MassIVE)
Dataset title: Proteomic analysis of bacteriophage fEV-1 infecting Yersinia pestis
Possible reference: Skurnik, M. et al. (2021) Bacteriophages fEV-1 and fD1 Infect Yersinia pestis., Viruses, PMID 34372590

PXD026763 Dataset with its publication pending (from PRIDE)
Dataset title: Human MDA-MB-231 breast cancer cells overexpressing miR-183-5p and its isomiRs
Possible reference: Telonis, AG. et al. (2015) Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity., Nucleic Acids Res, PMID 26400174

PXD026743 Dataset with its publication pending (from PRIDE)
Dataset title: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
Possible reference: Staneva, DP. et al. (2021) A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination., Genome Res, PMID 34407985

PXD026730 Dataset with its publication pending (from PRIDE)
Dataset title: Global profiling of phosphorylation-dependent changes in cysteine reactivity
Possible reference: Kemper, EK. et al. (2022) Global profiling of phosphorylation-dependent changes in cysteine reactivity., Nat Methods, PMID 35228727

PXD026724 Dataset with its publication pending (from PRIDE)
Dataset title: Cavin3 released from caveolae interacts with BRCA1 to regulate the cellular stress response
Possible reference: McMahon, KA. et al. (2021) Cavin3 released from caveolae interacts with BRCA1 to regulate the cellular stress response., Elife, PMID 34142659

PXD026704 Dataset with its publication pending (from PRIDE)
Dataset title: Coating and corruption of human neutrophils by bacterial outer membrane vesicles
Possible reference: du Teil Espina, M. et al. (2022) Coating and Corruption of Human Neutrophils by Bacterial Outer Membrane Vesicles., Microbiol Spectr, PMID 36000865

PXD026700 no publication (from MassIVE)
Dataset title: Growth Rate-Dependent Coordination of Catabolism and Anabolism in the Archaeon Methanococcus maripaludis under Phosphate Limitation
Possible reference: Gu, W. et al. (2022) Growth rate-dependent coordination of catabolism and anabolism in the archaeon Methanococcus maripaludis under phosphate limitation., ISME J, PMID 35780255

PXD026680 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic and Metabolomic Profiling of Acute and Chronic Stress Events Associated with Military Exercises
Possible reference: McKetney, J. et al. (2022) Proteomic and metabolomic profiling of acute and chronic stress events associated with military exercises., Mol Omics, PMID 34860218

PXD026671 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated transcriptomic and proteomic analysis of Tritipyrum provides insights into the molecular basis of salt tolerance
Possible reference: Yang, R. et al. (2021) Integrated transcriptomic and proteomic analysis of Tritipyrum provides insights into the molecular basis of salt tolerance., PeerJ, PMID 35036157

PXD026660 Dataset with its publication pending (from PRIDE)
Dataset title: Plasmodiophora brassicae-triggered cell enlargement and loss of cellular integrity in root systems is mediated by pectin demethylation.
Possible reference: Stefanowicz, K. et al. (2021) Plasmodiophora brassicae-Triggered Cell Enlargement and Loss of Cellular Integrity in Root Systems Are Mediated by Pectin Demethylation., Front Plant Sci, PMID 34394168

PXD026656 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis identified age-associated prognostic biomarkers in pneumonia-derived pediatric sepsis
Possible reference: Luo, T. et al. (2022) Proteomic analysis identified potential age-associated prognostic biomarkers in pneumonia-derived paediatric sepsis., Proteomics Clin Appl, PMID 34822739

PXD026653 Dataset with its publication pending (from PRIDE)
Dataset title: Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol
Possible reference: Verner, Z. et al. (2021) Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol., PLoS Pathog, PMID 34780573

PXD026633 Dataset with its publication pending (from PRIDE)
Dataset title: A small RNA regulates�pprM, a modulator of pleiotropic proteins promoting DNA repair, in�Deinococcus radiodurans�under ionizing radiation
Possible reference: Villa, JK. et al. (2021) A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation., Sci Rep, PMID 34155239

PXD026630 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping proteome changes in recurrent colon cancer reveals a significant immune system signature
Possible reference: Berle, M. et al. (2022) Mapping Proteome Changes in Microsatellite Stable, Recurrent Colon Cancer Reveals a Significant Immune System Signature., Cancer Genomics Proteomics, PMID 35181583

PXD026626 no publication (from MassIVE)
Dataset title: Pathogenic BRCA1 variants disrupt PLK1-regulation of mitotic spindle orientation and luminal differentiation
Possible reference: He, Z. et al. (2022) Pathogenic BRCA1 variants disrupt PLK1-regulation of mitotic spindle orientation., Nat Commun, PMID 35459234

PXD026620 no publication (from MassIVE)
Dataset title: Cardiolipin remodeling enables protein crowding in the inner mitochondrial membrane
Possible reference: Xu, Y. et al. (2021) Cardiolipin remodeling enables protein crowding in the inner mitochondrial membrane., EMBO J, PMID 34661298

PXD026619 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ
Possible reference: Hemmerle, L. et al. (2022) Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ., Nat Commun, PMID 35595740

PXD026605 Dataset with its publication pending (from PRIDE)
Dataset title: Listeria monocytogenes utilizes the ClpP1/2 proteolytic machinery for fine-tuned substrate degradation at elevated temperatures
Possible reference: Balogh, D. et al. (2022) Listeria monocytogenes utilizes the ClpP1/2 proteolytic machinery for fine-tuned substrate degradation at elevated temperatures., RSC Chem Biol, PMID 35866172

PXD026602 Dataset with its publication pending (from iProX)
Dataset title: Proteome of Pugionium cornutum
Possible reference: Wang, P. et al. (2023) Understanding the response in Pugionium cornutum (L.) Gaertn. seedling leaves under drought stress using transcriptome and proteome integrated analysis., PeerJ, PMID 37033724

PXD026599 Dataset with its publication pending (from PRIDE)
Dataset title: A phosphoproteomic approach reveals that PKD3 controls PKA-mediated glucose and tyrosine metabolism
Possible reference: Loza-Valdes, A. et al. (2021) A phosphoproteomic approach reveals that PKD3 controls PKA-mediated glucose and tyrosine metabolism., Life Sci Alliance, PMID 34145024

PXD026570 Dataset with its publication pending (from PRIDE)
Dataset title: Extensive Three-Dimensional Intratumor Proteomic Heterogeneity Revealed by Multiregion Sampling in High-Grade Serous Ovarian Tumor Specimens
Possible reference: Hunt, AL. et al. (2021) Extensive three-dimensional intratumor proteomic heterogeneity revealed by multiregion sampling in high-grade serous ovarian tumor specimens., iScience, PMID 34278265

PXD026541 Dataset with its publication pending (from PRIDE)
Dataset title: Chromatin enrichment for Proteomics in Plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in Jasmonate signaling
Possible reference: V�lez-Berm�dez, IC. et al. (2021) Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling., BMC Genomics, PMID 34809577

PXD026513 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic study of Desulfovibrio ferrophilus IS5 reveals overexpressed extracellular multi-heme cytochrome associated with severe microbiologically influenced corrosion
Possible reference: Chatterjee, M. et al. (2021) Proteomic study of Desulfovibrio ferrophilus IS5 reveals overexpressed extracellular multi-heme cytochrome associated with severe microbiologically influenced corrosion., Sci Rep, PMID 34326431

PXD026484 Dataset with its publication pending (from PRIDE)
Dataset title: Acute depletion of CTCF rewires genome-wide chromatin accessibility
Possible reference: Xu, B. et al. (2021) Acute depletion of CTCF rewires genome-wide chromatin accessibility., Genome Biol, PMID 34429148

PXD026473 no publication (from MassIVE)
Dataset title: Proximity labeling identifies a repertoire of site-specific R-loop modulators
Possible reference: Yan, Q. et al. (2022) Proximity labeling identifies a repertoire of site-specific R-loop modulators., Nat Commun, PMID 35013239

PXD026465 Dataset with its publication pending (from PRIDE)
Dataset title: Inositol signaling in the basidiomycete fungus Schizophyllum commune
Possible reference: Murry, R. et al. (2019) Crosstalk between Ras and inositol phosphate signaling revealed by lithium action on inositol monophosphatase in Schizophyllum commune., Adv Biol Regul, PMID 30639095

PXD026459 Dataset with its publication pending (from PRIDE)
Dataset title: Tryptic peptide imaging of an urothelial cancer tissue cohort
Possible reference: F�ll, MC. et al. (2022) Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the Galaxy framework., Clin Proteomics, PMID 35439943

PXD026424 Dataset with its publication pending (from PRIDE)
Dataset title: Mouse 129SV submandibular salivary gland. -Male vs Female- and -Wildtype vs ERdj5 knockout-
Possible reference: Moustardas, P. et al. (2021) Deregulation of the Kallikrein Protease Family in the Salivary Glands of the Sj�gren's Syndrome ERdj5 Knockout Mouse Model., Front Immunol, PMID 34305928

PXD026407 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of full-length hnRNP R isoform impairs DNA damage response in motoneurons by inhibiting Yb1 recruitment to chromatin
Possible reference: Ghanawi, H. et al. (2021) Loss of full-length hnRNP R isoform impairs DNA damage response in motoneurons by inhibiting Yb1 recruitment to chromatin., Nucleic Acids Res, PMID 34850154

PXD026393 no publication (from MassIVE)
Dataset title: Photoredox-catalyzed decarboxylative C-terminal differentiation for bulk and single molecule proteomics
Possible reference: Zhang, L. et al. (2021) Photoredox-Catalyzed Decarboxylative C-Terminal Differentiation for Bulk- and Single-Molecule Proteomics., ACS Chem Biol, PMID 34734691

PXD026378 Dataset with its publication pending (from PRIDE)
Dataset title: Variation in upstream open reading frames contributes to allelic diversity in protein abundance
Possible reference: Gage, JL. et al. (2022) Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance., Proc Natl Acad Sci U S A, PMID 35349347

PXD026374 Dataset with its publication pending (from PRIDE)
Dataset title: PLCG1 is required for AML1-ETO leukemia stem cell self-renewal
Possible reference: Schnoeder, TM. et al. (2022) PLCG1 is required for AML1-ETO leukemia stem cell self-renewal., Blood, PMID 34695195

PXD026373 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Aspergillus niger in Peanuts
Possible reference: Xu, M. et al. (2021) Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in Aspergillus niger in Peanuts., Front Microbiol, PMID 34489910

PXD026367 Dataset with its publication pending (from PRIDE)
Dataset title: Structural basis for the specificity of PPM1H phosphatase for Rab GTPases
Possible reference: Waschb�sch, D. et al. (2021) Structural basis for the specificity of PPM1H phosphatase for Rab GTPases., EMBO Rep, PMID 34580980

PXD026358 no publication (from MassIVE)
Dataset title: Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress
Possible reference: Li, X. et al. (2021) Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress., Redox Biol, PMID 34425387

PXD026356 Dataset with its publication pending (from iProX)
Dataset title: Dynamic FMR1 granule phase switch instructed by m6A modification contributes to maternal RNA decay
Possible reference: Zhang, G. et al. (2022) Dynamic FMR1 granule phase switch instructed by m6A modification contributes to maternal RNA decay., Nat Commun, PMID 35165263

PXD026343 Dataset with its publication pending (from PRIDE)
Dataset title: Tensin3 interaction with talin drives formation of fibronectin-associated fibrillar adhesions
Possible reference: Atherton, P. et al. (2022) Tensin3 interaction with talin drives the formation of fibronectin-associated fibrillar adhesions., J Cell Biol, PMID 36074065

PXD026301 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomics reveal elevated CCN2 in NGLY1 deficient cells
Possible reference: Hetz, R. et al. (2022) Comparative proteomics reveals elevated CCN2 in NGLY1-deficient cells., Biochem Biophys Res Commun, PMID 36209585

PXD026291 no publication (from MassIVE)
Dataset title: Synergistic PIM kinase and proteasome inhibition in MYC-overexpressing triple-negative breast cancer
Possible reference: Kunder, R. et al. (2022) Synergistic PIM kinase and proteasome inhibition as a therapeutic strategy for MYC-overexpressing triple-negative breast cancer., Cell Chem Biol, PMID 34525344

PXD026289 Dataset with its publication pending (from PRIDE)
Dataset title: Sorting nexin-27 regulates AMPA receptor trafficking through the synaptic adhesion protein LRFN2
Possible reference: McMillan, KJ. et al. (2021) Sorting nexin-27 regulates AMPA receptor trafficking through the synaptic adhesion protein LRFN2., Elife, PMID 34251337

PXD026288 Dataset with its publication pending (from PRIDE)
Dataset title: Tumor temporal proteome profiling reveals the immunological triple offensive induced by synthetic anti-cancer Salmonella
Possible reference: Yang, S. et al. (2021) Tumor Temporal Proteome Profiling Reveals the Immunological Triple Offensive Induced by Synthetic Anti-Cancer Salmonella., Front Immunol, PMID 34489962

PXD026271 Dataset with its publication pending (from jPOST)
Dataset title: Deep proteomics of HEK293 cells by DIA-MS with FAIMS
Possible reference: Kawashima, Y. et al. (2022) Single-Shot 10K Proteome Approach: Over 10,000 Protein Identifications by Data-Independent Acquisition-Based Single-Shot Proteomics with Ion Mobility Spectrometry., J Proteome Res, PMID 35522919

PXD026263 Dataset with its publication pending (from PRIDE)
Dataset title: Multiple regulatory intrinsically disordered motifs control FOXO4 transcription factor binding and function
Possible reference: Bourgeois, B. et al. (2021) Multiple regulatory intrinsically disordered motifs control FOXO4 transcription factor binding and function., Cell Rep, PMID 34320339

PXD026253 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of the Putative Nucleoporin POM33 in the Filamentous Fungus Sordaria macrospora
Possible reference: Groth, A. et al. (2021) Analysis of the Putative Nucleoporin POM33 in the Filamentous Fungus Sordaria macrospora., J Fungi (Basel), PMID 34575720

PXD026250 no publication (from MassIVE)
Dataset title: Data Independent Acquisition Mass Spectrometry of the Human Lens Enhances Spatiotemporal Measurement of Fiber Cell Aging
Possible reference: Cantrell, LS. et al. (2021) Data-Independent Acquisition Mass Spectrometry of the Human Lens Enhances Spatiotemporal Measurement of Fiber Cell Aging., J Am Soc Mass Spectrom, PMID 34705440

PXD026244 Dataset with its publication pending (from PRIDE)
Dataset title: Structural probing of Hsp26 activation and client binding by quantitative cross-linking mass spectrometry
Possible reference: F�rsch, J. et al. (2021) Structural Probing of Hsp26 Activation and Client Binding by Quantitative Cross-Linking Mass Spectrometry., Anal Chem, PMID 34542282

PXD026240 Dataset with its publication pending (from jPOST)
Dataset title: protein coverage improvement for mouse lung tissue by using cysteine modification method
Possible reference: Tomioka, R. et al. (2024) Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation., J Am Soc Mass Spectrom, PMID 38287222

PXD026237 Dataset with its publication pending (from PRIDE)
Dataset title: PfAP2-O Influences Virulence Gene Transcription and Sexual Development in Plasmodium falciparum
Possible reference: Cubillos, EFG. et al. (2021) The Transcription Factor PfAP2-O Influences Virulence Gene Transcription and Sexual Development in Plasmodium falciparum., Front Cell Infect Microbiol, PMID 34268135

PXD026232 no publication (from MassIVE)
Dataset title: Epigenetic regulation of nuclear lamina-associated heterochromatin domains by HAT1 and the acetylation of newly synthesized histones
Possible reference: Popova, LV. et al. (2021) Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones., Nucleic Acids Res, PMID 34788845

PXD026229 Dataset with its publication pending (from PRIDE)
Dataset title: Axonal and somatodendritic proteomes of dopamine neurons in the mouse brain
Possible reference: Hobson, BD. et al. (2022) Subcellular proteomics of dopamine neurons in the mouse brain., Elife, PMID 35098924

PXD026212 Dataset with its publication pending (from PRIDE)
Dataset title: Sex differences in the role of protein degradation in the hippocampus during memory formation
Possible reference: Turner, M. et al. (2026) Reductions in protein degradation in the retrosplenial cortex regulate contextual fear memory formation in a sex-independent manner., Neurobiol Learn Mem, PMID 41397580

PXD026181 Dataset with its publication pending (from PRIDE)
Dataset title: TINCR lncRNA encodes a ubiquitin-like protein that activates CDC42, promotes epithelial differentiation and suppresses tumor growth
Possible reference: Boix, O. et al. (2022) pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation., Nat Commun, PMID 36369429

PXD026110 Dataset with its publication pending (from PRIDE)
Dataset title: FASN-dependent de novo lipogenesis is required for brain development
Possible reference: Gonzalez-Bohorquez, D. et al. (2022) FASN-dependent de novo lipogenesis is required for brain development., Proc Natl Acad Sci U S A, PMID 34996870

PXD026103 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted mass spectrometry enables quantification of novel pharmacodynamic biomarkers of ATM kinase inhibitors
Possible reference: Whiteaker, JR. et al. (2021) Targeted Mass Spectrometry Enables Quantification of Novel Pharmacodynamic Biomarkers of ATM Kinase Inhibition., Cancers (Basel), PMID 34359745

PXD026086 Dataset with its publication pending (from PRIDE)
Dataset title: The Human Melanoma Proteome Atlas – Defining the Molecular Pathology & Complementing the Melanoma Transcriptome
Possible reference: Betancourt, LH. et al. (2021) The Human Melanoma Proteome Atlas-Complementing the melanoma transcriptome., Clin Transl Med, PMID 34323402

PXD026067 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of Actin Filament Interactors in Giardia lamblia
Possible reference: Steele-Ogus, MC. et al. (2021) Identification of Actin Filament-Associated Proteins in Giardia lamblia., Microbiol Spectr, PMID 34287056

PXD026032 Dataset with its publication pending (from iProX)
Dataset title: Phosphoproteome of mouse testis at postnatal days 30
Possible reference: Couto-Santos, F. et al. (2021) Prepubertal arsenic exposure alters phosphoproteins profile, quality, and fertility of epididymal spermatozoa in sexually mature rats., Toxicology, PMID 34352348

PXD026030 Dataset with its publication pending (from iProX)
Dataset title: Quantitative proteomics analysis of the effects of dietary deprivation of methionine and cystine upon A549 xenografts and its bearing mice
Possible reference: Yang, H. et al. (2021) Quantitative proteomic analysis of the effects of dietary deprivation of methionine and cystine on A549 xenograft and A549 xenograft-bearing mouse., Proteomics, PMID 34482643

PXD026009 Dataset with its publication pending (from jPOST)
Dataset title: Facile one-pot nanoproteomics for label-free proteome profiling of 50-1000 mammalian cells
Possible reference: Martin, K. et al. (2021) Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50-1000 Mammalian Cells., J Proteome Res, PMID 34351778

PXD026008 Dataset with its publication pending (from jPOST)
Dataset title: Facile one-pot nanoproteomics for label-free proteome profiling of 50-1000 mammalian cells
Possible reference: Martin, K. et al. (2021) Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50-1000 Mammalian Cells., J Proteome Res, PMID 34351778

PXD025990 no publication (from MassIVE)
Dataset title: An ultrasensitive method for analysis of viral spike N-glycoforms
Possible reference: Baboo, S. et al. (2021) DeGlyPHER: An Ultrasensitive Method for the Analysis of Viral Spike N-Glycoforms., Anal Chem, PMID 34597027

PXD025951 Dataset with its publication pending (from iProX)
Dataset title: Specific enrichment and glycosylation discrepancy profiling of cellular exosomes by dual-affinity probe
Possible reference: Zhang, N. et al. (2021) Specific enrichment and glycosylation discrepancy profiling of cellular exosomes using a dual-affinity probe., Chem Commun (Camb), PMID 34059853

PXD025943 no publication (from MassIVE)
Dataset title: Temporal dynamics of protein and post-translational modification abundances in Populus leaf across a diurnal period
Possible reference: Shrestha, HK. et al. (2021) Temporal dynamics of protein and post-translational modification abundances in Populus leaf across a diurnal period., Proteomics, PMID 34482644

PXD025939 Dataset with its publication pending (from PRIDE)
Dataset title: Unravelling subcellular and ultrastructural changes during vitrification of human spermatozoa: effect of mitochondria-targeted antioxidant and permeable cryoprotectant
Possible reference: Kumar, P. et al. (2021) Unraveling Subcellular and Ultrastructural Changes During Vitrification of Human Spermatozoa: Effect of a Mitochondria-Targeted Antioxidant and a Permeable Cryoprotectant., Front Cell Dev Biol, PMID 34277615

PXD025936 Dataset with its publication pending (from PRIDE)
Dataset title: The termite fungal cultivar Termitomyces combines diverse enzymes and oxidative reactions for plant biomass conversion
Possible reference: Schalk, F. et al. (2021) The Termite Fungal Cultivar Termitomyces Combines Diverse Enzymes and Oxidative Reactions for Plant Biomass Conversion., mBio, PMID 34126770

PXD025934 Dataset with its publication pending (from PRIDE)
Dataset title: Detecting mistranslation in yeast expressing tRNA variants
Possible reference: Berg, MD. et al. (2017) Evolving Mistranslating tRNAs Through a Phenotypically Ambivalent Intermediate in Saccharomyces cerevisiae., Genetics, PMID 28576863

PXD025902 Dataset with its publication pending (from PRIDE)
Dataset title: SEVERE CONSEQUENCES OF A HIGH-LIPID DIET INCLUDE HYDROGEN SULFIDE DYSFUNCTION AND DISEASE AGGRESSION IN GLIOBLASTOMA
Possible reference: Silver, DJ. et al. (2021) Severe consequences of a high-lipid diet include hydrogen sulfide dysfunction and enhanced aggression in glioblastoma., J Clin Invest, PMID 34255747

PXD025881 Dataset with its publication pending (from PRIDE)
Dataset title: Human EDEM2 proteomics and glycoproteomics datasets
Possible reference: Munteanu, CVA. et al. (2021) Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network., Mol Cell Proteomics, PMID 34332121

PXD025876 Dataset with its publication pending (from PRIDE)
Dataset title: BEMAP analysis of glycosylated YghJ
Possible reference: Riaz, S. et al. (2021) Characterization of Glycosylation-Specific Systemic and Mucosal IgA Antibody Responses to Escherichia coli Mucinase YghJ (SslE)., Front Immunol, PMID 34975849

PXD025869 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of Simulium damnosum salivary antigens
Possible reference: Willen, L. et al. (2021) Human immune response against salivary antigens of Simulium damnosum s.l.: A new epidemiological marker for exposure to blackfly bites in onchocerciasis endemic areas., PLoS Negl Trop Dis, PMID 34157020

PXD025857 Dataset with its publication pending (from jPOST)
Dataset title: Blood plasma proteome of Japanese medaka fish exposed to humic acid
Possible reference: Yurchenko, VV. et al. (2022) Proteomics Analysis in Japanese Medaka Oryzias latipes Exposed to Humic Acid Revealed Suppression of Innate Immunity and Coagulation Proteins., Biology (Basel), PMID 35625410

PXD025849 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular characterization of hematopoietic stem cells after in vitro amplification on biomimetic 3D PDMS cell culture scaffoldsMolecular characterization of hematopoietic stem cells after in vitro amplification on biomimetic 3D PDMS cell culture scaffold
Possible reference: Marx-Bl�mel, L. et al. (2021) Molecular characterization of hematopoietic stem cells after in vitro amplification on biomimetic 3D PDMS cell culture scaffolds., Sci Rep, PMID 34707135

PXD025842 Dataset with its publication pending (from PRIDE)
Dataset title: Comparison of extracellular matrix enrichment protocols for the improved characterization of the skin matrisome by mass spectrometry
Possible reference: Dussoyer, M. et al. (2022) Comparison of extracellular matrix enrichment protocols for the improved characterization of the skin matrisome by mass spectrometry., J Proteomics, PMID 34678517

PXD025832 Dataset with its publication pending (from PRIDE)
Dataset title: The interactome of site-specifically acetylated linker histone H1
Possible reference: H�llm�ller, E. et al. (2021) Interactome of Site-Specifically Acetylated Linker Histone H1., J Proteome Res, PMID 34351766

PXD025825 no publication (from MassIVE)
Dataset title: Proteomic profiling of ectosomes derived from paired urothelial bladder cancer and normal cells reveals the presence of biologically-relevant molecules
Possible reference: Surman, M. et al. (2021) Proteomic Profiling of Ectosomes Derived from Paired Urothelial Bladder Cancer and Normal Cells Reveals the Presence of Biologically-Relevant Molecules., Int J Mol Sci, PMID 34202855

PXD025771 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of differential phosphoproteins reveled complex responses of soybean to phosphate starvation through reversible protein phosphorylation
Possible reference: Jiang, W. et al. (2021) Soybean responds to phosphate starvation through reversible protein phosphorylation., Plant Physiol Biochem, PMID 34371392

PXD025754 Dataset with its publication pending (from PRIDE)
Dataset title: DDX21 is a p38-MAPK sensitive nucleolar protein necessary for mouse preimplantation embryo development and cell-fate specification
Possible reference: Bora, P. et al. (2021) DDX21 is a p38-MAPK-sensitive nucleolar protein necessary for mouse preimplantation embryo development and cell-fate specification., Open Biol, PMID 34255976

PXD025747 no publication (from MassIVE)
Dataset title: Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance
Possible reference: Shrestha, HK. et al. (2021) Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance., BMC Microbiol, PMID 34749649

PXD025744 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic-based research strategy identified laminin subunit alpha 2 as a potential urinary-specific biomarker for the medullary sponge kidney disease
Possible reference: Fabris, A. et al. (2017) Proteomic-based research strategy identified laminin subunit alpha 2 as a potential urinary-specific biomarker for the medullary sponge kidney disease., Kidney Int, PMID 27914711

PXD025742 no publication (from MassIVE)
Dataset title: In utero pulse-injection of isotopic amino acids quantifies protein turnover rates during murine fetal development
Possible reference: Baeza, J. et al. (2023) In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development., bioRxiv, PMID 37293076

PXD025738 Dataset with its publication pending (from PRIDE)
Dataset title: Pumilio2 and Staufen2 selectively balance the synaptic proteome
Possible reference: Schieweck, R. et al. (2021) Pumilio2 and Staufen2 selectively balance the synaptic proteome., Cell Rep, PMID 34161769

PXD025732 Dataset with its publication pending (from PRIDE)
Dataset title: Absolute proteome quantification in the gas-fermenting acetogen Clostridium autoethanogenum
Possible reference: Valgepea, K. et al. (2022) Absolute Proteome Quantification in the Gas-Fermenting Acetogen Clostridium autoethanogenum., mSystems, PMID 35384696

PXD025725 Dataset with its publication pending (from PRIDE)
Dataset title: POGLUT2 and POGLUT3 O-glucosylate multiple EGF repeats in fibrillin-1, -2, and LTBP1 and promote secretion of FBN1
Possible reference: Williamson, DB. et al. (2021) POGLUT2 and POGLUT3 O-glucosylate multiple EGF repeats in fibrillin-1, -2, and LTBP1 and promote secretion of fibrillin-1., J Biol Chem, PMID 34411563

PXD025714 no publication (from MassIVE)
Dataset title: Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome
Possible reference: Runge, AKW. et al. (2021) Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome., Proc Biol Sci, PMID 34229485

PXD025683 Dataset with its publication pending (from PRIDE)
Dataset title: Allergenicity Assessment and Allergen Profile Analysis of Different Chinese Wheat Cultivars
Possible reference: Wang, Y. et al. (2021) Allergenicity assessment and allergen profile analysis of different Chinese wheat cultivars., World Allergy Organ J, PMID 34257797

PXD025643 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic characterization of neuromelanin granules and substantia nigra in health and disease
Possible reference: Wulf, M. et al. (2021) Laser Microdissection-Based Protocol for the LC-MS/MS Analysis of the Proteomic Profile of Neuromelanin Granules., J Vis Exp, PMID 34978295

PXD025621 Dataset with its publication pending (from PRIDE)
Dataset title: Succinylation profiles of brain injury after intracerebral hemorrhage
Possible reference: Deng, YH. et al. (2021) Succinylation profiles of brain injury after intracerebral hemorrhage., PLoS One, PMID 34780519

PXD025618 Dataset with its publication pending (from PRIDE)
Dataset title: Disruption of nucleocytoplasmic trafficking as a cellular senescence driver
Possible reference: Park, JH. et al. (2021) Disruption of nucleocytoplasmic trafficking as a cellular senescence driver., Exp Mol Med, PMID 34188179

PXD025591 Dataset with its publication pending (from PRIDE)
Dataset title: A proteomics database for CNS proteins of the great pond snail Lymnaea stagnalis
Possible reference: Wooller, S. et al. (2022) A combined bioinformatics and LC-MS-based approach for the development and benchmarking of a comprehensive database of Lymnaea CNS proteins., J Exp Biol, PMID 35403696

PXD025586 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome analysis of Renibacterium salmoninarum reveals putative role of membrane vesicles in virulence
Possible reference: Kroniger, T. et al. (2022) Proteome analysis of the Gram-positive fish pathogen Renibacterium salmoninarum reveals putative role of membrane vesicles in virulence., Sci Rep, PMID 35194033

PXD025528 Dataset with its publication pending (from jPOST)
Dataset title: Mechanical stress induced protein precipitation method for drug target screening
Possible reference: Lyu, J. et al. (2021) Mechanical stress induced protein precipitation method for drug target screening., Anal Chim Acta, PMID 34051997

PXD025512 Dataset with its publication pending (from PRIDE)
Dataset title: The venom and telopodal defence systems of the centipede Lithobius forficatus are functionally convergent serial homologues
Possible reference: Schendel, V. et al. (2024) The venom and telopodal defence systems of the centipede Lithobius forficatus are functionally convergent serial homologues., BMC Biol, PMID 38867210

PXD025507 Dataset with its publication pending (from PRIDE)
Dataset title: Actinomycin targets NPM1c-primed mitochondria in AML
Possible reference: Wu, HC. et al. (2021) Actinomycin D Targets NPM1c-Primed Mitochondria to Restore PML-Driven Senescence in AML Therapy., Cancer Discov, PMID 34301789

PXD025490 Dataset with its publication pending (from PRIDE)
Dataset title: Isonicotinylation is Isonicotinylation is a histone mark induced by the anti-tuberculosis first-line drug isoniazida histone mark induced by the anti-tuberculosis first-line drug isoniazid
Possible reference: Jiang, Y. et al. (2021) Isonicotinylation is a histone mark induced by the anti-tuberculosis first-line drug isoniazid., Nat Commun, PMID 34545082

PXD025481 Dataset with its publication pending (from PRIDE)
Dataset title: Single cell chemical proteomics (SCCP) interrogates the timing and heterogeneity of cancer cell commitment to death
Possible reference: V�gv�ri, �. et al. (2022) Single-Cell Chemical Proteomics (SCCP) Interrogates the Timing and Heterogeneity of Cancer Cell Commitment to Death., Anal Chem, PMID 35731985

PXD025455 Dataset with its publication pending (from PRIDE)
Dataset title: A Panel of Glycopeptides as Candidate Biomarkers for Early Diagnosis of NASH Hepatocellular Carcinoma Using a Stepped HCD Method and PRM Evaluation
Possible reference: Lin, Y. et al. (2021) A Panel of Glycopeptides as Candidate Biomarkers for Early Diagnosis of NASH Hepatocellular Carcinoma Using a Stepped HCD Method and PRM Evaluation., J Proteome Res, PMID 33929864

PXD025443 Dataset with its publication pending (from PRIDE)
Dataset title: A proteomic approach for systematic mapping of human deubiquitinating enzymes substrates
Possible reference: Ramirez, J. et al. (2021) A Proteomic Approach for Systematic Mapping of Substrates of Human Deubiquitinating Enzymes., Int J Mol Sci, PMID 34063716

PXD025407 Dataset with its publication pending (from PRIDE)
Dataset title: A systematic evaluation of fragmentation methods for unlabeled and isobaric mass tag-labeled O-glycopeptides
Possible reference: Mao, Y. et al. (2021) Systematic Evaluation of Fragmentation Methods for Unlabeled and Isobaric Mass Tag-Labeled O-Glycopeptides., Anal Chem, PMID 34347445

PXD025400 Dataset with its publication pending (from PRIDE)
Dataset title: Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria
Possible reference: Herbert, CJ. et al. (2021) Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria., Nucleic Acids Res, PMID 34634819

PXD025394 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome and (ox)PTP profile analysis of diabetic NOD mouse under single (anti-CD3) or combined (anti-CD3 + IL1RA) treatment
Possible reference: Ablamunits, V. et al. (2012) Synergistic reversal of type 1 diabetes in NOD mice with anti-CD3 and interleukin-1 blockade: evidence of improved immune regulation., Diabetes, PMID 22043003

PXD025385 Dataset with its publication pending (from PRIDE)
Dataset title: DIAmeter: Matching peptides to data-independent acquisition mass spectrometry data
Possible reference: Lu, YY. et al. (2021) DIAmeter: matching peptides to data-independent acquisition mass spectrometry data., Bioinformatics, PMID 34252924

PXD025383 Dataset with its publication pending (from PRIDE)
Dataset title: The chimeric GaaR::XlnR transcription factor induces pectinolytic activities in the presence of D-xylose in Aspergillus niger
Possible reference: Kun, RS. et al. (2021) The chimeric GaaR-XlnR transcription factor induces pectinolytic activities in the presence of D-xylose in Aspergillus niger., Appl Microbiol Biotechnol, PMID 34236481

PXD025367 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic profiling reveals specific adaptation of Vibrio anguillarum to oxidative stress, iron deprivation and humoral components of innate immunity
Possible reference: Sk�ne, A. et al. (2022) Comparative proteomic profiling reveals specific adaption of Vibrio anguillarum to oxidative stress, iron deprivation and humoral components of innate immunity., J Proteomics, PMID 34737109

PXD025358 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic changes in adipose tissue and skeletal muscle in women with PCOS
Possible reference: Stener-Victorin, E. et al. (2024) Proteomic analysis shows decreased type I fibers and ectopic fat accumulation in skeletal muscle from women with PCOS., Elife, PMID 38180081

PXD025356 Dataset with its publication pending (from PRIDE)
Dataset title: Secretory autophagy mediates mitochondria clearance in the absence of the mATG8-conjugation machinery
Possible reference: Tan, HWS. et al. (2022) A degradative to secretory autophagy switch mediates mitochondria clearance in the absence of the mATG8-conjugation machinery., Nat Commun, PMID 35764633

PXD025339 Dataset with its publication pending (from PRIDE)
Dataset title: Adenovirus remodeling of the host proteome and of host factors associating with viral genomes
Possible reference: Dybas, JM. et al. (2021) Adenovirus Remodeling of the Host Proteome and Host Factors Associated with Viral Genomes., mSystems, PMID 34463575

PXD025326 no publication (from MassIVE)
Dataset title: An Acquired Acyltransferase Promotes Klebsiella pneumoniae ST258 Respiratory Infection
Possible reference: Ahn, D. et al. (2021) An acquired acyltransferase promotes Klebsiella pneumoniae ST258 respiratory infection., Cell Rep, PMID 34077733

PXD025317 no publication (from MassIVE)
Dataset title: Proteomic characterization of canine gastric fluid by liquid chromatography mass spectrometry (LCMS) for development of protein biomarkers in regurgitation, vomiting, and cough
Possible reference: Grobman, M. et al. (2021) Proteomic Characterization of Canine Gastric Fluid by Liquid Chromatography-Mass Spectrometry for Development of Protein Biomarkers in Regurgitation, Vomiting, and Cough., Front Vet Sci, PMID 34307522

PXD025315 Dataset with its publication pending (from PRIDE)
Dataset title: N471D WASH complex subunit strumpellin knock-in mice display BPTF and KLHL11 dysregulation in brain tissue
Possible reference: Clemen, CS. et al. (2022) N471D WASH complex subunit strumpellin knock-in mice display mild motor and cardiac abnormalities and BPTF and KLHL11 dysregulation in brain tissue., Neuropathol Appl Neurobiol, PMID 34312900

PXD025309 no publication (from MassIVE)
Dataset title: Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling
Possible reference: Ooi, SK. et al. (2021) Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling., Proc Natl Acad Sci U S A, PMID 34465625

PXD025297 Dataset with its publication pending (from PRIDE)
Dataset title: Small protein enrichment improves proteomics detection of sORF encoded peptides.
Possible reference: Cassidy, L. et al. (2021) Multidimensional separation schemes enhance the identification and molecular characterization of low molecular weight proteomes and short open reading frame-encoded peptides in top-down proteomics., J Proteomics, PMID 32949814

PXD025294 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens
Possible reference: Bezstarosti, K. et al. (2021) Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens., PLoS One, PMID 34762662

PXD025293 Dataset with its publication pending (from PRIDE)
Dataset title: Lima1 mediates the pluripotency control of membrane dynamics and cellular metabolism
Possible reference: Duethorn, B. et al. (2022) Lima1 mediates the pluripotency control of membrane dynamics and cellular metabolism., Nat Commun, PMID 35105859

PXD025286 Dataset with its publication pending (from PRIDE)
Dataset title: Synaptic protein S-palmitoylation as a novel mechanism underlying sex-dependent differences in neuronal plasticity
Possible reference: Zaręba-Kozioł, M. et al. (2021) S-Palmitoylation of Synaptic Proteins as a Novel Mechanism Underlying Sex-Dependent Differences in Neuronal Plasticity., Int J Mol Sci, PMID 34200797

PXD025285 Dataset with its publication pending (from PRIDE)
Dataset title: Endolysosomal processing of N-glycans on acid alpha-glucosidase is critical to attain the most active enzyme for hydrolyzing glycogen
Possible reference: Selvan, N. et al. (2021) Endolysosomal N-glycan processing is critical to attain the most active form of the enzyme acid alpha-glucosidase., J Biol Chem, PMID 33971197

PXD025279 Dataset with its publication pending (from PRIDE)
Dataset title: The molecular appearance of native TRPM7 channel complexes identified by high-resolution proteomics
Possible reference: Kollewe, A. et al. (2021) The molecular appearance of native TRPM7 channel complexes identified by high-resolution proteomics., Elife, PMID 34766907

PXD025272 Dataset with its publication pending (from PRIDE)
Dataset title: IKAROS and MENIN are Functionally Cooperative Therapeutic Targets in Acute Myeloid Leukemia
Possible reference: Aubrey, BJ. et al. (2022) IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia., Nat Cancer, PMID 35534777

PXD025258 Dataset with its publication pending (from PRIDE)
Dataset title: Site-specific ubiquitylation acts as a regulator of linker histone H1
Possible reference: H�llm�ller, E. et al. (2021) Site-specific ubiquitylation acts as a regulator of linker histone H1., Nat Commun, PMID 34108453

PXD025240 Dataset with its publication pending (from PRIDE)
Dataset title: Hippocampal disruptions of synaptic and astrocyte metabolism during early amyloid pathology in the 5xFAD mouse model of Alzheimer’s disease
Possible reference: Andersen, JV. et al. (2021) Hippocampal disruptions of synaptic and astrocyte metabolism are primary events of early amyloid pathology in the 5xFAD mouse model of Alzheimer's disease., Cell Death Dis, PMID 34657143

PXD025236 Dataset with its publication pending (from PRIDE)
Dataset title: Temperature influences the composition and cytotoxicity of extracellular vesicles in Staphylococcus aureus
Possible reference: Briaud, P. et al. (2021) Temperature Influences the Composition and Cytotoxicity of Extracellular Vesicles in Staphylococcus aureus., mSphere, PMID 34612674

PXD025234 Dataset with its publication pending (from PRIDE)
Dataset title: Cold acclimation process under limited light conditions in Arabidopsis thaliana
Possible reference: Nunes, C. et al. (2013) Regulation of growth by the trehalose pathway: relationship to temperature and sucrose., Plant Signal Behav, PMID 24084646

PXD025232 Dataset with its publication pending (from PRIDE)
Dataset title: IKAROS and MENIN are Functionally Cooperative Therapeutic Targets in Acute Myeloid Leukemia
Possible reference: Aubrey, BJ. et al. (2022) IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia., Nat Cancer, PMID 35534777

PXD025231 Dataset with its publication pending (from PRIDE)
Dataset title: IKAROS and MENIN are Functionally Cooperative Therapeutic Targets in Acute Myeloid Leukemia
Possible reference: Aubrey, BJ. et al. (2022) IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia., Nat Cancer, PMID 35534777

PXD025229 Dataset with its publication pending (from PRIDE)
Dataset title: IKAROS and MENIN are Functionally Cooperative Therapeutic Targets in Acute Myeloid Leukemia
Possible reference: Aubrey, BJ. et al. (2022) IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia., Nat Cancer, PMID 35534777

PXD025228 Dataset with its publication pending (from PRIDE)
Dataset title: IKAROS and MENIN are Functionally Cooperative Therapeutic Targets in Acute Myeloid Leukemia
Possible reference: Aubrey, BJ. et al. (2022) IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia., Nat Cancer, PMID 35534777

PXD025227 Dataset with its publication pending (from PRIDE)
Dataset title: IKAROS and MENIN are Functionally Cooperative Therapeutic Targets in Acute Myeloid Leukemia
Possible reference: Aubrey, BJ. et al. (2022) IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia., Nat Cancer, PMID 35534777

PXD025220 Dataset with its publication pending (from PRIDE)
Dataset title: Crosslinking mass spectrometry of the unconventional kinetoplastid kinetochore proteins KKT16-KKT17-KKT18
Possible reference: Ludzia, P. et al. (2021) Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein., Structure, PMID 33915106

PXD025219 Dataset with its publication pending (from PRIDE)
Dataset title: Bacterial RF3 Senses Chaperone Function in Co-translational Folding
Possible reference: Zhao, L. et al. (2021) Bacterial RF3 senses chaperone function in co-translational folding., Mol Cell, PMID 34107307

PXD025218 Dataset with its publication pending (from PRIDE)
Dataset title: N-linked glycoproteins from exosome-depleted excretory-secretory products of fourth-stage larval Angiostrongylus cantonensis promotes alternative activation of macrophages through metabolic reprogramming by the PI3K-Akt pathway
Possible reference: Wan, S. et al. (2021) Exosome-Depleted Excretory-Secretory Products of the Fourth-Stage Larval Angiostrongylus cantonensis Promotes Alternative Activation of Macrophages Through Metabolic Reprogramming by the PI3K-Akt Pathway., Front Immunol, PMID 34367145

PXD025217 Dataset with its publication pending (from PRIDE)
Dataset title: Topology of the redox network during induction of photosynthesis as revealed by time-resolved proteomics in tobacco
Possible reference: Zimmer, D. et al. (2021) Topology of the redox network during induction of photosynthesis as revealed by time-resolved proteomics in tobacco., Sci Adv, PMID 34919428

PXD025213 Dataset with its publication pending (from PRIDE)
Dataset title: Supermeres, a new functional extracellular nanoparticle replete with disease biomarkers and therapeutic target
Possible reference: Zhang, Q. et al. (2021) Supermeres are functional extracellular nanoparticles replete with disease biomarkers and therapeutic targets., Nat Cell Biol, PMID 34887515

PXD025212 Dataset with its publication pending (from PRIDE)
Dataset title: Biochemical and Proteomic proteomic changes in the roots of M4 grapevine rootstock in response to nitrate availability
Possible reference: Prinsi, B. et al. (2021) Biochemical and Proteomic Changes in the Roots of M4 Grapevine Rootstock in Response to Nitrate Availability., Plants (Basel), PMID 33920578

PXD025196 Dataset with its publication pending (from PRIDE)
Dataset title: Embryonic developmental arrest in the annual killifish Austrolebias charrua: a proteomic approach to diapause III.
Possible reference: Chalar, C. et al. (2021) Embryonic developmental arrest in the annual killifish Austrolebias charrua: A proteomic approach to diapause III., PLoS One, PMID 34086690

PXD025170 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic study of fig inflorescence and receptacle
Possible reference: Zhai, Y. et al. (2021) Papain-Like Cysteine Protease Gene Family in Fig (Ficus carica L.): Genome-Wide Analysis and Expression Patterns., Front Plant Sci, PMID 34122493

PXD025163 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of serial isolates of Trichosporon asahii
Possible reference: Yang, X. et al. (2021) Proteomic analysis of serial isolates of Trichosporon asahii identifies host-specific adaptations using the TMT/MRM approach., J Proteomics, PMID 34153541

PXD025149 Dataset with its publication pending (from PRIDE)
Dataset title: EROS is a selective chaperone regulating the phagocyte NADPH oxidase and purinergic signalling.
Possible reference: Randzavola, LO. et al. (2022) EROS is a selective chaperone regulating the phagocyte NADPH oxidase and purinergic signalling., Elife, PMID 36421765

PXD025146 Dataset with its publication pending (from PRIDE)
Dataset title: The global Proteome and Ubiquitinome of bacterial and viral co-infected Bronchial Epithelial Cells
Possible reference: Sura, T. et al. (2022) The global proteome and ubiquitinome of bacterial and viral co-infected bronchial epithelial cells., J Proteomics, PMID 34600154

PXD025140 Dataset with its publication pending (from PRIDE)
Dataset title: Labeling preferences of diazirines with protein biomolecules
Possible reference: West, AV. et al. (2021) Labeling Preferences of Diazirines with Protein Biomolecules., J Am Chem Soc, PMID 33876925

PXD025139 Dataset with its publication pending (from PRIDE)
Dataset title: Pathway-guided monitoring of the disease course in bladder cancer with longitudinal urine proteomics
Possible reference: Carvalho, LB. et al. (2023) Pathway-guided monitoring of the disease course in bladder cancer with longitudinal urine proteomics., Commun Med (Lond), PMID 36646893

PXD025138 Dataset with its publication pending (from PRIDE)
Dataset title: Prognostic accuracy of MALDI-TOF mass spectrometric analysis of plasma in COVID-19
Possible reference: Lazari, LC. et al. (2021) Prognostic accuracy of MALDI-TOF mass spectrometric analysis of plasma in COVID-19., Life Sci Alliance, PMID 34168074

PXD025123 Dataset with its publication pending (from PRIDE)
Dataset title: Dual roles of HSP70 chaperone HSPA1 in quality control of nascent and newly synthesized proteins
Possible reference: Tian, G. et al. (2021) Dual roles of HSP70 chaperone HSPA1 in quality control of nascent and newly synthesized proteins., EMBO J, PMID 34010456

PXD025107 Dataset with its publication pending (from PRIDE)
Dataset title: Data on nucleoid-associated proteins isolated from Mycoplasma gallisepticum after intracellular infection
Possible reference: Zubov, AI. et al. (2021) Data on nucleoid-associated proteins isolated from Mycoplasma gallisepticum after intracellular infection., Data Brief, PMID 34458519

PXD025102 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular characterization of a complex of Apoptosis Inducing Factor 1 (AIFM1) with cytochrome c oxidase of the mitochondrial respiratory chain
Possible reference: Hevler, JF. et al. (2021) Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain., Proc Natl Acad Sci U S A, PMID 34548399

PXD025101 Dataset with its publication pending (from PRIDE)
Dataset title: Contribution of IFIX to nuclear and cytoplasmic proteome changes during immune signaling
Possible reference: Howard, TR. et al. (2021) The DNA Sensor IFIX Drives Proteome Alterations To Mobilize Nuclear and Cytoplasmic Antiviral Responses, with Its Acetylation Acting as a Localization Toggle., mSystems, PMID 34156286

PXD025092 Dataset with its publication pending (from PRIDE)
Dataset title: Multimodality Assessment of HFpEF Skeletal Muscle Reveals Differences in the Machinery of Energy Fuel Metabolism
Possible reference: Zamani, P. et al. (2021) Multimodality assessment of heart failure with preserved ejection fraction skeletal muscle reveals differences in the machinery of energy fuel metabolism., ESC Heart Fail, PMID 33991175

PXD025087 Dataset with its publication pending (from PRIDE)
Dataset title: Genomic and proteomic study of Andreprevotia ripae isolated from an anthill reveals an extensive repertoire of chitinolytic enzymes
Possible reference: Lorentzen, SB. et al. (2021) Genomic and Proteomic Study of Andreprevotia ripae Isolated from an Anthill Reveals an Extensive Repertoire of Chitinolytic Enzymes., J Proteome Res, PMID 34191517

PXD025080 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of the coral symbiont Breviolum minutum under elevated temperature stress
Possible reference: Lust, B. et al. (2025) The Influence of Symbiont Identity on the Proteomic and Metabolomic Responses of the Model Cnidarian Aiptasia to Thermal Stress., Environ Microbiol, PMID 40056008

PXD025078 Dataset with its publication pending (from PRIDE)
Dataset title: Sequential N/O-glycosylation analysis of heavily glycosylated HIV-1 gp120 by combination of electron-transfer/higher-energy collisional dissociation and stepped collision energy/higher-energy collisional dissociation (EThcD-sceHCD)
Possible reference: Zhang, Y. et al. (2021) Sequential Analysis of the N/O-Glycosylation of Heavily Glycosylated HIV-1 gp120 Using EThcD-sceHCD-MS/MS., Front Immunol, PMID 34745128

PXD025066 Dataset with its publication pending (from PRIDE)
Dataset title: Furan warheads for covalent trapping of weak protein-protein interactions: specific cross-linking of thymosin Î²4 to actin
Possible reference: Miret-Casals, L. et al. (2021) Furan warheads for covalent trapping of weak protein-protein interactions: cross-linking of thymosin β4 to actin., Chem Commun (Camb), PMID 34036992

PXD025050 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of the coral symbiont Durusdinium trenchii under elevated temperature stress
Possible reference: Lust, B. et al. (2025) The Influence of Symbiont Identity on the Proteomic and Metabolomic Responses of the Model Cnidarian Aiptasia to Thermal Stress., Environ Microbiol, PMID 40056008

PXD025039 Dataset with its publication pending (from jPOST)
Dataset title: Matrix thermal shift assay for fast construction of multidimensional ligand targets space
Possible reference: Ruan, C. et al. (2022) Matrix Thermal Shift Assay for Fast Construction of Multidimensional Ligand-Target Space., Anal Chem, PMID 35442643

PXD025035 no publication (from MassIVE)
Dataset title: Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms
Possible reference: Song, E. et al. (2020) Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement., bioRxiv, PMID 32935102

PXD025031 no publication (from MassIVE)
Dataset title: Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry
Possible reference: Wei, T. et al. (2022) Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry., Elife, PMID 35439114

PXD025029 Dataset with its publication pending (from PRIDE)
Dataset title: A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis
Possible reference: Robertson, N. et al. (2022) A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis., Nat Commun, PMID 35115551

PXD025017 Dataset with its publication pending (from iProX)
Dataset title: Comprehensive iTRAQ based proteomic Characterization of Coronary Artery Diseases
Possible reference: Sharma, P. et al. (2024) A comprehensive proteomic profiling of urinary exosomes and the identification of early non-invasive biomarker in patients with coronary artery disease., J Proteomics, PMID 38151158

PXD025016 no publication (from MassIVE)
Dataset title: Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms
Possible reference: Song, E. et al. (2020) Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement., bioRxiv, PMID 32935102

PXD025015 no publication (from MassIVE)
Dataset title: Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms
Possible reference: Song, E. et al. (2020) Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement., bioRxiv, PMID 32935102

PXD025014 no publication (from MassIVE)
Dataset title: A CANCER UBIQUITOME LANDSCAPE IDENTIFIES METABOLIC REPROGRAMMING AS TARGET OF PARKIN TUMOR SUPPRESSION
Possible reference: Agarwal, E. et al. (2021) A cancer ubiquitome landscape identifies metabolic reprogramming as target of Parkin tumor suppression., Sci Adv, PMID 34433563

PXD025011 Dataset with its publication pending (from PRIDE)
Dataset title: Integrative cell type-specific multi-omics approaches reveal impaired programs of glial cell differentiation in mouse culture models of DM1
Possible reference: Gonz�lez-Barriga, A. et al. (2021) Integrative Cell Type-Specific Multi-Omics Approaches Reveal Impaired Programs of Glial Cell Differentiation in Mouse Culture Models of DM1., Front Cell Neurosci, PMID 34025359

PXD025005 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative Urinary Proteomics of UCPPS
Possible reference: Froehlich, JW. et al. (2022) The Urinary Proteomic Profile Implicates Key Regulators for Urologic Chronic Pelvic Pain Syndrome (UCPPS): A MAPP Research Network�Study., Mol Cell Proteomics, PMID 34774759

PXD024997 Dataset with its publication pending (from PRIDE)
Dataset title: Clinical Assay for the Early Detection of Colorectal Cancer Using Mass Spectrometric Wheat Germ Agglutinin Multiple Reaction Monitoring
Possible reference: Tsai, IJ. et al. (2021) Clinical Assay for the Early Detection of Colorectal Cancer Using Mass Spectrometric Wheat Germ Agglutinin Multiple Reaction Monitoring., Cancers (Basel), PMID 34063271

PXD024972 Dataset with its publication pending (from jPOST)
Dataset title: Comprehensive transcriptome sequencing of Tanaidacea with proteomic evidences for their silk
Possible reference: Kakui, K. et al. (2021) Comprehensive Transcriptome Sequencing of Tanaidacea with Proteomic Evidences for Their Silk., Genome Biol Evol, PMID 34904645

PXD024952 Dataset with its publication pending (from PRIDE)
Dataset title: The distinctive flagellar proteome of Euglena gracilis
Possible reference: Hammond, M. et al. (2021) The distinctive flagellar proteome of Euglena gracilis illuminates the complexities of protistan flagella adaptation., New Phytol, PMID 34292600

PXD024949 Dataset with its publication pending (from PRIDE)
Dataset title: Fast and global reorganization of the chloroplast protein biogenesis network during heat acclimation
Possible reference: Tr�sch, R. et al. (2022) Fast and global reorganization of the chloroplast protein biogenesis network during heat acclimation., Plant Cell, PMID 34958373

PXD024934 Dataset with its publication pending (from PRIDE)
Dataset title: C. albicans mtEXO mutant mitochondria
Possible reference: Łabędzka-Dmoch, K. et al. (2021) Pervasive transcription of the mitochondrial genome in Candida albicans is revealed in mutants lacking the mtEXO RNase complex., RNA Biol, PMID 34229573

PXD024933 Dataset with its publication pending (from PRIDE)
Dataset title: Examining pathways of iron and sulfur acquisition, trafficking, deployment, and storage in mineral-grown methanogen cells
Possible reference: Payne, D. et al. (2021) Examining Pathways of Iron and Sulfur Acquisition, Trafficking, Deployment, and Storage in Mineral-Grown Methanogen Cells., J Bacteriol, PMID 34251867

PXD024925 Dataset with its publication pending (from iProX)
Dataset title: Discovery of metal-binding proteins by thermal proteome profiling.
Possible reference: Zeng, X. et al. (2024) Discovery of metal-binding proteins by thermal proteome profiling., Nat Chem Biol, PMID 38409364

PXD024921 Dataset with its publication pending (from PRIDE)
Dataset title: TMT-based proteomic analysis of CSF in dogs with intervertebral disc herniation
Possible reference: Horvatić, A. et al. (2025) Combining Metabolomics and Proteomics to Reveal Key Serum Compounds Related to Canine Intervertebral Disc Herniation., Metabolites, PMID 40559419

PXD024906 Dataset with its publication pending (from PRIDE)
Dataset title: Spatial discordances between mRNAs and proteins in the intestinal epithelium
Possible reference: Harnik, Y. et al. (2021) Spatial discordances between mRNAs and proteins in the intestinal epithelium., Nat Metab, PMID 34931081

PXD024891 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic and lipidomic profiling of demyelinating lesions identifies fatty acids as modulators in inflammation resolution
Possible reference: Penkert, H. et al. (2021) Proteomic and lipidomic profiling of demyelinating lesions identifies fatty acids as modulators in lesion recovery., Cell Rep, PMID 34706241

PXD024873 Dataset with its publication pending (from PRIDE)
Dataset title: Synechocystis sp. PCC 6803(iron and/or copper starvation)-LC MS/MS
Possible reference: Huokko, T. et al. (2019) Thylakoid Localized Type 2 NAD(P)H Dehydrogenase NdbA Optimizes Light-Activated Heterotrophic Growth of Synechocystis sp. PCC 6803., Plant Cell Physiol, PMID 30847494

PXD024852 Dataset with its publication pending (from PRIDE)
Dataset title: Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through a NGFR-dependent mechanism
Possible reference: Garc�a-Silva, S. et al. (2021) Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism., Nat Cancer, PMID 34957415

PXD024842 no publication (from MassIVE)
Dataset title: Central nervous system immune response in postinfectious hydrocephalus
Possible reference: Robert, SM. et al. (2023) The choroid plexus links innate immunity to CSF dysregulation in hydrocephalus., Cell, PMID 36803604

PXD024830 Dataset with its publication pending (from PRIDE)
Dataset title: Proteogenomic Landscape of Uterine Leiomyomas from Hereditary Leiomyomatosis and Renal Cell Cancer Patients
Possible reference: Bateman, NW. et al. (2021) Proteogenomic landscape of uterine leiomyomas from hereditary leiomyomatosis and renal cell cancer patients., Sci Rep, PMID 33931688

PXD024829 Dataset with its publication pending (from PRIDE)
Dataset title: The proteome and phosphoproteome of acute stress in the mouse hippocampus
Possible reference: von Ziegler, LM. et al. (2022) Multiomic profiling of the acute stress response in the mouse hippocampus., Nat Commun, PMID 35383160

PXD024822 Dataset with its publication pending (from PRIDE)
Dataset title: The human GID complex engages two independent modules for substrate recruitment
Possible reference: Mohamed, WI. et al. (2021) The human GID complex engages two independent modules for substrate recruitment., EMBO Rep, PMID 34647674

PXD024816 Dataset with its publication pending (from PRIDE)
Dataset title: Mutation of Arabidopsis SME1 improves oxidative stress resilience
Possible reference: Willems, P. et al. (2023) Mutation of Arabidopsis SME1 and Sm core assembly improves oxidative stress resilience., Free Radic Biol Med, PMID 36870374

PXD024810 Dataset with its publication pending (from iProX)
Dataset title: Integrated multiomic analysis reveals comprehensive tumor heterogeneity in primary and recurrent hepatocellular carcinomas
Possible reference: Zhou, C. et al. (2023) Whole-exome sequencing reveals the metastatic potential of hepatocellular carcinoma from the perspective of tumor and circulating tumor DNA., Hepatol Int, PMID 37217808

PXD024789 Dataset with its publication pending (from PRIDE)
Dataset title: Wells Lab Primary T Cell Surfaceomics
Possible reference: Byrnes, JR. et al. (2022) Hypoxia Is a Dominant Remodeler of the Effector T�Cell Surface Proteome Relative to Activation and Regulatory T Cell Suppression., Mol Cell Proteomics, PMID 35217172

PXD024778 no publication (from MassIVE)
Dataset title: Tenrec ecaudatus liver proteome
Possible reference: Khudyakov, JI. et al. (2021) Liver proteome response to torpor in a basoendothermic mammal, Tenrec ecaudatus, provides insights into the evolution of homeothermy., Am J Physiol Regul Integr Comp Physiol, PMID 34431404

PXD024771 Dataset with its publication pending (from PRIDE)
Dataset title: Gefitinib results in robust host-directed immunity against Salmonella infection through proteo-metabolomic reprogramming.
Possible reference: Sadhu, S. et al. (2021) Gefitinib Results in Robust Host-Directed Immunity Against Salmonella Infection Through Proteo-Metabolomic Reprogramming., Front Immunol, PMID 33868285

PXD024733 Dataset with its publication pending (from PRIDE)
Dataset title: culture media formulations on extracellular vesicle production by amniotic epithelial cells
Possible reference: Zhu, D. et al. (2021) Impact of chemically defined culture media formulations on extracellular vesicle production by amniotic epithelial cells., Proteomics, PMID 34081834

PXD024730 Dataset with its publication pending (from PRIDE)
Dataset title: Global analysis of lysine 2-hydroxyisobutyrylation in Rheum palmatum
Possible reference: Qi, T. et al. (2021) Global analysis of protein lysine 2-hydroxyisobutyrylation (Khib) profiles in Chinese herb rhubarb (Dahuang)., BMC Genomics, PMID 34266380

PXD024728 Dataset with its publication pending (from PRIDE)
Dataset title: SOD1 is a possible predictor of COVID-19 progression as revealed by plasma proteomics
Possible reference: Xu, B. et al. (2021) SOD1 is a Possible Predictor of COVID-19 Progression as Revealed by Plasma Proteomics., ACS Omega, PMID 34250342

PXD024721 Dataset with its publication pending (from PRIDE)
Dataset title: Tetrahydrocurcumin ameliorates Alzheimer's pathological phenotypes by inhibition of microglial cell cycle arrest and apoptosis via Ras/ERK signaling
Possible reference: Xiao, Y. et al. (2021) Tetrahydrocurcumin ameliorates Alzheimer's pathological phenotypes by inhibition of microglial cell cycle arrest and apoptosis via Ras/ERK signaling., Biomed Pharmacother, PMID 34243602

PXD024720 Dataset with its publication pending (from PRIDE)
Dataset title: The evolution of Proteomics in the genus Flaveria
Possible reference: Aldous, SH. et al. (2014) Evolution of the Phosphoenolpyruvate Carboxylase Protein Kinase Family in C3 and C4 Flaveria spp., Plant Physiol, PMID 24850859

PXD024715 Dataset with its publication pending (from PRIDE)
Dataset title: Sox9 determines translational capacity during early chondrogenic differentiation of ATDC5 cells by regulating expression of ribosome biogenesis factors and ribosomal proteins
Possible reference: Caron, MMJ. et al. (2021) Sox9 Determines Translational Capacity During Early Chondrogenic Differentiation of ATDC5 Cells by Regulating Expression of Ribosome Biogenesis Factors and Ribosomal Proteins., Front Cell Dev Biol, PMID 34235151

PXD024700 Dataset with its publication pending (from PRIDE)
Dataset title: 1,2-Propanediol utilization mediated by bacterial microcompartments in Propionibacterium freudenreichii DSM 20271
Possible reference: Dank, A. et al. (2021) Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization of Propionibacterium freudenreichii., Front Microbiol, PMID 34054787

PXD024683 Dataset with its publication pending (from PRIDE)
Dataset title: Rational correction of pathogenic conformational defects in HTRA1
Possible reference: Beaufort, N. et al. (2024) Rational correction of pathogenic conformational defects in HTRA1., Nat Commun, PMID 39013852

PXD024682 Dataset with its publication pending (from PRIDE)
Dataset title: Chromosomal instability by mutations in the novel minor spliceosome component CENATAC
Possible reference: de Wolf, B. et al. (2021) Chromosomal instability by mutations in the novel minor spliceosome component CENATAC., EMBO J, PMID 34009673

PXD024676 no publication (from MassIVE)
Dataset title: A systematic evaluation of semispecific peptide search parameter enables identification of previously undescribed N-terminal peptides and conserved proteolytic processing in cancer cell lines
Possible reference: Fahrner, M. et al. (2021) A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines., Proteomes, PMID 34070654

PXD024638 Dataset with its publication pending (from PRIDE)
Dataset title: Venom proteomic analysis of two medically important Nigerian viperidae (Echis ocellatus and Bitis arietans) snake species
Possible reference: Dingwoke, EJ. et al. (2021) Venom proteomic analysis of medically important Nigerian viper Echis ocellatus and Bitis arietans snake species., Biochem Biophys Rep, PMID 34765747

PXD024605 Dataset with its publication pending (from PRIDE)
Dataset title: Too Hot to Handle: Antibacterial Peptides Identified in Ghost Pepper
Possible reference: Culver, KD. et al. (2021) Too Hot to Handle: Antibacterial Peptides Identified in Ghost Pepper., J Nat Prod, PMID 34445876

PXD024603 Dataset with its publication pending (from PRIDE)
Dataset title: ArfGAP1 inhibits mTORC1 lysosomal localization and activation
Possible reference: Meng, D. et al. (2021) ArfGAP1 inhibits mTORC1 lysosomal localization and activation., EMBO J, PMID 33988249

PXD024601 Dataset with its publication pending (from PRIDE)
Dataset title: Systematic analysis of the impact of R-methylation on RBPs-RNA interactions
Possible reference: Maniaci, M. et al. (2021) Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach., Front Mol Biosci, PMID 34557518

PXD024599 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamic methylation of histone H3K18 in differentiating Theileria parasites
Possible reference: Cheeseman, K. et al. (2021) Dynamic methylation of histone H3K18 in differentiating Theileria parasites., Nat Commun, PMID 34050145

PXD024592 Dataset with its publication pending (from PRIDE)
Dataset title: Effects of thermal acclimation on the proteome of the planarian Crenobia alpina from an alpine freshwater spring
Possible reference: Ebner, JN. et al. (2022) Effects of thermal acclimation on the proteome of the planarian Crenobia alpina from an alpine freshwater spring., J Exp Biol, PMID 35875852

PXD024590 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of the substrate specificities and reaction kinetics of the yeast oligosaccharyltransferase isoforms
Possible reference: Eyring, J. et al. (2021) Substrate specificities and reaction kinetics of the yeast oligosaccharyltransferase isoforms., J Biol Chem, PMID 34023382

PXD024588 Dataset with its publication pending (from PRIDE)
Dataset title: Protein identification of spermatozoa and seminal plasma in bottlenose dolphin (Tursiops truncatus)
Possible reference: Fuentes-Albero, MC. et al. (2021) Protein Identification of Spermatozoa and Seminal Plasma in Bottlenose Dolphin (Tursiops truncatus)., Front Cell Dev Biol, PMID 34336830

PXD024586 no publication (from MassIVE)
Dataset title: Listeria exploits IFITM3 to suppress antibacterial activity in phagocytes
Possible reference: Tan, JMJ. et al. (2021) Listeria exploits IFITM3 to suppress antibacterial activity in phagocytes., Nat Commun, PMID 34404769

PXD024579 Dataset with its publication pending (from PRIDE)
Dataset title: Ovalbumin antigen-specific activation of T cell receptor closely resembles antibody stimulation as revealed by BOOST phosphotyrosine proteomics
Possible reference: Chua, XY. et al. (2021) Ovalbumin Antigen-Specific Activation of Human T Cell Receptor Closely Resembles Soluble Antibody Stimulation as Revealed by BOOST Phosphotyrosine Proteomics., J Proteome Res, PMID 34018748

PXD024550 Dataset with its publication pending (from PRIDE)
Dataset title: Characterisation of the pseudokinase SCYL1
Possible reference: Kuliyev, E. et al. (2018) Overlapping Role of SCYL1 and SCYL3 in Maintaining Motor Neuron Viability., J Neurosci, PMID 29437892

PXD024540 Dataset with its publication pending (from PRIDE)
Dataset title: IGDQ motogenic peptide gradient induces directional cell migration through integrin (Î±v)Î²3 activation in metastatic breast cancer
Possible reference: Ayama-Canden, S. et al. (2022) IGDQ motogenic peptide gradient induces directional cell migration through integrin (αv)β3 activation in MDA-MB-231 metastatic breast cancer cells., Neoplasia, PMID 35763908

PXD024532 no publication (from MassIVE)
Dataset title: A highly conserved pocket on PP2A-B56 is required for hSgo1 binding and cohesion protection during mitosis
Possible reference: Ueki, Y. et al. (2021) A highly conserved pocket on PP2A-B56 is required for hSgo1 binding and cohesion protection during mitosis., EMBO Rep, PMID 33973335

PXD024521 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting Pancreatic Cancer by TAK-981, a SUMOylation Inhibitor that Activates the Immune System and Blocks Tumor Cell Cycle Progression
Possible reference: Kumar, S. et al. (2022) Targeting pancreatic cancer by TAK-981: a SUMOylation inhibitor that activates the immune system and blocks cancer cell cycle progression in a preclinical model., Gut, PMID 35074907

PXD024504 no publication (from MassIVE)
Dataset title: Global coordination of metabolic pathways in Escherichia coli by active and passive regulation
Possible reference: Kochanowski, K. et al. (2021) Global coordination of metabolic pathways in Escherichia coli by active and passive regulation., Mol Syst Biol, PMID 33852189

PXD024502 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of enteric neuronal Ndrg4 promotes colorectal cancer via increased release of Nid1 and Fbln2
Possible reference: Vaes, N. et al. (2021) Loss of enteric neuronal Ndrg4 promotes colorectal cancer via increased release of Nid1 and Fbln2., EMBO Rep, PMID 33890711

PXD024490 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics and transcriptomics analysis of fruit development and ripening in watermelon
Possible reference: Yu, Y. et al. (2022) Quantitative Transcriptomic and Proteomic Analysis of Fruit Development and Ripening in Watermelon (Citrullus lanatus)., Front Plant Sci, PMID 35392508

PXD024482 Dataset with its publication pending (from PRIDE)
Dataset title: Visualization and identification of bioorthogonally-labeled exosome proteins following systemic administration in mice
Possible reference: Zhang, E. et al. (2021) Visualization and Identification of Bioorthogonally Labeled Exosome Proteins Following Systemic Administration in Mice., Front Cell Dev Biol, PMID 33898459

PXD024472 no publication (from MassIVE)
Dataset title: Systematic characterization of gut microbiome-secreted molecules by integrated multi-omics
Possible reference: De Saedeleer, B. et al. (2021) Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics., ISME Commun, PMID 35106519

PXD024470 no publication (from MassIVE)
Dataset title: Succinylome-controlled antibiotic resistance in MRSA - Succinylome
Possible reference: Campbell, C. et al. (2021) Accumulation of Succinyl Coenzyme A Perturbs the Methicillin-Resistant Staphylococcus aureus (MRSA) Succinylome and Is Associated with Increased Susceptibility to Beta-Lactam Antibiotics., mBio, PMID 34182779

PXD024462 Dataset with its publication pending (from PRIDE)
Dataset title: GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme
Possible reference: Sherpa, D. et al. (2021) GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme., Mol Cell, PMID 33905682

PXD024457 Dataset with its publication pending (from PRIDE)
Dataset title: Allosteric transcription stimulation by super elongation complex
Possible reference: Chen, Y. et al. (2021) Allosteric transcription stimulation by RNA polymerase II super elongation complex., Mol Cell, PMID 34265249

PXD024426 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vimentin mimics VEGF and is a target for anti-angiogenic immunotherapy
Possible reference: van Beijnum, JR. et al. (2022) Extracellular vimentin mimics VEGF and is a target for anti-angiogenic immunotherapy., Nat Commun, PMID 35606362

PXD024412 Dataset with its publication pending (from PRIDE)
Dataset title: KRAS Epitope Identification Immunopeptidomics
Possible reference: Ade, CM. et al. (2023) Identification of neoepitope reactive T-cell receptors guided by HLA-A*03:01 and HLA-A*11:01 immunopeptidomics., J Immunother Cancer, PMID 37758652

PXD024388 Dataset with its publication pending (from PRIDE)
Dataset title: A KRAS-responsive long non-coding RNA controls microRNA
Possible reference: Shi, L. et al. (2021) A KRAS-responsive long non-coding RNA controls microRNA processing., Nat Commun, PMID 33795683

PXD024381 Dataset with its publication pending (from PRIDE)
Dataset title: Corynebacterium diphtheriae proteome adaptation to cell culture medium and serum
Possible reference: M�ller, J. et al. (2021) Corynebacterium diphtheriae Proteome Adaptation to Cell Culture Medium and Serum., Proteomes, PMID 33805816

PXD024370 no publication (from MassIVE)
Dataset title: Plasma proteomic profile associated with platelet dysfunction after trauma
Possible reference: Bateman, RM. et al. (2016) 36th International Symposium on Intensive Care and Emergency Medicine : Brussels, Belgium. 15-18 March 2016., Crit Care, PMID 27885969

PXD024359 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Clustering Reveals the Kinetics of Disease Biomarkers in Bovine and Human Models of Post-Traumatic Osteoarthritis
Possible reference: Black, RM. et al. (2021) Proteomic Clustering Reveals the Kinetics of Disease Biomarkers in Bovine and Human Models of Post-Traumatic Osteoarthritis., Osteoarthr Cartil Open, PMID 36313736

PXD024352 Dataset with its publication pending (from PRIDE)
Dataset title: Deletion of the transcription factors Hsf1, Msn2 and Msn4 in yeast uncovers transcriptional reprogramming in response to proteotoxic stress
Possible reference: M�hlhofer, M. et al. (2024) Deletion of the transcription factors Hsf1, Msn2 and Msn4 in yeast uncovers transcriptional reprogramming in response to proteotoxic stress., FEBS Lett, PMID 38366111

PXD024350 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of Ataxin-2 interactome using LC-MS/MS
Possible reference: Inagaki, H. et al. (2021) DDX6 is a positive regulator of Ataxin-2/PAPD4 cytoplasmic polyadenylation machinery., Biochem Biophys Res Commun, PMID 33756349

PXD024346 Dataset with its publication pending (from PRIDE)
Dataset title: Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave (Sicily, Italy)
Possible reference: Scorrano, G. et al. (2022) Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave., Commun Biol, PMID 36400919

PXD024343 Dataset with its publication pending (from PRIDE)
Dataset title: Coiled-Coil Domain-Containing 68 Downregulation Promotes Colorectal Cancer Cell Growth by Inhibiting ITCH-Mediated CDK4 Degradation
Possible reference: Wang, C. et al. (2021) Coiled-Coil Domain-Containing 68 Downregulation Promotes Colorectal Cancer Cell Growth by Inhibiting ITCH-Mediated CDK4 Degradation., Front Oncol, PMID 33968776

PXD024330 Dataset with its publication pending (from PRIDE)
Dataset title: Interactome of the Autophagy Receptor TAX1BP1 (T6BP)
Possible reference: Sarango, G. et al. (2022) The Autophagy Receptor TAX1BP1 (T6BP) improves antigen presentation by MHC-II molecules., EMBO Rep, PMID 36215666

PXD024321 Dataset with its publication pending (from PRIDE)
Dataset title: A SUPERFAMILY-WIDE ACTIVITY ATLAS OF SERINE HYDROLASES IN DROSOPHILA MELANOGASTER
Possible reference: Kumar, K. et al. (2021) A Superfamily-wide Activity Atlas of Serine Hydrolases in Drosophila melanogaster., Biochemistry, PMID 33827210

PXD024320 Dataset with its publication pending (from PRIDE)
Dataset title: SILAC-based quantitative proteomics of cancer cells treated with the anti-tumor antibody 14F7
Possible reference: Bousquet, PA. et al. (2022) SILAC-based quantitative proteomics and microscopy analysis of cancer cells treated with the N-glycolyl GM3-specific anti-tumor antibody 14F7., Front Immunol, PMID 36439103

PXD024301 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular basis of F-actin regulation and sarcomere assembly via myotilin
Possible reference: Kostan, J. et al. (2021) Molecular basis of F-actin regulation and sarcomere assembly via myotilin., PLoS Biol, PMID 33844684

PXD024294 Dataset with its publication pending (from PRIDE)
Dataset title: miR-146 modulation in ALS astrocytes
Possible reference: Gomes, C. et al. (2022) Neurotoxic Astrocytes Directly Converted from Sporadic and Familial ALS Patient Fibroblasts Reveal Signature Diversities and miR-146a Theragnostic Potential in Specific Subtypes., Cells, PMID 35406750

PXD024262 no publication (from MassIVE)
Dataset title: Resource allocation in the archaeon Methanococcus maripaludis during slow growth
Possible reference: M�ller, AL. et al. (2021) An alternative resource allocation strategy in the chemolithoautotrophic archaeon Methanococcus maripaludis., Proc Natl Acad Sci U S A, PMID 33879571

PXD024243 Dataset with its publication pending (from PRIDE)
Dataset title: Cellular proteomic changes in the immediate early phase of HIV-1 and 2 transduction
Possible reference: Linkner, TR. et al. (2021) Cellular Proteo-Transcriptomic Changes in the Immediate Early-Phase of Lentiviral Transduction., Microorganisms, PMID 34835333

PXD024219 Dataset with its publication pending (from PRIDE)
Dataset title: Network analysis of the CSF proteome characterises convergent pathways of cellular dysfunction in ALS
Possible reference: Thompson, AG. et al. (2021) Network Analysis of the CSF Proteome Characterizes Convergent Pathways of Cellular Dysfunction in ALS., Front Neurosci, PMID 33815045

PXD024200 Dataset with its publication pending (from PRIDE)
Dataset title: TWIST1 expression is associated with high-risk Neuroblastoma and promotes Primary and Metastatic Tumor Growth
Possible reference: Sepporta, MV. et al. (2022) TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth., Commun Biol, PMID 35022561

PXD024185 no publication (from MassIVE)
Dataset title: GTPBP8 is required for mitoribosomal biogenesis and mitochondrial translation
Possible reference: Wang, L. et al. (2023) GTPBP8 is required for mitoribosomal biogenesis and mitochondrial translation., Cell Mol Life Sci, PMID 37971521

PXD024167 Dataset with its publication pending (from jPOST)
Dataset title: Chromatin Proteome of Drosophila Ovarian somatic cells
Possible reference: Rivera, AJ. et al. (2025) Traffic Jam activates the Flamenco piRNA cluster locus and the Piwi pathway to ensure transposon silencing and Drosophila fertility., Cell Rep, PMID 40209716

PXD024163 no publication (from MassIVE)
Dataset title: Liceaga / Aguilar-Toala chia seed protein hydrolysate antimicrobial peptides
Possible reference: Aguilar-Toal�, JE. et al. (2020) New Insights into the Antimicrobial Properties of Hydrolysates and Peptide Fractions Derived from Chia Seed (Salvia hispanica L.)., Probiotics Antimicrob Proteins, PMID 32385579

PXD024160 Dataset with its publication pending (from PRIDE)
Dataset title: Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding
Possible reference: Taschner, M. et al. (2021) Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding., EMBO J, PMID 34191293

PXD024134 Dataset with its publication pending (from PRIDE)
Dataset title: Optimized Sample Preparation Workflow for Improved Identification of Ghost Proteins
Possible reference: Cardon, T. et al. (2020) Optimized Sample Preparation Workflow for Improved Identification of Ghost Proteins., Anal Chem, PMID 31829555

PXD024108 Dataset with its publication pending (from PRIDE)
Dataset title: Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis by a NGFR-dependent mechanism
Possible reference: Garc�a-Silva, S. et al. (2021) Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism., Nat Cancer, PMID 34957415

PXD024088 Dataset with its publication pending (from PRIDE)
Dataset title: Neddylation modification on cGAS of human and mouse
Possible reference: Li, C. et al. (2021) RNF111-facilitated neddylation potentiates cGAS-mediated antiviral innate immune response., PLoS Pathog, PMID 33720974

PXD024084 Dataset with its publication pending (from PRIDE)
Dataset title: Autocatalytic activation of a malarial egress protease is druggable and requires a protein cofactor
Possible reference: Tan, MSY. et al. (2021) Autocatalytic activation of a malarial egress protease is druggable and requires a protein cofactor., EMBO J, PMID 33932049

PXD024043 Dataset with its publication pending (from PRIDE)
Dataset title: Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation
Possible reference: Brunner, AD. et al. (2022) Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation., Mol Syst Biol, PMID 35226415

PXD024035 Dataset with its publication pending (from PRIDE)
Dataset title: Orphan nuclear receptor COUP-TFII enhances myofibroblasts glycolysis leading to kidney fibrosis
Possible reference: Li, L. et al. (2021) Orphan nuclear receptor COUP-TFII enhances myofibroblast glycolysis leading to kidney fibrosis., EMBO Rep, PMID 34031962

PXD024021 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative phosphoproteomic analysis of tomato genotypes with contrasting cadmium tolerance
Possible reference: Marques, DN. et al. (2021) Comparative phosphoproteomic analysis of tomato genotypes with contrasting cadmium tolerance., Plant Cell Rep, PMID 34410462

PXD024009 Dataset with its publication pending (from PRIDE)
Dataset title: Effects of the IDH1 R132H mutation on the energy metabolism: a comparison between tissue and corresponding primary glioma cell cultures
Possible reference: Dekker, LJM. et al. (2022) Effects of the IDH1 R132H Mutation on the Energy Metabolism: A Comparison between Tissue and Corresponding Primary Glioma Cell Cultures., ACS Omega, PMID 35128264

PXD023980 Dataset with its publication pending (from iProX)
Dataset title: GproDIA enables intact glycopeptide characterization using data‐independent acquisition glycoproteomics with comprehensive statistical control
Possible reference: Yang, Y. et al. (2021) GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control., Nat Commun, PMID 34663801

PXD023978 Dataset with its publication pending (from PRIDE)
Dataset title: Unresolved stalled ribosome complexes restrict cycle progression after genotoxic stress
Possible reference: Stoneley, M. et al. (2022) Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress., Mol Cell, PMID 35180429

PXD023976 Dataset with its publication pending (from PRIDE)
Dataset title: Unresolved stalled ribosome complexes restrict cycle progression after genotoxic stress
Possible reference: Stoneley, M. et al. (2022) Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress., Mol Cell, PMID 35180429

PXD023966 Dataset with its publication pending (from PRIDE)
Dataset title: A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals
Possible reference: Holoch, D. et al. (2021) A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals., Nat Genet, PMID 34782763

PXD023951 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation and Optimization of High-Field Asymmetric Waveform Ion Mobility Spectrometry for Multiplexed Quantitative Site-specific N-glycoproteomics
Possible reference: Fang, P. et al. (2021) Evaluation and Optimization of High-Field Asymmetric Waveform Ion-Mobility Spectrometry for Multiplexed Quantitative Site-Specific N-Glycoproteomics., Anal Chem, PMID 34133129

PXD023947 no publication (from MassIVE)
Dataset title: The Ubiquitin Interacting Motif Like Domain of Met4 is a K48 Polyubiquitin Chain Selective Binding Domain
Possible reference: Villamil, M. et al. (2022) The Ubiquitin Interacting Motif-Like Domain of Met4 Selectively Binds K48 Polyubiquitin Chains., Mol Cell Proteomics, PMID 34763062

PXD023943 Dataset with its publication pending (from PRIDE)
Dataset title: Glycoproteomic and phenotypic elucidation of B4GALNT2 expression variants in the SID histo-blood group system
Possible reference: Stenfelt, L. et al. (2022) Glycoproteomic and Phenotypic Elucidation of B4GALNT2 Expression Variants in the SID Histo-Blood Group System., Int J Mol Sci, PMID 35409292

PXD023939 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial membrane proteins and VPS35 orchestrate selective removal of mtDNA
Possible reference: Sen, A. et al. (2022) Mitochondrial membrane proteins and VPS35 orchestrate selective removal of mtDNA., Nat Commun, PMID 36344526

PXD023878 Dataset with its publication pending (from PRIDE)
Dataset title: Unresolved stalled ribosome complexes restrict cycle progression after genotoxic stress
Possible reference: Stoneley, M. et al. (2022) Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress., Mol Cell, PMID 35180429

PXD023873 Dataset with its publication pending (from PRIDE)
Dataset title: AMPylation profiling during neuronal differentiation reveals extensive variation on lysosomal proteins
Possible reference: Becker, T. et al. (2021) AMPylation profiling during neuronal differentiation reveals extensive variation on lysosomal proteins., iScience, PMID 34917898

PXD023861 Dataset with its publication pending (from PRIDE)
Dataset title: Unresolved stalled ribosome complexes restrict cycle progression after genotoxic stress
Possible reference: Stoneley, M. et al. (2022) Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress., Mol Cell, PMID 35180429

PXD023859 Dataset with its publication pending (from PRIDE)
Dataset title: Sex differences in the ventral tegmental area and nucleus accumbens proteome at baseline and following nicotine exposure
Possible reference: Lee, AM. et al. (2021) Sex Differences in the Ventral Tegmental Area and Nucleus Accumbens Proteome at Baseline and Following Nicotine Exposure., Front Mol Neurosci, PMID 34335180

PXD023855 Dataset with its publication pending (from PanoramaPublic)
Dataset title: RGI-GOLVEN signalling promotes FLS2 abundance to regulate plant immunity
Possible reference: Stegmann, M. et al. (2022) RGI-GOLVEN signaling promotes cell surface immune receptor abundance to regulate plant immunity., EMBO Rep, PMID 35229426

PXD023853 Dataset with its publication pending (from PRIDE)
Dataset title: OXI1 coordinates programmed cell death by promoting salicylic acid, N-hydroxypipecolic acid and reactive oxygen species accumulation in Arabidopsis
Possible reference: Rawat, AA. et al. (2023) OXIDATIVE SIGNAL-INDUCIBLE1 induces immunity by coordinating N-hydroxypipecolic acid, salicylic acid, and camalexin synthesis., New Phytol, PMID 36319610

PXD023851 Dataset with its publication pending (from PRIDE)
Dataset title: IgE antibodies increase honeybee venom responsiveness and detoxification efficiency of mast cells
Possible reference: Starkl, P. et al. (2022) IgE antibodies increase honeybee venom responsiveness and detoxification efficiency of mast cells., Allergy, PMID 33840121

PXD023834 Dataset with its publication pending (from PRIDE)
Dataset title: A type I IFN, prothrombotic hyperinflammatory neutrophil signature is distinct for COVID-19 ARDS
Possible reference: Reyes, L. et al. (2021) -------A type I IFN, prothrombotic hyperinflammatory neutrophil signature is distinct for COVID-19 ARDS--., Wellcome Open Res, PMID 33997298

PXD023814 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping AT1R biased signaling using proximity-labeling and proteomics identifies diverse actions of biased agonists
Possible reference: Pfeiffer, CT. et al. (2021) Mapping Angiotensin II Type 1 Receptor-Biased Signaling Using Proximity Labeling and Proteomics Identifies Diverse Actions of Biased Agonists., J Proteome Res, PMID 33950683

PXD023803 no publication (from MassIVE)
Dataset title: Phosphoproteomics of ATR Signaling in Prophase I of Mouse Meiosis
Possible reference: Sims, JR. et al. (2022) Phosphoproteomics of ATR signaling in mouse testes., Elife, PMID 35133275

PXD023786 Dataset with its publication pending (from PRIDE)
Dataset title: SNAPIN regulates Î² cell cycle progression to promote pancreatic Î² cell growth
Possible reference: Jiang, M. et al. (2021) SNAPIN Regulates Cell Cycle Progression to Promote Pancreatic β Cell Growth., Front Endocrinol (Lausanne), PMID 34194388

PXD023764 no publication (from MassIVE)
Dataset title: Multi-platform omics analysis of Nipah virus infection reveals viral glycoprotein modulation of mitochondria: proteomics
Possible reference: Johnston, GP. et al. (2025) Multi-platform omics analysis of Nipah virus infection reveals viral glycoprotein modulation of mitochondria., Cell Rep, PMID 40106432

PXD023749 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles shed by follicular lymphoma B cells promote the polarization of bone marrow stromal cell niche
Possible reference: Dumontet, E. et al. (2021) Extracellular vesicles shed by follicular lymphoma B cells promote polarization of the bone marrow stromal cell niche., Blood, PMID 33881493

PXD023743 no publication (from MassIVE)
Dataset title: Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry
Possible reference: Wei, T. et al. (2022) Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry., Elife, PMID 35439114

PXD023732 Dataset with its publication pending (from PRIDE)
Dataset title: PROBER Identifies Proteins Associated with Sequence- Specific DNA in Living Cells
Possible reference: Mondal, S. et al. (2022) PROBER identifies proteins associated with programmable sequence-specific DNA in living cells., Nat Methods, PMID 35927480

PXD023729 Dataset with its publication pending (from PRIDE)
Dataset title: Escherichia coli proteome during outgrowth from stationary phase
Possible reference: Hoch, PG. et al. (2015) Phenotypic characterization and complementation analysis of Bacillus subtilis 6S RNA single and double deletion mutants., Biochimie, PMID 25576829

PXD023720 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative Proteomic Analysis in Alveolar Type II Cells Reveals the Different Capacities of RAS and TGF-Î² to Induce EpithelialâMesenchymal Transition
Possible reference: Zhou, Y. et al. (2021) Quantitative Proteomic Analysis in Alveolar Type II Cells Reveals the Different Capacities of RAS and TGF-β to Induce Epithelial-Mesenchymal Transition., Front Mol Biosci, PMID 33869273

PXD023712 Dataset with its publication pending (from PRIDE)
Dataset title: The esterase PfeE, Achilles heel in the battle for iron between Pseudomonas aeruginosa and Escherichia coli
Possible reference: Gasser, V. et al. (2021) The Esterase PfeE, the Achilles' Heel in the Battle for Iron between Pseudomonas aeruginosa and Escherichia coli., Int J Mol Sci, PMID 33802163

PXD023705 Dataset with its publication pending (from PRIDE)
Dataset title: Tissue extracellular matrix hydrogels as alternative to Matrigel for culturing gastrointestinal organoid
Possible reference: Cherne, MD. et al. (2021) A Synthetic Hydrogel, VitroGel� ORGANOID-3, Improves Immune Cell-Epithelial Interactions in a Tissue Chip Co-Culture Model of Human Gastric Organoids and Dendritic Cells., Front Pharmacol, PMID 34552484

PXD023701 Dataset with its publication pending (from PRIDE)
Dataset title: Scaffold-free 3D cell culture of primary skin fibroblasts induces profound changes of the matrisome
Possible reference: Vu, B. et al. (2021) Scaffold-free 3D cell culture of primary skin fibroblasts induces profound changes of the matrisome., Matrix Biol Plus, PMID 34435183

PXD023685 Dataset with its publication pending (from PRIDE)
Dataset title: SEVERE CONSEQUENCES OF A HIGH-LIPID DIET INCLUDE HYDROGEN SULFIDE DYSFUNCTION AND DISEASE AGGRESSION IN GLIOBLASTOMA
Possible reference: Silver, DJ. et al. (2021) Severe consequences of a high-lipid diet include hydrogen sulfide dysfunction and enhanced aggression in glioblastoma., J Clin Invest, PMID 34255747

PXD023653 Dataset with its publication pending (from PRIDE)
Dataset title: Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype
Possible reference: Kojic, M. et al. (2021) Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype., Nat Commun, PMID 33976153

PXD023641 no publication (from MassIVE)
Dataset title: Atase1 and Atase2 differentially regulate reticulophagy and cellular acetyl-CoA metabolism
Possible reference: Rigby, MJ. et al. (2021) Endoplasmic reticulum acetyltransferases Atase1 and Atase2 differentially regulate reticulophagy, macroautophagy and cellular acetyl-CoA metabolism., Commun Biol, PMID 33846551

PXD023639 no publication (from MassIVE)
Dataset title: The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFNb pathway Proteome
Possible reference: Takahashi, M. et al. (2021) The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway., Nat Immunol, PMID 33767426

PXD023633 Dataset with its publication pending (from PRIDE)
Dataset title: Chemo-proteomics exploration of HDAC degradability by small molecule degraders
Possible reference: Xiong, Y. et al. (2021) Chemo-proteomics exploration of HDAC degradability by small molecule degraders., Cell Chem Biol, PMID 34314730

PXD023630 Dataset with its publication pending (from PRIDE)
Dataset title: Chemo-proteomics exploration of HDAC degradability by small molecule degraders
Possible reference: Xiong, Y. et al. (2021) Chemo-proteomics exploration of HDAC degradability by small molecule degraders., Cell Chem Biol, PMID 34314730

PXD023612 Dataset with its publication pending (from PRIDE)
Dataset title: Allergenicity Assessment and Allergen Profile Analysis of Different Chinese Wheat Cultivars
Possible reference: Wang, Y. et al. (2021) Allergenicity assessment and allergen profile analysis of different Chinese wheat cultivars., World Allergy Organ J, PMID 34257797

PXD023591 Dataset with its publication pending (from PRIDE)
Dataset title: Orthogonal degron system for controlled protein degradation in cyanobacteria
Possible reference: Sakkos, JK. et al. (2021) Orthogonal Degron System for Controlled Protein Degradation in Cyanobacteria., ACS Synth Biol, PMID 34232633

PXD023579 Dataset with its publication pending (from PRIDE)
Dataset title: K27-linked ubiquitylation promotes p97 substrate processing and is essential for cell proliferation
Possible reference: Shearer, RF. et al. (2022) K27-linked ubiquitylation promotes p97 substrate processing and is essential for cell proliferation., EMBO J, PMID 35349166

PXD023553 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery and evaluation of protein biomarkers as a signature of wellness in late stage cancer patients in early phase clinical trials
Possible reference: Geary, B. et al. (2021) Discovery and Evaluation of Protein Biomarkers as a Signature of Wellness in Late-Stage Cancer Patients in Early Phase Clinical Trials., Cancers (Basel), PMID 34069985

PXD023543 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic analysis of different parts of Taenia hydatigena
Possible reference: Cai, M. et al. (2021) Comparative Proteomic Analysis of Different Parts of Taenia Hydatigena., Front Vet Sci, PMID 33981740

PXD023542 Dataset with its publication pending (from PRIDE)
Dataset title: Targeted in situ cross-linking for determination of structure and interactions of SARS-CoV-2 proteins in the cellular context
Possible reference: Slavin, M. et al. (2021) Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2., Proc Natl Acad Sci U S A, PMID 34373319

PXD023530 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic characterization of bacteriophage peptides from mastitis producer Staphylococcus aureus by LC-ESI-MS/MS and their bacteriophage phylogenomic analysis
Possible reference: Abril, AG. et al. (2021) Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis., Foods, PMID 33917943

PXD023506 Dataset with its publication pending (from PRIDE)
Dataset title: Sexual dimorphism in zebrafish heart associated proteins
Possible reference: Niksirat, H. et al. (2021) High-Resolution Proteomic Profiling Shows Sexual Dimorphism in Zebrafish Heart-Associated Proteins., J Proteome Res, PMID 34185526

PXD023459 Dataset with its publication pending (from PRIDE)
Dataset title: Stenotrophomonas bentonitica BII-R7proteome in presence of Se(IV)
Possible reference: Ruiz-Fresneda, MA. et al. (2023) Combined bioreduction and volatilization of SeVI by Stenotrophomonas bentonitica: Formation of trigonal selenium nanorods and methylated species., Sci Total Environ, PMID 36356742

PXD023421 no publication (from MassIVE)
Dataset title: The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry
Possible reference: Negretti, NM. et al. (2021) The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry., Nat Commun, PMID 33637714

PXD023396 Dataset with its publication pending (from PRIDE)
Dataset title: Secretome Analysis of Anoxybacillus caldiproteolyticus 1A02591
Possible reference: Cheng, JH. et al. (2021) Characterization and Diversity Analysis of the Extracellular Proteases of Thermophilic Anoxybacillus caldiproteolyticus 1A02591 From Deep-Sea Hydrothermal Vent Sediment., Front Microbiol, PMID 33796092

PXD023361 Dataset with its publication pending (from PRIDE)
Dataset title: The Cdk8 kinase module regulates Mediator-RNA polymerase II interaction
Possible reference: Tsai, KL. et al. (2013) A conserved Mediator-CDK8 kinase module association regulates Mediator-RNA polymerase II interaction., Nat Struct Mol Biol, PMID 23563140

PXD023357 Dataset with its publication pending (from PRIDE)
Dataset title: Metaproteogenomic profiling of chemosynthetic microbial biofilms reveals metabolic flexibility during colonization of a shallow-water gas vent
Possible reference: Patwardhan, S. et al. (2021) Metaproteogenomic Profiling of Chemosynthetic Microbial Biofilms Reveals Metabolic Flexibility During Colonization of a Shallow-Water Gas Vent., Front Microbiol, PMID 33889140

PXD023333 Dataset with its publication pending (from jPOST)
Dataset title: Proteome analysis of high affinity mouse C3H/HeN saliva-1proteins to hydroxyapatite
Possible reference: Ohshima, K. et al. (2022) Proteome analysis of high affinity mouse saliva proteins to hydroxyapatite., Heliyon, PMID 36033281

PXD023332 Dataset with its publication pending (from jPOST)
Dataset title: Proteome analysis of high affinity mouse BALB/cA saliva-1proteins to hydroxyapatite
Possible reference: Ohshima, K. et al. (2022) Proteome analysis of high affinity mouse saliva proteins to hydroxyapatite., Heliyon, PMID 36033281

PXD023314 Dataset with its publication pending (from PRIDE)
Dataset title: TMT-based quantitative proteomic analysis reveals defense mechanism of wheat against the crown rot pathogen Fusarium pseudograminearum
Possible reference: Qiao, F. et al. (2021) TMT-based quantitative proteomic analysis reveals defense mechanism of wheat against the crown rot pathogen Fusarium pseudograminearum., BMC Plant Biol, PMID 33557748

PXD023311 Dataset with its publication pending (from PRIDE)
Dataset title: Novel Proteome and N-glycoproteome of the Thermophilic Fungus Chaetomium thermophilugm in Response to High Temperature
Possible reference: Gao, J. et al. (2021) Novel Proteome and N-Glycoproteome of the Thermophilic Fungus Chaetomium thermophilum in Response to High Temperature., Front Microbiol, PMID 34163440

PXD023292 Dataset with its publication pending (from PRIDE)
Dataset title: N-degradomic analysis of proteolytic processing in WT1 heterozygous mice
Possible reference: Rinschen, MM. et al. (2017) N-Degradomic Analysis Reveals a Proteolytic Network Processing the Podocyte Cytoskeleton., J Am Soc Nephrol, PMID 28724775

PXD023289 Dataset with its publication pending (from PRIDE)
Dataset title: The GORKY Glycoalkaloid Transporter is Indispensable for Preventing Tomato Bitterness
Possible reference: Kazachkova, Y. et al. (2021) The GORKY glycoalkaloid transporter is indispensable for preventing tomato bitterness., Nat Plants, PMID 33707737

PXD023282 Dataset with its publication pending (from iProX)
Dataset title: iTRAQ-TMT mass spectrometry in K562 cells
Possible reference: Savitski, MM. et al. (2013) Measuring and managing ratio compression for accurate iTRAQ/TMT quantification., J Proteome Res, PMID 23768245

PXD023244 Dataset with its publication pending (from PRIDE)
Dataset title: Bioinformatic analysis of the wound peptidome reveals potential biomarkers and antimicrobial peptides
Possible reference: Hartman, E. et al. (2020) Bioinformatic Analysis of the Wound Peptidome Reveals Potential Biomarkers and Antimicrobial Peptides., Front Immunol, PMID 33613550

PXD023218 Dataset with its publication pending (from PRIDE)
Dataset title: Linking post-translational modifications and protein turnover by site-resolved protein turnover (SPOT) profiling
Possible reference: Zecha, J. et al. (2022) Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling., Nat Commun, PMID 35013197

PXD023209 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive analysis of the host-virus interactome of SARS-CoV-2
Possible reference: Kamel, W. et al. (2021) Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection., Mol Cell, PMID 34118193

PXD023180 Dataset with its publication pending (from PRIDE)
Dataset title: Age-dependent changes in protein incorporation into collagen-rich tissues of mice by in vivo pulsed SILAC labelling
Possible reference: Ariosa-Morejon, Y. et al. (2021) Age-dependent changes in protein incorporation into collagen-rich tissues of mice by in vivo pulsed SILAC labelling., Elife, PMID 34581667

PXD023167 Dataset with its publication pending (from PRIDE)
Dataset title: Systematic profiling of protein complex dynamics reveals DNA-PK phosphorylation of IFI16 en route to herpesvirus immunity
Possible reference: Justice, JL. et al. (2021) Systematic profiling of protein complex dynamics reveals DNA-PK phosphorylation of IFI16 en route to herpesvirus immunity., Sci Adv, PMID 34144993

PXD023143 Dataset with its publication pending (from PRIDE)
Dataset title: Immunopeptidome of isolated patient- derived hepatocytes in Hepatitis B viral infection and hepatocellular carcinoma
Possible reference: de Beijer, MTA. et al. (2022) Immunopeptidome of hepatocytes isolated from patients with HBV infection and hepatocellular carcinoma., JHEP Rep, PMID 36185575

PXD023142 Dataset with its publication pending (from PRIDE)
Dataset title: Serine biosynthesis is a metabolic vulnerability in IDH2-driven breast cancer progression
Possible reference: Barnabas, GD. et al. (2021) Serine Biosynthesis Is a Metabolic Vulnerability in IDH2-Driven Breast Cancer Progression., Cancer Res, PMID 33500247

PXD023126 Dataset with its publication pending (from PRIDE)
Dataset title: The type III secretion system effector EspO of enterohemorrhagic Escherichia coli inhibits apoptosis through an interaction with HAX-1
Possible reference: Chatterjee, S. et al. (2021) The type III secretion system effector EspO of enterohaemorrhagic Escherichia coli inhibits apoptosis through an interaction with HAX-1., Cell Microbiol, PMID 34021690

PXD023122 Dataset with its publication pending (from PRIDE)
Dataset title: Pseudouridine-modified tRNA fragments repress malignant protein synthesis and predict leukemic progression in myelodysplastic syndrome
Possible reference: Guzzi, N. et al. (2022) Pseudouridine-modified tRNA fragments repress aberrant protein synthesis and predict leukaemic progression in myelodysplastic syndrome., Nat Cell Biol, PMID 35292784

PXD023109 Dataset with its publication pending (from PRIDE)
Dataset title: Protein-based vaccine protect against Piscirickettsia salmonis in Atlantic salmon (Salmo salar)
Possible reference: Pontigo, JP. et al. (2021) Protein-Based Vaccine Protect Against Piscirickettsia salmonis in Atlantic Salmon (Salmo salar)., Front Immunol, PMID 33679740

PXD023092 Dataset with its publication pending (from PRIDE)
Dataset title: Galactolipid and Phospholipid Profile and Proteome Alterations in Soybean Leaves at the Onset of Salt Stress
Possible reference: Liu, A. et al. (2021) Galactolipid and Phospholipid Profile and Proteome Alterations in Soybean Leaves at the Onset of Salt Stress., Front Plant Sci, PMID 33815451

PXD023091 Dataset with its publication pending (from PRIDE)
Dataset title: Glycosylation Limits Forward Trafficking of the Tetraspan Membrane Protein PMP22
Possible reference: Marinko, JT. et al. (2021) Glycosylation limits forward trafficking of the tetraspan membrane protein PMP22., J Biol Chem, PMID 33933451

PXD023086 Dataset with its publication pending (from PRIDE)
Dataset title: African swine fever virus ubiquitinconjugating enzyme interacts with host translation machinery to regulate the host protein synthesis
Possible reference: Barrado-Gil, L. et al. (2020) African Swine Fever Virus Ubiquitin-Conjugating Enzyme Interacts With Host Translation Machinery to Regulate the Host Protein Synthesis., Front Microbiol, PMID 33384682

PXD023071 Dataset with its publication pending (from PRIDE)
Dataset title: Protein composition in thylakoids of Arabidopsis without Lhcb3 and Lhcb6
Possible reference: Kouřil, R. et al. (2013) High-light vs. low-light: effect of light acclimation on photosystem II composition and organization in Arabidopsis thaliana., Biochim Biophys Acta, PMID 23274453

PXD023064 Dataset with its publication pending (from PRIDE)
Dataset title: Systematic HLA Epitope Ranking Pan Algorithm (SHERPA)
Possible reference: Pyke, RM. et al. (2023) Precision Neoantigen Discovery Using Large-Scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation., Mol Cell Proteomics, PMID 36796642

PXD023050 Dataset with its publication pending (from PRIDE)
Dataset title: High levels of TFAM repress in vivo transcription of mitochondrial DNA
Possible reference: Bonekamp, NA. et al. (2021) High levels of TFAM repress mammalian mitochondrial DNA transcription in vivo., Life Sci Alliance, PMID 34462320

PXD023048 Dataset with its publication pending (from PRIDE)
Dataset title: iTRAQ-based proteomic analysis of dentate gyrus in temporal lobe epilepsy with hippocampal sclerosis
Possible reference: Xiao, W. et al. (2020) iTRAQ-Based Proteomic Analysis of Dentate Gyrus in Temporal Lobe Epilepsy With Hippocampal Sclerosis., Front Neurol, PMID 33569037

PXD023047 Dataset with its publication pending (from PRIDE)
Dataset title: Arabidopsis EARLY RESPONSIVE TO DEHYDRATION 7 associates with lipid droplets via its senescence domain
Possible reference: Doner, NM. et al. (2021) Arabidopsis thaliana EARLY RESPONSIVE TO DEHYDRATION 7 Localizes to Lipid Droplets via Its Senescence Domain., Front Plant Sci, PMID 33936146

PXD023045 Dataset with its publication pending (from PRIDE)
Dataset title: Mycofactocin is critical for Mycobacterium tuberculosis adaptation into microaerophilic conditions
Possible reference: Krishnamoorthy, G. et al. (2021) Role of Premycofactocin Synthase in Growth, Microaerophilic Adaptation, and Metabolism of Mycobacterium tuberculosis., mBio, PMID 34311585

PXD023039 Dataset with its publication pending (from PRIDE)
Dataset title: Staphylococcus aureus responds to physiologically relevant temperature changes by altering its global transcript and protein profile
Possible reference: Bastock, RA. et al. (2021) Staphylococcus aureus Responds to Physiologically Relevant Temperature Changes by Altering Its Global Transcript and Protein Profile., mSphere, PMID 33731473

PXD023019 Dataset with its publication pending (from PRIDE)
Dataset title: Isoginkgetin derivative IP2 enhances the adaptive immune response against tumor antigens
Possible reference: Darrigrand, R. et al. (2021) Isoginkgetin derivative IP2 enhances the adaptive immune response against tumor antigens., Commun Biol, PMID 33649389

PXD023013 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome-wide analysis of Lysine 2-Hydroxyisobutyrylation in Candida albicans
Possible reference: Zheng, H. et al. (2021) Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in Candida albicans., mSystems, PMID 33531408

PXD023011 Dataset with its publication pending (from PRIDE)
Dataset title: Lysine lactylation critically regulated energy metabolism of the protozoan parasite Trypanosoma brucei
Possible reference: Zhang, N. et al. (2021) Protein Lactylation Critically Regulates Energy Metabolism in the Protozoan Parasite Trypanosoma brucei., Front Cell Dev Biol, PMID 34722503

PXD022992 Dataset with its publication pending (from PRIDE)
Dataset title: Data-independent Acquisition-based Proteome and Phosphoproteome Profiling across Six Melanoma Cell Lines
Possible reference: Gao, E. et al. (2021) Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypes., Mol Omics, PMID 33728422

PXD022988 Dataset with its publication pending (from PRIDE)
Dataset title: Counterion Optimization Dramatically Improves Selectivity for Phosphopeptides and Glycopeptides in Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC)
Possible reference: Cui, Y. et al. (2021) Counterion Optimization Dramatically Improves Selectivity for Phosphopeptides and Glycopeptides in Electrostatic Repulsion-Hydrophilic Interaction Chromatography., Anal Chem, PMID 34042420

PXD022979 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic identification of the UDP-GlcNAc : PI Î±1-6 GlcNAc-transferase subunits of the glycosylphosphatidylinositol biosynthetic pathway of Trypanosoma brucei.
Possible reference: Ji, Z. et al. (2021) Proteomic identification of the UDP-GlcNAc: PI α1-6 GlcNAc-transferase subunits of the glycosylphosphatidylinositol biosynthetic pathway of Trypanosoma brucei., PLoS One, PMID 33735232

PXD022935 no publication (from MassIVE)
Dataset title: Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function
Possible reference: Palanikumar, L. et al. (2021) Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function., Nat Commun, PMID 34172723

PXD022913 Dataset with its publication pending (from PRIDE)
Dataset title: TALEN-based HvMPK3 knockout attenuates proteome and phenotype responses to flg22 in barley
Possible reference: Takáč, T. et al. (2021) TALEN-Based HvMPK3 Knock-Out Attenuates Proteome and Root Hair Phenotypic Responses to flg22 in Barley., Front Plant Sci, PMID 33995462

PXD022872 Dataset with its publication pending (from PRIDE)
Dataset title: GENETIC SUBTYPE- AND CELL TYPE-SPECIFIC PROTEIN SIGNATURES IN FRONTOTEMPORAL DEMENTIA
Possible reference: Miedema, SSM. et al. (2022) Distinct cell type-specific protein signatures in GRN and MAPT genetic subtypes of frontotemporal dementia., Acta Neuropathol Commun, PMID 35799292

PXD022870 Dataset with its publication pending (from PRIDE)
Dataset title: MALDI-IMS combined with shotgun proteomics identify and localize new factors in male infertility
Possible reference: Lahiri, S. et al. (2021) MALDI-IMS combined with shotgun proteomics identify and localize new factors in male infertility., Life Sci Alliance, PMID 33408244

PXD022858 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular reprogramming and phenotype switching in Staphylococcus aureus lead to high antibiotic persistence and affect therapy success
Possible reference: Huemer, M. et al. (2021) Molecular reprogramming and phenotype switching in Staphylococcus aureus lead to high antibiotic persistence and affect therapy success., Proc Natl Acad Sci U S A, PMID 33574060

PXD022852 Dataset with its publication pending (from PRIDE)
Dataset title: Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis
Possible reference: Lan, Y. et al. (2021) Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis., Nat Commun, PMID 33608555

PXD022851 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles derived from adult and fetal bone marrow mesenchymal stromal cells differentially promote expansion of hematopoietic stem and progenitor cells
Possible reference: Ghebes, CA. et al. (2021) Extracellular Vesicles Derived From Adult and Fetal Bone Marrow Mesenchymal Stromal Cells Differentially Promote ex vivo Expansion of Hematopoietic Stem and Progenitor Cells., Front Bioeng Biotechnol, PMID 33718342

PXD022842 Dataset with its publication pending (from PRIDE)
Dataset title: Patagonin - CRISP: Antimicrobial activity and source of antimicrobial molecules in Duvernoy's gland secretion - Philodryas patagoniensis snake
Possible reference: Badari, JC. et al. (2020) Patagonin-CRISP: Antimicrobial Activity and Source of Antimicrobial Molecules in Duvernoy's Gland Secretion (Philodryas patagoniensis Snake)., Front Pharmacol, PMID 33603660

PXD022828 no publication (from MassIVE)
Dataset title: The neomycin resistance cassette in the targeted allele of Shank3B knock-out mice has potential off-target effects to produce an unusual Shank3 isoform
Possible reference: Jin, C. et al. (2020) The Neomycin Resistance Cassette in the Targeted Allele of Shank3B Knock-Out Mice Has Potential Off-Target Effects to Produce an Unusual Shank3 Isoform., Front Mol Neurosci, PMID 33505245

PXD022821 Dataset with its publication pending (from PRIDE)
Dataset title: The proteomic response of the coral symbiont Symbiodinium microadriaticum to thermal and nutrient stress
Possible reference: Oakley, CA. et al. (2023) The Symbiodinium Proteome Response to Thermal and Nutrient Stresses., Plant Cell Physiol, PMID 36565060

PXD022811 Dataset with its publication pending (from PRIDE)
Dataset title: SOX4 AND SMARCA4 COOPERATIVELY REGULATE PI3K SIGNALING THROUGH TRANSCRIPTIONAL ACTIVATION OF TGFBR2 IN BASAL LIKE BREAST CANCER
Possible reference: Mehta, GA. et al. (2021) SOX4 and SMARCA4 cooperatively regulate PI3k signaling through transcriptional activation of TGFBR2., NPJ Breast Cancer, PMID 33837205

PXD022808 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic alterations in oral cancer patients delineated by tobacco using habits
Possible reference: Bhat, FA. et al. (2021) Proteomic Alterations Associated with Oral Cancer Patients with Tobacco Using Habits., OMICS, PMID 33794113

PXD022805 Dataset with its publication pending (from PRIDE)
Dataset title: OXPHOS deficiency activates global adaptations to maintain mitochondrial membrane potential
Possible reference: Liu, S. et al. (2021) OXPHOS deficiency activates global adaptation pathways to maintain mitochondrial membrane potential., EMBO Rep, PMID 33655635

PXD022796 no publication (from MassIVE)
Dataset title: Towards predicting the fate of reef corals
Possible reference: Wolanski, E. et al. (2014) Oceanographic and behavioural assumptions in models of the fate of coral and coral reef fish larvae., J R Soc Interface, PMID 24966233

PXD022791 Dataset with its publication pending (from PRIDE)
Dataset title: FAIMS single cellUltrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell
Possible reference: Cong, Y. et al. (2020) Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell., Chem Sci, PMID 34163866

PXD022788 Dataset with its publication pending (from PRIDE)
Dataset title: An environmental ecocorona influences the formation and evolution of the biological corona on the surface of single-walled carbon nanotubes - proteome
Possible reference: Abdolahpur Monikh, F. et al. (2021) An environmental ecocorona influences the formation and evolution of the biological corona on the surface of single-walled carbon nanotubes., NanoImpact, PMID 35559972

PXD022758 Dataset with its publication pending (from PRIDE)
Dataset title: A proteomic approach to understand the clinical significance of acute myeloid leukemia-derived extracellular vesicles reflecting essential characteristics of leukemia
Possible reference: Kang, KW. et al. (2021) A Proteomic Approach to Understand the Clinical Significance of Acute Myeloid Leukemia-Derived Extracellular Vesicles Reflecting Essential Characteristics of Leukemia., Mol Cell Proteomics, PMID 33592500

PXD022755 Dataset with its publication pending (from PRIDE)
Dataset title: SCF-Fbxo42 promotes synaptonemal complex assembly by downregulating PP2A-B56
Possible reference: Barbosa, P. et al. (2021) SCF-Fbxo42 promotes synaptonemal complex assembly by downregulating PP2A-B56., J Cell Biol, PMID 33382409

PXD022744 Dataset with its publication pending (from jPOST)
Dataset title: Rapid enzyme-mediated biotinylation for cell surface proteome profiling
Possible reference: Li, Y. et al. (2021) Rapid Enzyme-Mediated Biotinylation for Cell Surface Proteome Profiling., Anal Chem, PMID 33660993

PXD022743 no publication (from MassIVE)
Dataset title: Salmonella effector SopD promotes plasma membrane scission by inhibiting Rab10
Possible reference: Boddy, KC. et al. (2021) Salmonella effector SopD promotes plasma membrane scission by inhibiting Rab10., Nat Commun, PMID 34349110

PXD022734 Dataset with its publication pending (from PRIDE)
Dataset title: Oxygen sensitive regulation of TFAM linking the von Hippel-Lindau cancer syndrome to impaired mitochondrial biogenesis
Possible reference: Li, S. et al. (2022) Impaired oxygen-sensitive regulation of mitochondrial biogenesis within the von Hippel-Lindau syndrome., Nat Metab, PMID 35760869

PXD022722 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of REPLICANT Perfusate Detects Changes in the Metastatic Lymph Node Microenvironment
Possible reference: Stevenson, J. et al. (2021) Proteomics of REPLICANT perfusate detects changes in the metastatic lymph node microenvironment., NPJ Breast Cancer, PMID 33674617

PXD022713 Dataset with its publication pending (from PRIDE)
Dataset title: An Alveolata secretory machinery adapted to parasite-host cell invasion
Possible reference: Aquilini, E. et al. (2021) An Alveolata secretory machinery adapted to parasite host cell invasion., Nat Microbiol, PMID 33495622

PXD022711 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome-wide analysis of heat-stress in Pinus radiata somatic embryos reveals a combined response of sugar metabolism and translational regulation mechanisms
Possible reference: Castander-Olarieta, A. et al. (2021) Proteome-Wide Analysis of Heat-Stress in Pinus radiata Somatic Embryos Reveals a Combined Response of Sugar Metabolism and Translational Regulation Mechanisms., Front Plant Sci, PMID 33912202

PXD022708 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative chemical proteomics of Leishmania mexicana
Possible reference: Kalesh, K. et al. (2019) A BONCAT-iTRAQ method enables temporally resolved quantitative profiling of newly synthesised proteins in Leishmania mexicana parasites during starvation., PLoS Negl Trop Dis, PMID 31856154

PXD022701 Dataset with its publication pending (from PRIDE)
Dataset title: The ubiquitin ligase Ariadne-1 regulates NSF for neurotransmitter release
Possible reference: Ram�rez, J. et al. (2021) The ubiquitin ligase Ariadne-1 regulates neurotransmitter release via ubiquitination of NSF., J Biol Chem, PMID 33581113

PXD022689 Dataset with its publication pending (from PRIDE)
Dataset title: Calpain-mediated Protein Targets in Cardiac Mitochondria following Ischemia-Reperfusion
Possible reference: Li, L. et al. (2022) Calpain-mediated protein targets in cardiac mitochondria following ischemia-reperfusion., Sci Rep, PMID 34997008

PXD022684 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of FPA interactors
Possible reference: Zheng, YS. et al. (2017) Identification of interacting proteins of the TaFVE protein involved in spike development in bread wheat., Proteomics, PMID 28225203

PXD022682 Dataset with its publication pending (from PRIDE)
Dataset title: Lipocalin 13 enhances insulin secretion but is dispensable for systemic metabolic control
Possible reference: B�hler, L. et al. (2021) Lipocalin 13 enhances insulin secretion but is dispensable for systemic metabolic control., Life Sci Alliance, PMID 33536239

PXD022677 Dataset with its publication pending (from PRIDE)
Dataset title: Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: Unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay
Possible reference: Wencker, FDR. et al. (2021) Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: unusual RNase�III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay., Nucleic Acids Res, PMID 33450025

PXD022676 Dataset with its publication pending (from PRIDE)
Dataset title: The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis
Possible reference: Scheer, H. et al. (2021) The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis., Nat Commun, PMID 33637717

PXD022673 Dataset with its publication pending (from PRIDE)
Dataset title: Chemotherapy-polarized macrophages from human breast cancer
Possible reference: Liu, J. et al. (2021) The IRENA lncRNA converts chemotherapy-polarized tumor-suppressing macrophages to tumor-promoting phenotypes in breast cancer., Nat Cancer, PMID 35122000

PXD022612 no publication (from MassIVE)
Dataset title: A comprehensive urine proteome database generated from patients with various renal conditions and prostate cancer
Possible reference: Swensen, AC. et al. (2021) A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer., Front Med (Lausanne), PMID 33928097

PXD022599 Dataset with its publication pending (from PRIDE)
Dataset title: The contact allergen NiSO4 triggers a distinct molecular response in primary human dendritic cells compared to bacterial LPS
Possible reference: H�per, T. et al. (2021) The Contact Allergen NiSO4 Triggers a Distinct Molecular Response in Primary Human Dendritic Cells Compared to Bacterial LPS., Front Immunol, PMID 33777040

PXD022594 no publication (from MassIVE)
Dataset title: Fully Integrated and Multiplexed Sample Preparation Technology for Sensitive Interactome Profiling
Possible reference: Mao, Y. et al. (2021) Fully Integrated and Multiplexed Sample Preparation Technology for Sensitive Interactome Profiling., Anal Chem, PMID 33522225

PXD022576 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomics provides insights into diapause program of Bactrocera minax (Diptera: Tephritidae)
Possible reference: Wang, J. et al. (2020) Comparative proteomics provides insights into diapause program of Bactrocera minax (Diptera: Tephritidae)., PLoS One, PMID 33382763

PXD022566 Dataset with its publication pending (from PRIDE)
Dataset title: Human EDEM2 proteomics and glycoproteomics datasets
Possible reference: Munteanu, CVA. et al. (2021) Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network., Mol Cell Proteomics, PMID 34332121

PXD022562 Dataset with its publication pending (from PRIDE)
Dataset title: Interaction of Chinese cabbage (Brassica rapa ssp. pekinensis) cell wall proteins with mustard leaf beetle (Phaedon cochleariae) polygalacturonase family members
Possible reference: Haeger, W. et al. (2021) New Players in the Interaction Between Beetle Polygalacturonases and Plant Polygalacturonase-Inhibiting Proteins: Insights From Proteomics and Gene Expression Analyses., Front Plant Sci, PMID 34149758

PXD022557 Dataset with its publication pending (from PRIDE)
Dataset title: Sex Impacts Cardiac Function and the Proteome Response to Thyroid Hormone in Aged Mice
Possible reference: Zhu, WZ. et al. (2020) Sex impacts cardiac function and the proteome response to thyroid hormone in aged mice., Proteome Sci, PMID 33372611

PXD022549 Dataset with its publication pending (from PRIDE)
Dataset title: Multiparametric characterization of red blood cells physiology after hypotonic dialysis based drug encapsulation process.
Possible reference: Robert, M. et al. (2022) Multiparametric characterization of red blood cell physiology after hypotonic dialysis based drug encapsulation process., Acta Pharm Sin B, PMID 35847505

PXD022547 Dataset with its publication pending (from PRIDE)
Dataset title: Reduced Nicotinamide Mononucleotide (NMNH) Potently Enhances NAD+, Suppresses Glycolysis and Cell Growth
Possible reference: Liu, Y. et al. (2021) Reduced Nicotinamide Mononucleotide (NMNH) Potently Enhances NAD+ and Suppresses Glycolysis, the TCA Cycle, and Cell Growth., J Proteome Res, PMID 33793246

PXD022543 Dataset with its publication pending (from PRIDE)
Dataset title: lMoniliella spathulata an oil-degrading yeast, which promotes growth of barley in oil polluted soil
Possible reference: Mikolasch, A. et al. (2021) Moniliella spathulata, an oil-degrading yeast, which promotes growth of barley in oil-polluted soil., Appl Microbiol Biotechnol, PMID 33219393

PXD022516 Dataset with its publication pending (from PRIDE)
Dataset title: Fasciola hepatica egg lysates - investigation of proteolytic activity
Possible reference: Ilgov�, J. et al. (2022) Transcriptomic and proteomic profiling of peptidase expression in Fasciola hepatica eggs developing at host's body temperature., Sci Rep, PMID 35725898

PXD022483 Dataset with its publication pending (from PRIDE)
Dataset title: Global profiling of N-glycosylated proteins in the diatom Phaeodactylum tricornutum
Possible reference: Xie, X. et al. (2021) Global Profiling of N-Glycoproteins and N-Glycans in the Diatom Phaeodactylum tricornutum., Front Plant Sci, PMID 34925422

PXD022478 Dataset with its publication pending (from PRIDE)
Dataset title: Chronic pain susceptibility is associated with anhedonic behavior and alterations in the accumbal ubiquitin-proteasome system
Possible reference: Guimar�es, MR. et al. (2021) Chronic pain susceptibility is associated with anhedonic behavior and alterations in the accumbal ubiquitin-proteasome system., Pain, PMID 33449505

PXD022475 Dataset with its publication pending (from PanoramaPublic)
Dataset title: Validation of host proteins differentially expressed between COVID severe and non-severe plasma samples
Possible reference: Suvarna, K. et al. (2021) Proteomics and Machine Learning Approaches Reveal a Set of Prognostic Markers for COVID-19 Severity With Drug Repurposing Potential., Front Physiol, PMID 33995121

PXD022471 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular biomarkers of neovascular age-related macular degeneration with incomplete response to anti-vascular endothelial growth factor treatment
Possible reference: Mantel, I. et al. (2020) Molecular Biomarkers of Neovascular Age-Related Macular Degeneration With Incomplete Response to Anti-Vascular Endothelial Growth Factor Treatment., Front Pharmacol, PMID 33447243

PXD022467 Dataset with its publication pending (from PRIDE)
Dataset title: Loss of full-length hnRNP R isoform impairs DNA damage response in motoneurons by inhibiting Yb1 recruitment to Chromatin
Possible reference: Ghanawi, H. et al. (2021) Loss of full-length hnRNP R isoform impairs DNA damage response in motoneurons by inhibiting Yb1 recruitment to chromatin., Nucleic Acids Res, PMID 34850154

PXD022459 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome changes in pepper (Capsicum annuum L.) leaves induced by the green peach aphid
Possible reference: Florencio-Ortiz, V. et al. (2021) Proteome changes in pepper (Capsicum annuum L.) leaves induced by the green peach aphid (Myzus persicae Sulzer)., BMC Plant Biol, PMID 33407137

PXD022426 Dataset with its publication pending (from PRIDE)
Dataset title: A tailored phosphoaspartate probe unravels CprR as a response regulator in Pseudomonas aeruginosa interkingdom signaling
Possible reference: Allihn, PWA. et al. (2021) A tailored phosphoaspartate probe unravels CprR as a response regulator in Pseudomonas aeruginosa interkingdom signaling., Chem Sci, PMID 34168754

PXD022425 Dataset with its publication pending (from PRIDE)
Dataset title: Universal antimicrobial resistance detection from clinical bacterial isolates using proteomics
Possible reference: Luna, BM. et al. (2019) Adjunctive transferrin to reduce the emergence of antibiotic resistance in Gram-negative bacteria., J Antimicrob Chemother, PMID 31170282

PXD022417 no publication (from MassIVE)
Dataset title: Dysregulation of the complement and coagulation cascade in treated schizophrenia and bipolar disorder patients
Possible reference: Santa Cruz, EC. et al. (2021) A pilot study indicating the dysregulation of the complement and coagulation cascades in treated schizophrenia and bipolar disorder patients., Biochim Biophys Acta Proteins Proteom, PMID 33839315

PXD022408 Dataset with its publication pending (from PRIDE)
Dataset title: Cryo-EM structural analysis of FADD: Caspase-8 complexes defines the catalytic dimer architecture for co-ordinated control of cell fate
Possible reference: Fox, JL. et al. (2021) Cryo-EM structural analysis of FADD:Caspase-8 complexes defines the catalytic dimer architecture for co-ordinated control of cell fate., Nat Commun, PMID 33547302

PXD022401 Dataset with its publication pending (from PRIDE)
Dataset title: Nicotiana benthamiana AP-MS for TSWV NSs
Possible reference: Zhai, Y. et al. (2021) Identification and Characterization of Plant-Interacting Targets of Tomato Spotted Wilt Virus Silencing Suppressor., Pathogens, PMID 33401462

PXD022397 Dataset with its publication pending (from PRIDE)
Dataset title: TbSAP is a novel chromatin protein repressing metacyclic Variant Surface Glycoprotein expression sites in bloodstream form Trypanosoma brucei
Possible reference: Davies, C. et al. (2021) TbSAP is a novel chromatin protein repressing metacyclic variant surface glycoprotein expression sites in bloodstream form Trypanosoma brucei., Nucleic Acids Res, PMID 33660774

PXD022389 Dataset with its publication pending (from jPOST)
Dataset title: O-GlcNAcylation suppresses the ion current IClswell by preventing the binding of the protein ICln to Î±-integrin
Possible reference: Costa, R. et al. (2020) O-GlcNAcylation Suppresses the Ion Current IClswell by Preventing the Binding of the Protein ICln to α-Integrin., Front Cell Dev Biol, PMID 33330510

PXD022372 Dataset with its publication pending (from PRIDE)
Dataset title: A ciliopathy complex restrains centriolar length and builds distal appendages to initiate ciliogenesis.
Possible reference: Kumar, D. et al. (2021) A ciliopathy complex builds distal appendages to initiate ciliogenesis., J Cell Biol, PMID 34241634

PXD022371 Dataset with its publication pending (from PRIDE)
Dataset title: Neuroserpin Is Strongly Expressed in the Developing and Adult Mouse Neocortex but Its Absence Does Not Perturb Cortical Lamination and Synaptic Proteome
Possible reference: Kement, D. et al. (2021) Neuroserpin Is Strongly Expressed in the Developing and Adult Mouse Neocortex but Its Absence Does Not Perturb Cortical Lamination and Synaptic Proteome., Front Neuroanat, PMID 33708076

PXD022330 Dataset with its publication pending (from PRIDE)
Dataset title: Two-dimensional low-flow liquid-chromatography setup for shotgun proteomics
Possible reference: Roca, LS. et al. (2021) Development of comprehensive two-dimensional low-flow liquid-chromatography setup coupled to high-resolution mass spectrometry for shotgun proteomics., Anal Chim Acta, PMID 33781465

PXD022323 Dataset with its publication pending (from PRIDE)
Dataset title: Deletion of Allele-Specific HLAs (DASH)
Possible reference: Pyke, RM. et al. (2022) A machine learning algorithm with subclonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity., Nat Commun, PMID 35414054

PXD022321 Dataset with its publication pending (from PRIDE)
Dataset title: Disturbed intramitochondrial phosphatidic acid transport impairs cellular stress signaling
Possible reference: Eiyama, A. et al. (2021) Disturbed intramitochondrial phosphatidic acid transport impairs cellular stress signaling., J Biol Chem, PMID 33497623

PXD022307 Dataset with its publication pending (from jPOST)
Dataset title: Arabidopsis membrane protein phosphoproteomics in early cold response
Possible reference: Kamal, MM. et al. (2020) Large-Scale Phosphoproteomic Study of Arabidopsis Membrane Proteins Reveals Early Signaling Events in Response to Cold., Int J Mol Sci, PMID 33207747

PXD022296 Dataset with its publication pending (from PRIDE)
Dataset title: Mass-spectrometry based plasma proteomics identifies biomarkers for the detection of COVID-19 progression
Possible reference: Suvarna, K. et al. (2021) Proteomics and Machine Learning Approaches Reveal a Set of Prognostic Markers for COVID-19 Severity With Drug Repurposing Potential., Front Physiol, PMID 33995121

PXD022291 no publication (from MassIVE)
Dataset title: Decoding functional high-density lipoprotein particle surfaceome interactions
Possible reference: Frey, K. et al. (2022) Decoding Functional High-Density Lipoprotein Particle Surfaceome Interactions., Int J Mol Sci, PMID 36012766

PXD022290 Dataset with its publication pending (from PRIDE)
Dataset title: Epithelial to mesenchymal transition shed microvesicle proteome
Possible reference: Carrasco-Ram�rez, P. et al. (2016) Podoplanin is a component of extracellular vesicles that reprograms cell-derived exosomal proteins and modulates lymphatic vessel formation., Oncotarget, PMID 26893367

PXD022259 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of rest and activated Tregs
Possible reference: Harrison, R. et al. (2026) Chaperone-mediated autophagy is required for regulatory T cell function., Nat Commun, PMID 42173902

PXD022257 Dataset with its publication pending (from PRIDE)
Dataset title: Integrative analysis of proteomics and DNA methylation in orbital fibroblasts from Graves
Possible reference: Virakul, S. et al. (2020) Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves' Ophthalmopathy., Front Endocrinol (Lausanne), PMID 33658982

PXD022250 Dataset with its publication pending (from PRIDE)
Dataset title: Adaptive Laboratory Evolution of microbial co-cultures for improved metabolite secretion
Possible reference: Konstantinidis, D. et al. (2021) Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion., Mol Syst Biol, PMID 34370382

PXD022245 Dataset with its publication pending (from PRIDE)
Dataset title: PTENÎµ, a new isoform of PTEN, suppresses tumor metastasis through filopodia formation regulation.
Possible reference: Zhang, Q. et al. (2021) PTENε suppresses tumor metastasis through regulation of filopodia formation., EMBO J, PMID 33755220

PXD022239 Dataset with its publication pending (from PRIDE)
Dataset title: Bacterial RF3 Senses Chaperone Function in Co-translational Folding
Possible reference: Zhao, L. et al. (2021) Bacterial RF3 senses chaperone function in co-translational folding., Mol Cell, PMID 34107307

PXD022225 Dataset with its publication pending (from PRIDE)
Dataset title: Combining mass spectrometry and machine learning to discover bioactive peptides
Possible reference: Madsen, CT. et al. (2022) Combining mass spectrometry and machine learning to discover bioactive peptides., Nat Commun, PMID 36266275

PXD022190 Dataset with its publication pending (from PRIDE)
Dataset title: Integrity of the short arm of nuclear pore Y-complex is required for mouse embryonic stem cell growth and differentiation
Possible reference: Gonzalez-Estevez, A. et al. (2021) Integrity of the short arm of the nuclear pore Y-complex is required for mouse embryonic stem cell growth and differentiation., J Cell Sci, PMID 34037234

PXD022189 Dataset with its publication pending (from PRIDE)
Dataset title: Label-Free LC-MS/MS Proteomic�Analysis of Urinary Identification in Diabetic Vascular Dementia
Possible reference: Chen, R. et al. (2021) Label-Free Liquid Chromatography-Mass Spectrometry Proteomic Analysis of Urinary Identification in Diabetic Vascular Dementia in a Han Chinese Population., Front Aging Neurosci, PMID 33597859

PXD022186 Dataset with its publication pending (from PRIDE)
Dataset title: Detection and Quantification of Novel C-terminal TDP-43 Fragments in ALS-TDP
Possible reference: Feneberg, E. et al. (2021) Detection and quantification of novel C-terminal TDP-43 fragments in ALS-TDP., Brain Pathol, PMID 33300249

PXD022149 Dataset with its publication pending (from PRIDE)
Dataset title: Ceragenins and antimicrobial peptides kill bacteria through distinct mechanisms
Possible reference: Mitchell, G. et al. (2022) Ceragenins and Antimicrobial Peptides Kill Bacteria through Distinct Mechanisms., mBio, PMID 35073755

PXD022112 Dataset with its publication pending (from PRIDE)
Dataset title: Harnessing machine learning to unravel protein degradation in Escherichia coli
Possible reference: Nagar, N. et al. (2021) Harnessing Machine Learning To Unravel Protein Degradation in Escherichia coli., mSystems, PMID 33531410

PXD022105 Dataset with its publication pending (from PRIDE)
Dataset title: Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila
Possible reference: Eastwood, EL. et al. (2021) Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila., Elife, PMID 33538693

PXD022103 Dataset with its publication pending (from PRIDE)
Dataset title: Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila
Possible reference: Eastwood, EL. et al. (2021) Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila., Elife, PMID 33538693

PXD022071 Dataset with its publication pending (from jPOST)
Dataset title: Damage-associated molecular patterns in S100 proteins are recognized by Signal Inhibitory Receptor on Leukocytes-1
Possible reference: Rumpret, M. et al. (2021) Recognition of S100 proteins by Signal Inhibitory Receptor on Leukocytes-1 negatively regulates human neutrophils., Eur J Immunol, PMID 34145909

PXD022068 Dataset with its publication pending (from PRIDE)
Dataset title: Endothelial cells exposed to atheroprotective flow secrete follistatin-like protein 1 which reduces transcytosis and inflammation
Possible reference: Ghim, M. et al. (2021) Endothelial cells exposed to atheroprotective flow secrete follistatin-like 1 protein which reduces transcytosis and inflammation., Atherosclerosis, PMID 34425528

PXD022067 Dataset with its publication pending (from PRIDE)
Dataset title: The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes
Possible reference: Davydova, E. et al. (2021) The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes., Nat Commun, PMID 33563959

PXD022061 Dataset with its publication pending (from PRIDE)
Dataset title: Structure of autoinhibited Akt1 reveals mechanism of PIP 3 -mediated activation
Possible reference: Truebestein, L. et al. (2021) Structure of autoinhibited Akt1 reveals mechanism of PIP3-mediated activation., Proc Natl Acad Sci U S A, PMID 34385319

PXD022039 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of Histoplasma capsulatum under zinc deprivation
Possible reference: Assun��o, LDP. et al. (2020) Insights Into Histoplasma capsulatum Behavior on Zinc Deprivation., Front Cell Infect Microbiol, PMID 33330123

PXD022028 Dataset with its publication pending (from PRIDE)
Dataset title: Host cholesterol modulates the generation and enrichment of persister population during Mycobacterium tuberculosis infection.
Possible reference: Talwar, S. et al. (2020) Role of VapBC12 Toxin-Antitoxin Locus in Cholesterol-Induced Mycobacterial Persistence., mSystems, PMID 33323416

PXD022023 Dataset with its publication pending (from PRIDE)
Dataset title: FAX-RIC enables robust RNA interactome profiling in multicellular organisms in vivo
Possible reference: Na, Y. et al. (2021) FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo., Nucleic Acids Res, PMID 33332543

PXD022019 Dataset with its publication pending (from PRIDE)
Dataset title: The influence of delay in mononuclear cell isolation on acute myeloid leukemia phosphorylation profiles
Possible reference: van Alphen, C. et al. (2021) The influence of delay in mononuclear cell isolation on acute myeloid leukemia phosphorylation profiles., J Proteomics, PMID 33561558

PXD022013 no publication (from MassIVE)
Dataset title: Evidence for structural protein damage and membrane lipid remodeling in red blood cells from COVID-19 patients
Possible reference: Thomas, T. et al. (2020) Evidence for structural protein damage and membrane lipid remodeling in red blood cells from COVID-19 patients., medRxiv, PMID 32637980

PXD021992 Dataset with its publication pending (from PRIDE)
Dataset title: Large-scale identification of ubiquitination sites on membrane-associated proteins in Arabidopsis thaliana seedlings
Possible reference: Grubb, LE. et al. (2021) Large-scale identification of ubiquitination sites on membrane-associated proteins in Arabidopsis thaliana seedlings., Plant Physiol, PMID 33585938

PXD021981 no publication (from MassIVE)
Dataset title: Synechococcus Sp. RS9916 Lyase Isomerase MpeV Characterization
Possible reference: Carrigee, LA. et al. (2021) MpeV is a lyase isomerase that ligates a doubly linked phycourobilin on the β-subunit of phycoerythrin I and II in marine Synechococcus., J Biol Chem, PMID 33154169

PXD021966 Dataset with its publication pending (from PRIDE)
Dataset title: Composition and origin of lung fluid proteome in premature infants and relationship to respiratory outcome
Possible reference: Ballard, PL. et al. (2020) Composition and origin of lung fluid proteome in premature infants and relationship to respiratory outcome., PLoS One, PMID 33301538

PXD021961 Dataset with its publication pending (from PRIDE)
Dataset title: Rapid degradation pathways of host proteins during HCMV infection revealed by quantitative proteomics
Possible reference: Lin, KM. et al. (2020) Rapid Degradation Pathways of Host Proteins During HCMV Infection Revealed by Quantitative Proteomics., Front Cell Infect Microbiol, PMID 33585265

PXD021947 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanism and function of DNA replication-independent DNA-protein crosslink repair via the SUMO pathway
Possible reference: Liu, JCY. et al. (2021) Mechanism and function of DNA replication-independent DNA-protein crosslink repair via the SUMO-RNF4 pathway., EMBO J, PMID 34346517

PXD021937 Dataset with its publication pending (from PRIDE)
Dataset title: Rat retinae data for use as spectral library, for pathway remodelling as well as protein mapping
Possible reference: Reinehr, S. et al. (2021) Rat retinae data for use as spectral library, for pathway remodeling as well as protein mapping., Data Brief, PMID 34222568

PXD021905 no publication (from MassIVE)
Dataset title: Respiratory vinyl chloride reductive dechlorination to ethene in TceA-expressing Dehalococcoides mccartyi
Possible reference: Yan, J. et al. (2021) Respiratory Vinyl Chloride Reductive Dechlorination to Ethene in TceA-Expressing Dehalococcoides mccartyi., Environ Sci Technol, PMID 33683880

PXD021901 Dataset with its publication pending (from PRIDE)
Dataset title: An NSD3-targeting PROTAC suppresses the NSD3 and cMyc oncogenic nodes in cancer cells
Possible reference: Xu, C. et al. (2022) A NSD3-targeted PROTAC suppresses NSD3 and cMyc oncogenic nodes in cancer cells., Cell Chem Biol, PMID 34469831

PXD021897 Dataset with its publication pending (from PRIDE)
Dataset title: Drosophila Sex Peptide Controls the Assembly of Lipid Microcarriers in Seminal Fluid
Possible reference: Wainwright, SM. et al. (2021) Drosophila Sex Peptide controls the assembly of lipid microcarriers in seminal fluid., Proc Natl Acad Sci U S A, PMID 33495334

PXD021888 Dataset with its publication pending (from PRIDE)
Dataset title: The lytic polysaccharide monooxygenase of Pseudomonas aeruginosa promotes bacterial survival during systemic infection
Possible reference: Askarian, F. et al. (2021) The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection., Nat Commun, PMID 33623002

PXD021880 Dataset with its publication pending (from PRIDE)
Dataset title: TDP-43 aggregation induced by oxidative stress causes global mitochondrial imbalance in ALS
Possible reference: Zuo, X. et al. (2021) TDP-43 aggregation induced by oxidative stress causes global mitochondrial imbalance in ALS., Nat Struct Mol Biol, PMID 33398173

PXD021876 Dataset with its publication pending (from PRIDE)
Dataset title: Axonal TDP-43 Drives NMJ Disruption through Inhibition of Local Protein Synthesis
Possible reference: Ionescu, A. et al. (2025) Muscle-derived miR-126 regulates TDP-43 axonal local synthesis and NMJ integrity in ALS models., Nat Neurosci, PMID 41044342

PXD021861 Dataset with its publication pending (from PRIDE)
Dataset title: The velvet protein Vel1 controls initial plant root colonization and conidia formation for xylem distribution in Verticillium wilt
Possible reference: H�fer, AM. et al. (2021) The velvet protein Vel1 controls initial plant root colonization and conidia formation for xylem distribution in Verticillium wilt., PLoS Genet, PMID 33720931

PXD021858 Dataset with its publication pending (from PRIDE)
Dataset title: ApoC-III is a novel inducer of human valvular calcification
Possible reference: Schlotter, F. et al. (2021) ApoC-III is a novel inducer of calcification in human aortic valves., J Biol Chem, PMID 33334888

PXD021856 Dataset with its publication pending (from PRIDE)
Dataset title: Human plasma small extracellular vesicle proteome (disease, non-disease)
Possible reference: Reale, A. et al. (2021) Human myeloma cell- and plasma-derived extracellular vesicles contribute to functional regulation of stromal cells., Proteomics, PMID 33580572

PXD021848 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of anatomical sections of the gut of Nosema-infected Western honey bee (Apis mellifera) reveals different early responses to Nosema spp. isolates
Possible reference: Houdelet, C. et al. (2021) Proteomics of Anatomical Sections of the Gut of Nosema-Infected Western Honeybee (Apis mellifera) Reveals Different Early Responses to Nosema spp. Isolates., J Proteome Res, PMID 33305956

PXD021846 no publication (from MassIVE)
Dataset title: Proteomic profile of bone collagen extracted for stable isotopes: implications for bulk and single amino acid analyses
Possible reference: Cleland, TP. et al. (2021) Proteomic profile of bone "collagen" extracted for stable isotopes: Implications for bulk and single amino acid analyses., Rapid Commun Mass Spectrom, PMID 33332665

PXD021843 Dataset with its publication pending (from PRIDE)
Dataset title: The malaria parasite sheddase SUB2 governs host red blood cell membrane sealing at invasion
Possible reference: Collins, CR. et al. (2020) The malaria parasite sheddase SUB2 governs host red blood cell membrane sealing at invasion., Elife, PMID 33287958

PXD021841 Dataset with its publication pending (from PRIDE)
Dataset title: A redirected protein secretion stress response in the genome-engineered midiBacillus-II
Possible reference: Aguilar Su�rez, R. et al. (2021) Redirected Stress Responses in a Genome-Minimized 'midiBacillus' Strain with Enhanced Capacity for Protein Secretion., mSystems, PMID 34904864

PXD021832 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic approache of the response to iron-limited condition in Staphylococcus lugdunensis
Possible reference: Aubourg, M. et al. (2020) Phenotypic and proteomic approaches of the response to iron-limited condition in Staphylococcus lugdunensis., BMC Microbiol, PMID 33115407

PXD021831 Dataset with its publication pending (from PRIDE)
Dataset title: A comprehensive landscape of 60S ribosome biogenesis factors
Possible reference: Sailer, C. et al. (2022) A comprehensive landscape of 60S ribosome biogenesis factors., Cell Rep, PMID 35139378

PXD021830 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of Btk haemolymph stimulon
Possible reference: Sun, Y. et al. (2021) Tandem Mass Tag-Based Quantitative Proteomics and Virulence Phenotype of Hemolymph-Treated Bacillus thuringiensis kurstaki Cells Reveal New Insights on Bacterial Pathogenesis in Insects., Microbiol Spectr, PMID 34704785

PXD021826 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondria-rough-ER Contacts in The Liver Regulate Systemic Lipid Homeostasis
Possible reference: Anastasia, I. et al. (2021) Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis., Cell Rep, PMID 33730569

PXD021802 no publication (from MassIVE)
Dataset title: Characterization and Complete Genome Sequence of Privateer, a Highly Prolate Proteus mirabilis Podophage
Possible reference: Corban, JE. et al. (2021) Characterization and complete genome sequence of Privateer, a highly prolate Proteus mirabilis podophage., PeerJ, PMID 33614267

PXD021793 Dataset with its publication pending (from PRIDE)
Dataset title: Unbiased label-free quantitative proteomics of Amyotrophic lateral sclerosis (ALS) mutations in CCNF reveals activation of the apoptosis pathway
Possible reference: Cheng, F. et al. (2021) Unbiased Label-Free Quantitative Proteomics of Cells Expressing Amyotrophic Lateral Sclerosis (ALS) Mutations in CCNF Reveals Activation of the Apoptosis Pathway: A Workflow to Screen Pathogenic Gene Mutations., Front Mol Neurosci, PMID 33986643

PXD021757 Dataset with its publication pending (from PRIDE)
Dataset title: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix
Possible reference: Gordevicius, J. et al. (2021) Epigenetic inactivation of the autophagy-lysosomal system in appendix in Parkinson's disease., Nat Commun, PMID 34446734

PXD021738 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibition of CBP synergizes with the RNA-dependent mechanisms of azacitidine by limiting protein translation
Possible reference: Diesch, J. et al. (2021) Inhibition of CBP synergizes with the RNA-dependent mechanisms of Azacitidine by limiting protein synthesis., Nat Commun, PMID 34663789

PXD021733 Dataset with its publication pending (from iProX)
Dataset title: VWCE inhibited the proliferation, migration, invasion, and chemoresistance of the breast cancer cell lines
Possible reference: Zhang, D. et al. (2020) VWCE Functions as a Tumor Suppressor in Breast Cancer Cells., Front Oncol, PMID 33194737

PXD021728 Dataset with its publication pending (from PRIDE)
Dataset title: Caspase-3 cleaves extracellular vesicle proteins during auditory brainstem development
Possible reference: Weghorst, F. et al. (2020) Caspase-3 Cleaves Extracellular Vesicle Proteins During Auditory Brainstem Development., Front Cell Neurosci, PMID 33281555

PXD021716 Dataset with its publication pending (from PRIDE)
Dataset title: Genetic and physiological mechanisms underlying flower induction in apple
Possible reference: Guitton, B. et al. (2016) Analysis of transcripts differentially expressed between fruited and deflowered 'Gala' adult trees: a contribution to biennial bearing understanding in apple., BMC Plant Biol, PMID 26924309

PXD021685 Dataset with its publication pending (from PRIDE)
Dataset title: SARS-CoV-2 Evades immune detection in Alveolar Macrophages
Possible reference: Dalskov, L. et al. (2020) SARS-CoV-2 evades immune detection in alveolar macrophages., EMBO Rep, PMID 33112036

PXD021684 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Adaptation of Clostridioides difficile to Treatment with the Antimicrobial Peptide Nisin
Possible reference: Maa�, S. et al. (2021) Proteomic Adaptation of Clostridioides difficile to Treatment with the Antimicrobial Peptide Nisin., Cells, PMID 33670309

PXD021682 Dataset with its publication pending (from PRIDE)
Dataset title: N-glycomic signature of stage II colorectal cancer and its association with the tumor microenvironment
Possible reference: Boyaval, F. et al. (2021) N-Glycomic Signature of Stage II Colorectal Cancer and Its Association With the Tumor Microenvironment., Mol Cell Proteomics, PMID 33581319

PXD021673 Dataset with its publication pending (from PRIDE)
Dataset title: LC-MS/MS analysis of lesional and normally looking psoriatic skin
Possible reference: Sobolev, VV. et al. (2021) LC-MS/MS analysis of lesional and normally looking psoriatic skin reveals significant changes in protein metabolism and RNA processing., PLoS One, PMID 34038424

PXD021663 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteomic analysis reveals Rio1 regulated protein metabolism in response to UV irradiation and multiple cellular processes in Sulfolobus islandicus REY15A
Possible reference: Huang, Q. et al. (2020) Phosphoproteomic Analysis Reveals Rio1-Related Protein Phosphorylation Changes in Response to UV Irradiation in Sulfolobus islandicus REY15A., Front Microbiol, PMID 33343525

PXD021658 Dataset with its publication pending (from PRIDE)
Dataset title: Thiol-ene microfluidic chip for fast on-chip sample clean-up, separation and ESI mass analysis of peptides and proteins
Possible reference: Svejdal, RR. et al. (2020) Thiol-ene microfluidic chip for fast on-chip sample clean-up, separation and ESI mass spectrometry of peptides and proteins., Anal Chim Acta, PMID 33218478

PXD021646 Dataset with its publication pending (from PRIDE)
Dataset title: The STRIPAK signaling complex regulates dephosphorylation of GUL1, an RNA-binding protein that shuttles on endosomes
Possible reference: Stein, V. et al. (2020) The STRIPAK signaling complex regulates dephosphorylation of GUL1, an RNA-binding protein that shuttles on endosomes., PLoS Genet, PMID 32997654

PXD021616 Dataset with its publication pending (from PRIDE)
Dataset title: MLL4-associated condensates counterbalance Polycomb-mediated nuclear mechanical stress in Kabuki Syndrome
Possible reference: Fasciani, A. et al. (2020) MLL4-associated condensates counterbalance Polycomb-mediated nuclear mechanical stress in Kabuki syndrome., Nat Genet, PMID 33169020

PXD021602 Dataset with its publication pending (from PRIDE)
Dataset title: Cell type-selective secretome profiling in vivo
Possible reference: Wei, W. et al. (2021) Cell type-selective secretome profiling in vivo., Nat Chem Biol, PMID 33199915

PXD021601 Dataset with its publication pending (from PRIDE)
Dataset title: Regulatory function of sympathetic innervation on the endo/lysosomal trafficking of acetylcholine receptor
Possible reference: Straka, T. et al. (2021) Regulatory Function of Sympathetic Innervation on the Endo/Lysosomal Trafficking of Acetylcholine Receptor., Front Physiol, PMID 33776791

PXD021598 no publication (from MassIVE)
Dataset title: Regulation of PP2A-subfamily holoenzyme function by carboxyl-terminal methylation
Possible reference: Nasa, I. et al. (2020) Effects of carboxyl-terminal methylation on holoenzyme function of the PP2A subfamily., Biochem Soc Trans, PMID 33125487

PXD021588 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative Host-Coronavirus Protein Interaction Networks Reveal Pan-Viral Disease Mechanisms
Possible reference: Gordon, DE. et al. (2020) Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms., Science, PMID 33060197

PXD021584 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative analysis of systemic and tumor microenvironment proteomes of children with b-cell acute lymphocytic leukemia at diagnosis and after induction treatment.
Possible reference: Broto, GE. et al. (2020) Comparative Analysis of Systemic and Tumor Microenvironment Proteomes From Children With B-Cell Acute Lymphocytic Leukemia at Diagnosis and After Induction Treatment., Front Oncol, PMID 33381445

PXD021581 Dataset with its publication pending (from PRIDE)
Dataset title: Prognostic accuracy of Mass Spectrometric Analysis of Plasma in COVID-19
Possible reference: Lazari, LC. et al. (2021) Prognostic accuracy of MALDI-TOF mass spectrometric analysis of plasma in COVID-19., Life Sci Alliance, PMID 34168074

PXD021569 no publication (from MassIVE)
Dataset title: Sex-specific effects of in vitro fertilization on adult metabolic phenotypes and hepatic transcriptomic and proteomic pathways in mouse
Possible reference: Narapareddy, L. et al. (2021) Sex-specific effects of in vitro fertilization on adult metabolic outcomes and hepatic transcriptome and proteome in mouse., FASEB J, PMID 33734487

PXD021564 Dataset with its publication pending (from PRIDE)
Dataset title: Protein and Signaling Pathway Responses to rhIL-6 Intervention before Lobaplatin Treatment in Osteosarcoma Cells using LC-MS/MS
Possible reference: Wang, H. et al. (2021) Protein and Signaling Pathway Responses to rhIL-6 Intervention Before Lobaplatin Treatment in Osteosarcoma Cells., Front Oncol, PMID 33791202

PXD021539 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of drivers of breast cancer invasion by secretome analysis: insight into CTGF signaling
Possible reference: Hellinger, JW. et al. (2020) Identification of drivers of breast cancer invasion by secretome analysis: insight into CTGF signaling., Sci Rep, PMID 33087801

PXD021521 no publication (from MassIVE)
Dataset title: In-depth analysis of proteomic and genomic fluctuations during the time course of human embryonic stem cells directed differentiation into beta cells
Possible reference: Budnik, B. et al. (2022) In-depth analysis of proteomic and genomic fluctuations during the time course of human embryonic stem cells directed differentiation into beta cells., Proteomics, PMID 35094488

PXD021520 no publication (from MassIVE)
Dataset title: Differential Peptide Subtraction: mass spectrometry for human cancer virus discovery
Possible reference: Toptan, T. et al. (2020) Proteomic approach to discover human cancer viruses from formalin-fixed tissues., JCI Insight, PMID 33055416

PXD021497 Dataset with its publication pending (from PanoramaPublic)
Dataset title: NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency
Possible reference: Matlock, AD. et al. (2023) NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency., Sci Data, PMID 36631473

PXD021457 Dataset with its publication pending (from PRIDE)
Dataset title: Critical role of Aquaporin-1 and telocytes in infantile hemangioma response to propranolol beta-blockade
Possible reference: Moisan, F. et al. (2021) Critical role of Aquaporin-1 and telocytes in infantile hemangioma response to propranolol beta blockade., Proc Natl Acad Sci U S A, PMID 33558238

PXD021437 Dataset with its publication pending (from PRIDE)
Dataset title: Control of synaptic vesicle release probability via VAMP4 targeting to endolysosomes
Possible reference: Ivanova, D. et al. (2021) Control of synaptic vesicle release probability via VAMP4 targeting to endolysosomes., Sci Adv, PMID 33931449

PXD021414 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of Extracellular Vesicles Produced by Granulicatella adiacens, which causes Infective Endocarditis
Possible reference: Alkandari, SA. et al. (2020) Proteomics of extracellular vesicles produced by Granulicatella adiacens, which causes infective endocarditis., PLoS One, PMID 33216751

PXD021399 Dataset with its publication pending (from jPOST)
Dataset title: Microparticle assisted precipitation screening method for robust drug target identification
Possible reference: Lyu, J. et al. (2020) Microparticle-Assisted Precipitation Screening Method for Robust Drug Target Identification., Anal Chem, PMID 32933243

PXD021372 Dataset with its publication pending (from jPOST)
Dataset title: Comparative phosphoproteomic analysis of raf22raf36 in Arabidopsis
Possible reference: Kamiyama, Y. et al. (2021) Arabidopsis group C Raf-like protein kinases negatively regulate abscisic acid signaling and are direct substrates of SnRK2., Proc Natl Acad Sci U S A, PMID 34282011

PXD021371 Dataset with its publication pending (from PRIDE)
Dataset title: DCLK1 small extracellular vesicle proteome
Possible reference: Carli, ALE. et al. (2021) Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells., Proteomics, PMID 33991177

PXD021368 Dataset with its publication pending (from PRIDE)
Dataset title: Isolation and characterization of multi-protein complexes enriched in the K-Cl co-transporter 2 from brain plasma membranes
Possible reference: Smalley, JL. et al. (2020) Isolation and Characterization of Multi-Protein Complexes Enriched in the K-Cl Co-transporter 2 From Brain Plasma Membranes., Front Mol Neurosci, PMID 33192291

PXD021366 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteome profiling uncovers a key role for CDKs in TNF signaling
Possible reference: Tanzer, MC. et al. (2021) Phosphoproteome profiling uncovers a key role for CDKs in TNF signaling., Nat Commun, PMID 34663829

PXD021363 no publication (from MassIVE)
Dataset title: Receptor-mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy
Possible reference: Ohnstad, AE. et al. (2020) Receptor-mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy., EMBO J, PMID 33226137

PXD021347 no publication (from MassIVE)
Dataset title: Proteomic analysis of Exaiptasia pallida
Possible reference: Cziesielski, MJ. et al. (2018) Summarized datasheet for multi-omics response of three Exaiptasia strains to heat stress: a new way to process omics data., BMC Res Notes, PMID 30563556

PXD021342 Dataset with its publication pending (from jPOST)
Dataset title: Microbial processing of jellyfish detritus in the ocean
Possible reference: Tinta, T. et al. (2020) Microbial Processing of Jellyfish Detritus in the Ocean., Front Microbiol, PMID 33193256

PXD021332 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanism of extractive degradation by Phlebiopsis gigantea
Possible reference: Hori, C. et al. (2014) Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood., PLoS Genet, PMID 25474575

PXD021327 no publication (from MassIVE)
Dataset title: Tyrosine phosphorylation of IQGAP1 in the MET pathway
Possible reference: Hedman, AC. et al. (2020) Tyrosine phosphorylation of the scaffold protein IQGAP1 in the MET pathway alters function., J Biol Chem, PMID 33087447

PXD021326 no publication (from MassIVE)
Dataset title: Tyrosine phosphorylation of IQGAP1 in the MET pathway
Possible reference: Hedman, AC. et al. (2020) Tyrosine phosphorylation of the scaffold protein IQGAP1 in the MET pathway alters function., J Biol Chem, PMID 33087447

PXD021324 Dataset with its publication pending (from jPOST)
Dataset title: Analysis of infant gut microbiome reveals metabolic functional roles associated with healthy and atopic dermatitis using metaproteomics
Possible reference: Kingkaw, A. et al. (2020) Analysis of the infant gut microbiome reveals metabolic functional roles associated with healthy infants and infants with atopic dermatitis using metaproteomics., PeerJ, PMID 33033661

PXD021290 no publication (from MassIVE)
Dataset title: A poplar rust effector protein associates with protein disulfide isomerase and enhance plant susceptibility
Possible reference: Madina, MH. et al. (2020) A Poplar Rust Effector Protein Associates with Protein Disulfide Isomerase and Enhances Plant Susceptibility., Biology (Basel), PMID 32947987

PXD021286 Dataset with its publication pending (from PRIDE)
Dataset title: Linkage-specific ubiquitin chain formation depends on a lysine hydrocarbon ruler
Possible reference: Liwocha, J. et al. (2021) Linkage-specific ubiquitin chain formation depends on a lysine hydrocarbon ruler., Nat Chem Biol, PMID 33288957

PXD021276 no publication (from MassIVE)
Dataset title: eEF2K inhibition synergizes with Glutaminase and eIF4EBP1 inhibitors to suppress triple-negative breast cancer cell growth; impact on the proteome
Possible reference: Ju, Y. et al. (2021) Inhibition of eEF2K synergizes with glutaminase inhibitors or 4EBP1 depletion to suppress growth of triple-negative breast cancer cells., Sci Rep, PMID 33911160

PXD021275 Dataset with its publication pending (from PRIDE)
Dataset title: N-glycomic signature of stage II colorectal cancer and its association with the tumor microenvironment
Possible reference: Boyaval, F. et al. (2021) N-Glycomic Signature of Stage II Colorectal Cancer and Its Association With the Tumor Microenvironment., Mol Cell Proteomics, PMID 33581319

PXD021266 Dataset with its publication pending (from PRIDE)
Dataset title: Structure dynamics of ApoA-I amyloidogenic variants in small HDL increase their ability to mediate cholesterol efflux
Possible reference: Nilsson, O. et al. (2021) Structure dynamics of ApoA-I amyloidogenic variants in small HDL increase their ability to mediate cholesterol efflux., J Lipid Res, PMID 33410751

PXD021265 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling reveals CDK6 upregulation as a targetable resistance mechanism for lenalidomide in multiple myeloma
Possible reference: Ng, YLD. et al. (2022) Proteomic profiling reveals CDK6 upregulation as a targetable resistance mechanism for lenalidomide in multiple myeloma., Nat Commun, PMID 35197447

PXD021258 no publication (from MassIVE)
Dataset title: Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation
Possible reference: Devitt, CC. et al. (2021) Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation., J Cell Sci, PMID 34060614

PXD021249 Dataset with its publication pending (from PRIDE)
Dataset title: Ablation of Btn1a1 leads to concurrent cell death and renewal in the mammary epithelium during lactation
Possible reference: Jeong, J. et al. (2021) The butyrophilin 1a1 knockout mouse revisited: Ablation of Btn1a1 leads to concurrent cell death and renewal in the mammary epithelium during lactation., FASEB Bioadv, PMID 34938960

PXD021222 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibiting coronavirus replication by chemical ER stress, including SARS-CoV-2 and MERS-CoV
Possible reference: Shaban, MS. et al. (2021) Multi-level inhibition of coronavirus replication by chemical ER stress., Nat Commun, PMID 34545074

PXD021218 Dataset with its publication pending (from PRIDE)
Dataset title: Quantifying gene expression control by growth and metabolism reveals distinct regulation of central carbon metabolism genes in yeast
Possible reference: Yu, R. et al. (2021) Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast., Elife, PMID 33720010

PXD021201 Dataset with its publication pending (from PRIDE)
Dataset title: Differential analysis of nucleolar proteomics in triple negative breast cancer
Possible reference: Weeks, SE. et al. (2021) Inhibiting β-catenin disables nucleolar functions in triple-negative breast cancer., Cell Death Dis, PMID 33664239

PXD021190 Dataset with its publication pending (from PRIDE)
Dataset title: Seven Novel Genes Related to Cell Proliferation and Migration of VHL-Mutated Pheochromocytoma
Possible reference: Gao, S. et al. (2021) Seven Novel Genes Related to Cell Proliferation and Migration of VHL-Mutated Pheochromocytoma., Front Endocrinol (Lausanne), PMID 33828526

PXD021173 Dataset with its publication pending (from PRIDE)
Dataset title: The mitochondrial surface receptor Tom70 protects the cytosol against mitoprotein-induced stress
Possible reference: Backes, S. et al. (2021) The chaperone-binding activity of the mitochondrial surface receptor Tom70 protects the cytosol against mitoprotein-induced stress., Cell Rep, PMID 33826901

PXD021165 Dataset with its publication pending (from PRIDE)
Dataset title: Overexpression of the human mutation P209L of cochaperone BAG3 in mouse
Possible reference: Fang, X. et al. (2019) P209L mutation in Bag3 does not cause cardiomyopathy in mice., Am J Physiol Heart Circ Physiol, PMID 30499714

PXD021160 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of Rat Proximal-Tubule Cell-Culture Models
Possible reference: Khundmiri, SJ. et al. (2021) Transcriptomes of Major Proximal Tubule Cell Culture Models., J Am Soc Nephrol, PMID 33122286

PXD021143 Dataset with its publication pending (from PRIDE)
Dataset title: Interactome of S65 phosphorylated NEDD8 and Ub
Possible reference: Stuber, K. et al. (2021) Structural and functional consequences of NEDD8 phosphorylation., Nat Commun, PMID 34642328

PXD021136 Dataset with its publication pending (from PRIDE)
Dataset title: Decoding the signalling profile of hematopoietic progenitor kinase 1 (HPK1) in innate immunity: a proteomic approach
Possible reference: Bader, A. et al. (2022) Decoding the signaling profile of hematopoietic progenitor kinase 1 (HPK1) in innate immunity: A proteomic approach., Eur J Immunol, PMID 35099066

PXD021126 Dataset with its publication pending (from PRIDE)
Dataset title: Structural analysis of the PTEN:P-Rex2 signaling node reveals how cancer-associated mutations coordinate to hyperactivate Rac1
Possible reference: D'Andrea, L. et al. (2021) Structural analysis of the PTEN:P-Rex2 signaling complex reveals how cancer-associated mutations coordinate to hyperactivate Rac1., Sci Signal, PMID 33947796

PXD021124 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of IgE reactive proteins from Aspergillus terreus using mass spectrometry.
Possible reference: Karmakar, B. et al. (2020) Identification and biochemical characterization of Asp t 36, a new fungal allergen from Aspergillus terreus., J Biol Chem, PMID 33454019

PXD021103 Dataset with its publication pending (from iProX)
Dataset title: Omics study reveals abnormal alterations of breastmilk proteins and metabolites in puerperant women with COVID-19
Possible reference: Zhao, Y. et al. (2020) Omics study reveals abnormal alterations of breastmilk proteins and metabolites in puerperant women with COVID-19., Signal Transduct Target Ther, PMID 33097684

PXD021096 Dataset with its publication pending (from PRIDE)
Dataset title: Human Neutrophils Phosphoproteome in Systemic Lupus Erythematosus
Possible reference: Bashant, KR. et al. (2021) Proteomic, biomechanical and functional analyses define neutrophil heterogeneity in systemic lupus erythematosus., Ann Rheum Dis, PMID 32988843

PXD021088 Dataset with its publication pending (from PRIDE)
Dataset title: Dystrophin domains R4-15 and R20-23
Possible reference: Nelson, DM. et al. (2020) Rapid, redox-mediated mechanical susceptibility of the cortical microtubule lattice in skeletal muscle., Redox Biol, PMID 33002761

PXD021086 Dataset with its publication pending (from PRIDE)
Dataset title: Proteo-metabolomic study of olive (cv. ‘Chondrolia Chalkidikis’) drupe development and maturation
Possible reference: Karagiannis, E. et al. (2021) Proteo-metabolomic journey across olive drupe development and maturation., Food Chem, PMID 34147896

PXD021085 Dataset with its publication pending (from PRIDE)
Dataset title: Chromatin modifiers and recombination factors promote a telomere fold-back structure, that is lost during replicative senescence
Possible reference: Wagner, T. et al. (2020) Chromatin modifiers and recombination factors promote a telomere fold-back structure, that is lost during replicative senescence., PLoS Genet, PMID 33370275

PXD021059 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in the Phytopathogenic Fungus Botrytis cinerea
Possible reference: Xu, Y. et al. (2020) Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Phytopathogenic Fungus Botrytis cinerea., Front Microbiol, PMID 33329453

PXD021049 Dataset with its publication pending (from jPOST)
Dataset title: High accurate and precise quantification analysis of GeLC-MS/MS with dimethyl labeling.
Possible reference: Konno, R. et al. (2021) Highly accurate and precise quantification strategy using stable isotope dimethyl labeling coupled with GeLC-MS/MS., Biochem Biophys Res Commun, PMID 33684618

PXD021042 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative analysis of maca (Lepidium meyenii) proteome profiles reveals insights into response mechanisms of herbal plants to high-temperature stress
Possible reference: Wang, ZQ. et al. (2020) Comparative analysis of maca (Lepidium meyenii) proteome profiles reveals insights into response mechanisms of herbal plants to high-temperature stress., BMC Plant Biol, PMID 32938390

PXD021029 Dataset with its publication pending (from iProX)
Dataset title: Dissection of anti-tumor activity of histone deacetylase inhibitor SAHA in NPC cells via quantitative phosphoproteomics
Possible reference: Huang, H. et al. (2020) Dissection of Anti-tumor Activity of Histone Deacetylase Inhibitor SAHA in Nasopharyngeal Carcinoma Cells via Quantitative Phosphoproteomics., Front Cell Dev Biol, PMID 33324635

PXD021026 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics characterisation of the L929 cell supernatant and its role in BMDM differentiation
Possible reference: Heap, RE. et al. (2021) Proteomics characterisation of the L929 cell supernatant and its role in BMDM differentiation., Life Sci Alliance, PMID 33853969

PXD021014 Dataset with its publication pending (from PRIDE)
Dataset title: Compartmentalized proteomic profiling outlines the crucial role of the Classical secretory pathway during recombinant protein production in Chinese hamster ovary cells
Possible reference: P�rez-Rodriguez, S. et al. (2021) Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells., ACS Omega, PMID 34056395

PXD021004 Dataset with its publication pending (from PRIDE)
Dataset title: HUMAN BLOOD SERUM PROTEOME CHANGES AFTER 6 HOURS OF SLEEP DEPRIVATION AT NIGHT
Possible reference: Bj�rkum, AA. et al. (2024) Human serum proteomics reveals a molecular signature after one night of sleep deprivation., Sleep Adv, PMID 39131770

PXD020924 Dataset with its publication pending (from PRIDE)
Dataset title: Different research approaches in unraveling the venom proteome of Naja ashei
Possible reference: Hus, KK. et al. (2020) Different Research Approaches in Unraveling the Venom Proteome of Naja ashei., Biomolecules, PMID 32899462

PXD020916 no publication (from MassIVE)
Dataset title: Selective dephosphorylation by PP2A-B55 directs the meiosis I - meiosis II transition in oocytes
Possible reference: Swartz, SZ. et al. (2021) Selective dephosphorylation by PP2A-B55 directs the meiosis I-meiosis II transition in oocytes., Elife, PMID 34342579

PXD020902 Dataset with its publication pending (from PRIDE)
Dataset title: Fecal metaproteomics reveals reduced gut inflammation and changed microbial metabolism following lifestyle-induced weight loss
Possible reference: Biemann, R. et al. (2021) Fecal Metaproteomics Reveals Reduced Gut Inflammation and Changed Microbial Metabolism Following Lifestyle-Induced Weight Loss., Biomolecules, PMID 34066026

PXD020870 Dataset with its publication pending (from PRIDE)
Dataset title: Nuclear phosphatidylinositol (3,4,5) triphosphate interactome uncovers an enrichment in nucleolar proteins
Possible reference: Mazloumi Gavgani, F. et al. (2021) Nuclear Phosphatidylinositol 3,4,5-Trisphosphate Interactome Uncovers an Enrichment in Nucleolar Proteins., Mol Cell Proteomics, PMID 34048982

PXD020866 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative phosphoproteomics of classical bordetellae elucidates the role of serine, threonine and tyrosine phosphorylation in Bordetella biology and virulence
Possible reference: Luu, LDW. et al. (2021) Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence., Front Cell Infect Microbiol, PMID 33928046

PXD020859 Dataset with its publication pending (from PRIDE)
Dataset title: Cross-linking mass spectrometry uncovers protein interactions and functional assemblies in synaptic vesicle membranes
Possible reference: Wittig, S. et al. (2021) Cross-linking mass spectrometry uncovers protein interactions and functional assemblies in synaptic vesicle membranes., Nat Commun, PMID 33558502

PXD020857 Dataset with its publication pending (from PRIDE)
Dataset title: Implementation of microfluidics for antimicrobial susceptibility assays: issues and optimization requirements
Possible reference: Parsley, NC. et al. (2020) Implementation of Microfluidics for Antimicrobial Susceptibility Assays: Issues and Optimization Requirements., Front Cell Infect Microbiol, PMID 33042872

PXD020856 Dataset with its publication pending (from PRIDE)
Dataset title: Harnessing Ionic Selectivity In Acetyltransferase Chemoproteomic Probes
Possible reference: Jing, Y. et al. (2021) Harnessing Ionic Selectivity in Acetyltransferase Chemoproteomic Probes., ACS Chem Biol, PMID 33373188

PXD020854 no publication (from MassIVE)
Dataset title: Proteomes of Robust Yarrowia lipolytica Isolates Cultivated in Biomass Hydrolysate Reveal Key Processes Impacting Sugar Utilization and Lipid Degradation
Possible reference: Walker, C. et al. (2021) Exploring Proteomes of Robust Yarrowia lipolytica Isolates Cultivated in Biomass Hydrolysate Reveals Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation., mSystems, PMID 34342539

PXD020849 Dataset with its publication pending (from PRIDE)
Dataset title: Structural inventory of native ribosomal ABCE1-43S pre-initiation complex
Possible reference: Kratzat, H. et al. (2021) A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes., EMBO J, PMID 33289941

PXD020805 Dataset with its publication pending (from PRIDE)
Dataset title: A vascular phosphoproteome atlas unveils a functional Tie‑Wnt signalling axis in the liver
Possible reference: Inverso, D. et al. (2021) A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie-Wnt signaling axis in the liver., Dev Cell, PMID 34038707

PXD020804 Dataset with its publication pending (from PRIDE)
Dataset title: The GAR Domain Determines Subcellular Localization of the Growth Controlling RNA Binding Protein Nucleolin
Possible reference: Doron-Mandel, E. et al. (2021) The glycine arginine-rich domain of the RNA-binding protein nucleolin regulates its subcellular localization., EMBO J, PMID 34515347

PXD020801 no publication (from MassIVE)
Dataset title: HUPO HPP Phosphopeptide Challenge
Possible reference: Hoopmann, MR. et al. (2020) Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project., J Proteome Res, PMID 33166149

PXD020796 no publication (from MassIVE)
Dataset title: Elongin A regulates transcription in vivo through enhanced RNA polymerase processivity
Possible reference: Wang, Y. et al. (2021) Elongin A regulates transcription in�vivo through enhanced RNA polymerase processivity., J Biol Chem, PMID 33298525

PXD020795 Dataset with its publication pending (from PRIDE)
Dataset title: Five microRNAs in serum are able to differentiate breast cancer patients from healthy individuals
Possible reference: Feliciano, A. et al. (2020) Five microRNAs in Serum Are Able to Differentiate Breast Cancer Patients From Healthy Individuals., Front Oncol, PMID 33224883

PXD020792 Dataset with its publication pending (from PRIDE)
Dataset title: Trans-2-enoyl-CoA reductase limits Ca2+ accumulation in the endoplasmic reticulum by inhibiting SERCA2b Ca2+ pump
Possible reference: Uchida, Y. et al. (2021) Trans-2-enoyl-CoA reductase limits Ca2+ accumulation in the endoplasmic reticulum by inhibiting the Ca2+ pump SERCA2b., J Biol Chem, PMID 33482198

PXD020790 Dataset with its publication pending (from PRIDE)
Dataset title: Global analysis of lysine 2-hydroxyisobutyrylation in wheat leaf
Possible reference: Feng, B. et al. (2021) Systematic analysis of lysine 2-hydroxyisobutyrylation posttranslational modification in wheat leaves., PLoS One, PMID 34138952

PXD020788 Dataset with its publication pending (from PRIDE)
Dataset title: Global analysis of lysine 2-hydroxyisobutyrylation in wheat leaf
Possible reference: Feng, B. et al. (2021) Systematic analysis of lysine 2-hydroxyisobutyrylation posttranslational modification in wheat leaves., PLoS One, PMID 34138952

PXD020775 Dataset with its publication pending (from PRIDE)
Dataset title: An integrated multi-omics protocol for swine feces reveals congruent longitudinal dynamics in microbiome structure and function.
Possible reference: Gierse, LC. et al. (2020) A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function., Microorganisms, PMID 33260576

PXD020760 Dataset with its publication pending (from PRIDE)
Dataset title: A vascular phosphoproteome atlas unveils a functional Tie‑Wnt signalling axis in the liver
Possible reference: Inverso, D. et al. (2021) A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie-Wnt signaling axis in the liver., Dev Cell, PMID 34038707

PXD020757 Dataset with its publication pending (from PRIDE)
Dataset title: Mechanisms and Novel Proteins for Iron Oxide Mineral Reduction in the Hyperthermophilic Crenarchaeon Pyrodictium delaneyi
Possible reference: Kashyap, S. et al. (2021) Microbe-Mineral Interaction and Novel Proteins for Iron Oxide Mineral Reduction in the Hyperthermophilic Crenarchaeon Pyrodictium delaneyi., Appl Environ Microbiol, PMID 33419739

PXD020756 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of dexamethasone effects on cartilage breakdown
Possible reference: Black, RM. et al. (2020) Proteomic analysis reveals dexamethasone rescues matrix breakdown but not anabolic dysregulation in a cartilage injury model., Osteoarthr Cartil Open, PMID 34322675

PXD020746 Dataset with its publication pending (from PRIDE)
Dataset title: Global Proteomic Analysis of Lysine lactylation in The Plant Pathogen Botrytis cinerea
Possible reference: Gao, M. et al. (2020) Systematic Analysis of Lysine Lactylation in the Plant Fungal Pathogen Botrytis cinerea., Front Microbiol, PMID 33193272

PXD020740 Dataset with its publication pending (from PRIDE)
Dataset title: Chemical proteomic profiling reveals protein interactors of the alarmones diadenosine triphosphate and tetraphosphate
Possible reference: Kr�ger, L. et al. (2021) Chemical proteomic profiling reveals protein interactors of the alarmones diadenosine triphosphate and tetraphosphate., Nat Commun, PMID 34608152

PXD020736 no publication (from MassIVE)
Dataset title: The Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation
Possible reference: Buck, TM. et al. (2020) The Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation., Mol Cell Proteomics, PMID 32868373

PXD020731 Dataset with its publication pending (from PRIDE)
Dataset title: ErbB2 drives Yap activation during cardiac regeneration
Possible reference: Aharonov, A. et al. (2020) ERBB2 drives YAP activation and EMT-like processes during cardiac regeneration., Nat Cell Biol, PMID 33046882

PXD020719 Dataset with its publication pending (from PRIDE)
Dataset title: Integration of JAK/STAT receptor-ligand trafficking, signalling and gene expression in Drosophila melanogaster cells
Possible reference: Moore, R. et al. (2020) Integration of JAK/STAT receptor-ligand trafficking, signalling and gene expression in Drosophila melanogaster cells., J Cell Sci, PMID 32917740

PXD020716 Dataset with its publication pending (from iProX)
Dataset title: Deep eutectic solvents-based polymer monolith incorporated with titanium dioxide nanotubes (TNTs) for specific recognition of the proteins
Possible reference: Zhang, X. et al. (2020) Deep eutectic solvents-based polymer monolith incorporated with titanium dioxide nanotubes for specific recognition of proteins., Anal Chim Acta, PMID 33190706

PXD020679 Mayfield AB. Proteomic Signatures of Corals from Thermodynamic Reefs. Mayfield AB (2020) Proteomic Signatures of Corals from Thermodynamic Reefs. Microorganisms (in press). (from MassIVE)
Dataset title: Proteomic signatures of corals from thermodynamic reefs
Possible reference: Ricaurte, M. et al. (2016) Proteomic analysis of bleached and unbleached Acropora palmata, a threatened coral species of the Caribbean., Mar Pollut Bull, PMID 27105725

PXD020644 Dataset with its publication pending (from PRIDE)
Dataset title: A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens
Possible reference: Renuse, S. et al. (2021) A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens., EBioMedicine, PMID 34229274

PXD020636 Dataset with its publication pending (from PRIDE)
Dataset title: A structural mechanism for PP2A-B56alpha inhibition by CIP2A
Possible reference: Pavic, K. et al. (2023) Structural mechanism for inhibition of PP2A-B56α and oncogenicity by CIP2A., Nat Commun, PMID 36854761

PXD020633 Dataset with its publication pending (from PRIDE)
Dataset title: Polydisperse molecular architecture of connexin 26/30 heteromeric hemichannels revealed by AFM imaging
Possible reference: Naulin, PA. et al. (2020) Polydisperse molecular architecture of connexin 26/30 heteromeric hemichannels revealed by atomic force microscopy imaging., J Biol Chem, PMID 32887797

PXD020618 Dataset with its publication pending (from PRIDE)
Dataset title: Clinical Proteomics of Metastatic Melanoma Reveals Profiles of Organ-Specificity and Treatment Resistance
Possible reference: Beck, L. et al. (2021) Clinical Proteomics of Metastatic Melanoma Reveals Profiles of Organ Specificity and Treatment Resistance., Clin Cancer Res, PMID 33446566

PXD020612 Dataset with its publication pending (from PRIDE)
Dataset title: USP15 deubiquitinase safeguards hematopoiesis and genome integrity in hematopoietic stem cells and leukemia cells
Possible reference: van den Berk, P. et al. (2020) USP15 Deubiquitinase Safeguards Hematopoiesis and Genome Integrity in Hematopoietic Stem Cells and Leukemia Cells., Cell Rep, PMID 33378683

PXD020607 Dataset with its publication pending (from PRIDE)
Dataset title: The component parts of bacteriophage virions accurately defined by a new machine-learning approach built on evolutionary features.
Possible reference: Thung, TY. et al. (2021) Component Parts of Bacteriophage Virions Accurately Defined by a Machine-Learning Approach Built on Evolutionary Features., mSystems, PMID 34042467

PXD020601 Dataset with its publication pending (from PRIDE)
Dataset title: Serum proteomics in COVID-19 patients: Altered coagulation and complement status as a function of IL-6 level
Possible reference: D'Alessandro, A. et al. (2020) Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level., J Proteome Res, PMID 32786691

PXD020594 no publication (from MassIVE)
Dataset title: Novel proteomic profiling of epididymal extracellular vesicles in the domestic cat reveals proteins related to sequential sperm maturation with differences observed between normospermic and teratospermic individuals
Possible reference: Rowlison, T. et al. (2020) Novel Proteomic Profiling of Epididymal Extracellular Vesicles in the Domestic Cat Reveals Proteins Related to Sequential Sperm Maturation with Differences Observed between Normospermic and Teratospermic Individuals., Mol Cell Proteomics, PMID 33008835

PXD020575 Dataset with its publication pending (from PRIDE)
Dataset title: An FGF-2 signaling pathway that is activated in aged skeletal muscle promotes intramuscular adipogenesis
Possible reference: Mathes, S. et al. (2021) FGF-2-dependent signaling activated in aged human skeletal muscle promotes intramuscular adipogenesis., Proc Natl Acad Sci U S A, PMID 34493647

PXD020565 Dataset with its publication pending (from PRIDE)
Dataset title: "Analysis of Zika virus capsid-Aedes aegypti mosquito interactome reveals pro-viral host factors critical for establishing infection"
Possible reference: Gestuveo, RJ. et al. (2021) Analysis of Zika virus capsid-Aedes aegypti mosquito interactome reveals pro-viral host factors critical for establishing infection., Nat Commun, PMID 33986255

PXD020539 Dataset with its publication pending (from PRIDE)
Dataset title: Contribution of the Unfolded Protein Response (UPR) transcription factor XBP1 to brain aging
Possible reference: Marcora, MS. et al. (2017) Amyloid-β42 clearance and neuroprotection mediated by X-box binding protein 1 signaling decline with aging in the Drosophila brain., Neurobiol Aging, PMID 28917667

PXD020511 Dataset with its publication pending (from PRIDE)
Dataset title: Numerous post-translational modifications of RNA polymerase II subunit Rpb4 link transcription to post-transcriptional mechanisms
Possible reference: Richard, S. et al. (2021) Numerous Post-translational Modifications of RNA Polymerase II Subunit Rpb4/7 Link Transcription to Post-transcriptional Mechanisms., Cell Rep, PMID 33440147

PXD020488 no publication (from MassIVE)
Dataset title: Sialylation of Asparagine 612 inhibits Aconitase activity during mouse sperm capacitation; A possible mechanism for the switch from oxidative phosphorylation to glycolysis.
Possible reference: Silva Balbin Villaverde, AI. et al. (2020) Sialylation of Asparagine 612 Inhibits Aconitase Activity during Mouse Sperm Capacitation; a Possible Mechanism for the Switch from Oxidative Phosphorylation to Glycolysis., Mol Cell Proteomics, PMID 32839225

PXD020481 Dataset with its publication pending (from PRIDE)
Dataset title: Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks
Possible reference: M�ller, M. et al. (2021) Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks., Nat Commun, PMID 34857745

PXD020426 Dataset with its publication pending (from PRIDE)
Dataset title: Heterotypic signaling between dermal fibroblasts and melanoma cells induces phenotypic plasticity and proteome rearrangement in malignant cells
Possible reference: Pessotti, DS. et al. (2020) Heterotypic signaling between dermal fibroblasts and melanoma cells induces phenotypic plasticity and proteome rearrangement in malignant cells., Biochim Biophys Acta Proteins Proteom, PMID 32866629

PXD020419 no publication (from MassIVE)
Dataset title: Mammalian telomeres reforged with non-telomeric sequences
Possible reference: Kim, C. et al. (2021) Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells., Nat Commun, PMID 33597549

PXD020414 Dataset with its publication pending (from PRIDE)
Dataset title: Label-free quantitative proteomic analysis of insect larval and metamorphic molts
Possible reference: Si, W. et al. (2020) Label-free quantitative proteomic analysis of insect larval and metamorphic molts., BMC Dev Biol, PMID 33234135

PXD020407 Dataset with its publication pending (from jPOST)
Dataset title: Retention Time Prediction Using Neural Networks Increases Identifications in Crosslinking Mass Spectrometry
Possible reference: Giese, SH. et al. (2021) Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry., Nat Commun, PMID 34050149

PXD020401 Dataset with its publication pending (from PRIDE)
Dataset title: TPL-2 kinase induces phagosome acidification to promote macrophage killing of Staphylococcus aureus
Possible reference: Breyer, F. et al. (2021) TPL-2 kinase induces phagosome acidification to promote macrophage killing of bacteria., EMBO J, PMID 33881780

PXD020400 Dataset with its publication pending (from PRIDE)
Dataset title: Cellular and extracellular proteome of the animal pathogen Corynebacterium silvaticum, a close relative of zoonotic Corynebacterium ulcerans and Corynebacterium pseudotuberculosis
Possible reference: M�ller, J. et al. (2020) Cellular and Extracellular Proteome of the Animal Pathogen Corynebacterium silvaticum, a Close Relative of Zoonotic Corynebacterium ulcerans and Corynebacterium pseudotuberculosis., Proteomes, PMID 32806579

PXD020398 Dataset with its publication pending (from PRIDE)
Dataset title: Support-vector-machine learning analysis of the human cerebrovascular thrombi proteome: an exploratory study
Possible reference: Dargazanli, C. et al. (2020) Machine Learning Analysis of the Cerebrovascular Thrombi Proteome in Human Ischemic Stroke: An Exploratory Study., Front Neurol, PMID 33240201

PXD020394 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: detection of viral proteins and host’s biological processes altered by the infection
Possible reference: Rivera, B. et al. (2020) Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: Detection of viral proteins and host's biological processes altered by the infection., Data Brief, PMID 32835036

PXD020381 Dataset with its publication pending (from PRIDE)
Dataset title: A multipass membrane protein interacts with the cGMP-dependent protein kinase to regulate critical calcium signals in malaria parasites
Possible reference: Balestra, AC. et al. (2021) Ca2+ signals critical for egress and gametogenesis in malaria parasites depend on a multipass membrane protein that interacts with PKG., Sci Adv, PMID 33762339

PXD020378 Dataset with its publication pending (from PRIDE)
Dataset title: Phenotypical adaptation of Pseudomonas aeruginosa in the presence of siderophore-antibiotic conjugates during epithelial cell infection
Possible reference: Perraud, Q. et al. (2020) Phenotypic Adaptation of Pseudomonas aeruginosa in the Presence of Siderophore-Antibiotic Conjugates during Epithelial Cell Infection., Microorganisms, PMID 33218210

PXD020372 Dataset with its publication pending (from iProX)
Dataset title: TMT proteomic analysis of Methanogenic archaeon
Possible reference: Mosier, AC. et al. (2015) Elevated temperature alters proteomic responses of individual organisms within a biofilm community., ISME J, PMID 25050524

PXD020365 Dataset with its publication pending (from PRIDE)
Dataset title: Spleen proteomics data from high fat diet fed mice
Possible reference: Svahn, SL. et al. (2020) Spleen proteomics data from high fat diet fed mice., Data Brief, PMID 32904176

PXD020355 Dataset with its publication pending (from PRIDE)
Dataset title: Prothrombin is a binding partner of the human Receptor of Advanced Glycation End products
Possible reference: Degani, G. et al. (2020) Prothrombin is a binding partner of the human receptor of advanced glycation end products., J Biol Chem, PMID 32665403

PXD020343 Dataset with its publication pending (from PRIDE)
Dataset title: Specific proteome changes in platelets from individuals with GATA1-, GFI1B- and RUNX1-linked bleeding disorders
Possible reference: Van Bergen, MGJM. et al. (2021) Specific proteome changes in platelets from individuals with GATA1-, GFI1B-, and RUNX1-linked bleeding disorders., Blood, PMID 33690840

PXD020286 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling of human spermatozoa glycoproteins by LC/MS/MS
Possible reference: Selvaraju, S. et al. (2018) Current status of sperm functional genomics and its diagnostic potential of fertility in bovine (Bos taurus)., Syst Biol Reprod Med, PMID 29537884

PXD020281 Dataset with its publication pending (from PRIDE)
Dataset title: MacroD1 sustains mitochondrial integrity and oxidative metabolism
Possible reference: Hopp, AK. et al. (2025) MacroD1 sustains mitochondrial integrity and oxidative metabolism., Nat Commun, PMID 40817374

PXD020260 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative Proteomics Identifies Sytenin-1 as a Universal Biomarker of Exosomes
Possible reference: Navajas, R. et al. (2019) Serum Exosome Isolation by Size-Exclusion Chromatography for the Discovery and Validation of Preeclampsia-Associated Biomarkers., Methods Mol Biol, PMID 30852814

PXD020258 Dataset with its publication pending (from PRIDE)
Dataset title: Therapeutic anti-glioma effect of the combined action of PCSK inhibitor with the anti-tumoral factors secreted by Poly (I:C) - stimulated macrophages
Possible reference: Rose, M. et al. (2022) Therapeutic anti-glioma effect of the combined action of PCSK inhibitor with the anti-tumoral factors secreted by Poly (I:C)-stimulated macrophages., Cancer Gene Ther, PMID 33402730

PXD020255 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of adipose depots after intermittent fasting reveals visceral fat preservation mechanisms
Possible reference: Harney, DJ. et al. (2021) Proteomics analysis of adipose depots after intermittent fasting reveals visceral fat preservation mechanisms., Cell Rep, PMID 33657384

PXD020247 Dataset with its publication pending (from PRIDE)
Dataset title: TPL-2 kinase induces phagosome acidification to promote macrophage killing of bacteria
Possible reference: Breyer, F. et al. (2021) TPL-2 kinase induces phagosome acidification to promote macrophage killing of bacteria., EMBO J, PMID 33881780

PXD020229 Dataset with its publication pending (from PRIDE)
Dataset title: Crosslinking mass spectrometry of the unconventional kinetoplastid kinetochore protein KKT4
Possible reference: Ludzia, P. et al. (2021) Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein., Structure, PMID 33915106

PXD020204 Dataset with its publication pending (from PRIDE)
Dataset title: A phosphoproteomic analysis of platelets in severe obesity uncovers platelet reactivity and signaling pathways alterations
Possible reference: Barrachina, MN. et al. (2021) Phosphoproteomic Analysis of Platelets in Severe Obesity Uncovers Platelet Reactivity and Signaling Pathways Alterations., Arterioscler Thromb Vasc Biol, PMID 33147989

PXD020197 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of brain mitochondrial-derived vesicles
Possible reference: Roberts, RF. et al. (2021) Proteomic Profiling of Mitochondrial-Derived Vesicles in Brain Reveals Enrichment of Respiratory Complex Sub-assemblies and Small TIM Chaperones., J Proteome Res, PMID 33242952

PXD020154 no publication (from MassIVE)
Dataset title: Quantitative Proteomic Analysis of Mouse Fetal and Adult Hematopoietic Progenitor Cells
Possible reference: Pimkova, K. et al. (2022) Quantitative analysis of redox proteome reveals oxidation-sensitive protein thiols acting in fundamental processes of developmental hematopoiesis., Redox Biol, PMID 35640380

PXD020153 Witzel, K., Matros, A. Fructans are differentially distributed in root tissues of asparagus. Cells, 2020, 9(9). doi: 10.3390/cells9091943. (from MassIVE)
Dataset title: Fructooligosaccharides are differentially distributed in root tissues of asparagus
Possible reference: Witzel, K. et al. (2020) Fructans Are Differentially Distributed in Root Tissues of Asparagus., Cells, PMID 32842694

PXD020151 Dataset with its publication pending (from PRIDE)
Dataset title: Biliary Tract Carcinogenesis Model Based on Bile Metaproteomics
Possible reference: Arteta, AA. et al. (2020) Biliary Tract Carcinogenesis Model Based on Bile Metaproteomics., Front Oncol, PMID 32793466

PXD020136 Dataset with its publication pending (from PRIDE)
Dataset title: The role of RodAp-conserved cysteine residues in the Aspergillus fumigatus conidial surface organization
Possible reference: Valsecchi, I. et al. (2020) The Role of RodA-Conserved Cysteine Residues in the Aspergillus fumigatus Conidial Surface Organization., J Fungi (Basel), PMID 32859091

PXD020115 Dataset with its publication pending (from jPOST)
Dataset title: The Liquid Chromatography/Tandem Mass Spectrometry-Based Quantification of Angiotensin Peptides
Possible reference: He, C. et al. (2020) Development of a novel nanoflow liquid chromatography-parallel reaction monitoring mass spectrometry-based method for quantification of angiotensin peptides in HUVEC cultures., PeerJ, PMID 32983648

PXD020104 Dataset with its publication pending (from PRIDE)
Dataset title: Generation and validation of recombinant antibodies to study tRNA synthetases in health and disease
Possible reference: Preger, C. et al. (2020) Generation and validation of recombinant antibodies to study human aminoacyl-tRNA synthetases., J Biol Chem, PMID 32817337

PXD020079 Dataset with its publication pending (from PRIDE)
Dataset title: CIITA-transduced glioblastoma cells uncover a rich repertoire of clinically relevant tumor-associated HLA-II antigens
Possible reference: Forlani, G. et al. (2021) CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens., Mol Cell Proteomics, PMID 33592498

PXD020078 Dataset with its publication pending (from PRIDE)
Dataset title: Urinary Glycoproteomic profiling of Non-Muscle Invasive and Muscle Invasive Bladder Carcinoma Patients reveals distinct N-glycosylation pattern of CD44, MGAM and GINM1
Possible reference: Sathe, G. et al. (2020) Urinary glycoproteomic profiling of non-muscle invasive and muscle invasive bladder carcinoma patients reveals distinct N-glycosylation pattern of CD44, MGAM, and GINM1., Oncotarget, PMID 32922663

PXD020064 no publication (from MassIVE)
Dataset title: Salinity-dependent proteome dynamics in Nile tilapia gills
Possible reference: Root, L. et al. (2021) Nonlinear effects of environmental salinity on the gill transcriptome versus proteome of Oreochromis niloticus modulate epithelial cell turnover., Genomics, PMID 34298068

PXD020056 no publication (from MassIVE)
Dataset title: Salinity-dependent proteome dynamics in Nile tilapia kidneys
Possible reference: Root, L. et al. (2021) A data-independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticus., Mol Ecol Resour, PMID 34101993

PXD020051 Dataset with its publication pending (from PRIDE)
Dataset title: ERR agonism reverses mitochondrial dysfunction and inflammation in the aging kidney
Possible reference: Wang, XX. et al. (2023) Estrogen-Related Receptor Agonism Reverses Mitochondrial Dysfunction and Inflammation in the Aging Kidney., Am J Pathol, PMID 37717940

PXD020015 Dataset with its publication pending (from PanoramaPublic)
Dataset title: S-Adenosylmethionine Depletion Activates La Ribonucleoprotein Domain Family Member 1 to Induce Protein Translation
Possible reference: Ramani, K. et al. (2022) S-adenosylmethionine inhibits la ribonucleoprotein domain family member 1 in murine liver and human liver cancer cells., Hepatology, PMID 34449924

PXD020014 Dataset with its publication pending (from PRIDE)
Dataset title: "In-gel cross-linking mass spectrometry (IGX-MS) of proteins and protein complexes"
Possible reference: Hevler, JF. et al. (2021) Selective cross-linking of coinciding protein assemblies by in-gel cross-linking mass spectrometry., EMBO J, PMID 33459420

PXD020009 Dataset with its publication pending (from PRIDE)
Dataset title: The previously uncharacterized HCMV protein pUL13 increases mitochondrial bioenergetics during infection
Possible reference: Betsinger, CN. et al. (2021) The human cytomegalovirus protein pUL13 targets mitochondrial cristae architecture to increase cellular respiration during infection., Proc Natl Acad Sci U S A, PMID 34344827

PXD019970 Dataset with its publication pending (from iProX)
Dataset title: Tissue proteomics dataset of COVID-19 patients
Possible reference: Zhou, Y. et al. (2020) A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19., PLoS Biol, PMID 33156843

PXD019953 Dataset with its publication pending (from PRIDE)
Dataset title: (p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains
Possible reference: Roghanian, M. et al. (2021) (p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains., Mol Cell, PMID 34416138

PXD019915 Dataset with its publication pending (from jPOST)
Dataset title: Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer
Possible reference: Oka, M. et al. (2021) Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer., Genome Biol, PMID 33397462

PXD019914 no publication (from MassIVE)
Dataset title: Glycoproteomic Characterization of Human High-Grade Serous Ovarian Cancer
Possible reference: Sheta, R. et al. (2016) A metabolic labeling approach for glycoproteomic analysis reveals altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells., J Proteomics, PMID 27095597

PXD019901 Dataset with its publication pending (from PRIDE)
Dataset title: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases
Possible reference: Stamatakis, G. et al. (2020) Generation of SARS-CoV-2 S1 Spike Glycoprotein Putative Antigenic Epitopes in Vitro by Intracellular Aminopeptidases., J Proteome Res, PMID 32931291

PXD019900 Dataset with its publication pending (from PRIDE)
Dataset title: Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli
Possible reference: H�r, J. et al. (2020) Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia�coli., Nucleic Acids Res, PMID 32813020

PXD019858 Dataset with its publication pending (from PRIDE)
Dataset title: Validation of itaconate modification on model proteins
Possible reference: Deng, X. et al. (2025) Itaconate reduces viral endocytosis by targeting Cys128 of the adaptor-related protein complex 1 gamma 1 subunit in the host, providing a novel target for antiviral drug development., Mol Biomed, PMID 41212381

PXD019826 Dataset with its publication pending (from PRIDE)
Dataset title: The mitochondrial transporter SFXN1 is critical for Complex III integrity and cellular metabolism
Possible reference: Acoba, MG. et al. (2021) The mitochondrial carrier SFXN1 is critical for complex III integrity and cellular metabolism., Cell Rep, PMID 33730581

PXD019821 Dataset with its publication pending (from jPOST)
Dataset title: A Marine Photosynthetic Microbial Cell Factory as a Platform for Spider Silk Production
Possible reference: Foong, CP. et al. (2020) A marine photosynthetic microbial cell factory as a platform for spider silk production., Commun Biol, PMID 32641733

PXD019816 Dataset with its publication pending (from PRIDE)
Dataset title: Engineering transplantable jejunal mucosal grafts using primary patient-derived organoids for children with intestinal failure
Possible reference: Meran, L. et al. (2020) Engineering transplantable jejunal mucosal grafts using patient-derived organoids from children with intestinal failure., Nat Med, PMID 32895569

PXD019788 Dataset with its publication pending (from PRIDE)
Dataset title: Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit
Possible reference: Holder, J. et al. (2020) Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit., Elife, PMID 32869743

PXD019787 Dataset with its publication pending (from PRIDE)
Dataset title: Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit
Possible reference: Holder, J. et al. (2020) Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit., Elife, PMID 32869743

PXD019786 Dataset with its publication pending (from PRIDE)
Dataset title: Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit
Possible reference: Holder, J. et al. (2020) Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit., Elife, PMID 32869743

PXD019784 Dataset with its publication pending (from PRIDE)
Dataset title: Hypoxis hemerocallidea (Afrtican potato) corm, leaf and flower transcriptomics and proteomics
Possible reference: Tomescu, MS. et al. (2021) Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato)., PLoS One, PMID 34283859

PXD019755 Dataset with its publication pending (from PRIDE)
Dataset title: Lkb1 suppresses amino acid-driven gluconeogenesis in the liver
Possible reference: Just, PA. et al. (2020) Lkb1 suppresses amino acid-driven gluconeogenesis in the liver., Nat Commun, PMID 33257663

PXD019734 Dataset with its publication pending (from iProX)
Dataset title: Bis(zinc(II)-dipicolylamine) functionalized sub-2 Î¼m core-shell microspheres for analysis of N-phosphoproteome
Possible reference: Hu, Y. et al. (2020) Bis(zinc(II)-dipicolylamine)-functionalized sub-2 μm core-shell microspheres for the analysis of N-phosphoproteome., Nat Commun, PMID 33277485

PXD019725 Dataset with its publication pending (from PRIDE)
Dataset title: Metabolic Changes Contribute to Melphalan Resistance in Multiple Myeloma
Possible reference: Khin, ZP. et al. (2014) A preclinical assay for chemosensitivity in multiple myeloma., Cancer Res, PMID 24310398

PXD019701 Dataset with its publication pending (from PRIDE)
Dataset title: DIPG harbour alterations targetable by MEK inhibitors, with acquired resistance mechanisms overcome by combinatorial inhibition
Possible reference: Izquierdo, E. et al. (2022) DIPG Harbors Alterations Targetable by MEK Inhibitors, with Acquired Resistance Mechanisms Overcome by Combinatorial Inhibition., Cancer Discov, PMID 34737188

PXD019679 Dataset with its publication pending (from PRIDE)
Dataset title: GHB analogs confer neuroprotection through specific interaction with the CaMKII hub domain
Possible reference: Leurs, U. et al. (2021) GHB analogs confer neuroprotection through specific interaction with the CaMKIIα hub domain., Proc Natl Acad Sci U S A, PMID 34330837

PXD019674 Dataset with its publication pending (from PRIDE)
Dataset title: Requirement of Nuclear Pore Complex subunits for transposon silencing in Drosophila
Possible reference: Munaf�, M. et al. (2021) Channel nuclear pore complex subunits are required for transposon silencing in Drosophila., Elife, PMID 33856346

PXD019665 Dataset with its publication pending (from PRIDE)
Dataset title: Characterization of the Novel Mitochondrial Genome Segregation Factor TAP110 in Trypanosoma brucei
Possible reference: Amodeo, S. et al. (2021) Characterization of the novel mitochondrial genome segregation factor TAP110 in Trypanosoma brucei., J Cell Sci, PMID 33589495

PXD019664 (from jPOST)
Dataset title: Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs
Possible reference: Niinae, T. et al. (2021) Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs., Mol Cell Proteomics, PMID 34186244

PXD019663 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of exudate of Cercospora armoraciae from Armoracia rusticana
Possible reference: Wang, H. et al. (2020) Proteomic analysis of exudate of Cercospora armoraciae from Armoracia rusticana., PeerJ, PMID 33005484

PXD019647 Dataset with its publication pending (from PRIDE)
Dataset title: PP2A-Rts1 antagonizes Rck2-mediated hyperosmotic stress signaling in yeast
Possible reference: Hollenstein, DM. et al. (2022) PP2ARts1 antagonizes Rck2-mediated hyperosmotic stress signaling in yeast., Microbiol Res, PMID 35461031

PXD019618 no publication (from MassIVE)
Dataset title: Quantitative Proteomics of human relevance of the dietary fiber-induced liver cancer murine model
Possible reference: Chandrashekar, DS. et al. (2020) Fermentable fiber-induced hepatocellular carcinoma in mice recapitulates gene signatures found in human liver cancer., PLoS One, PMID 32559205

PXD019600 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome landscape of epithelial to mesenchymal transition (EMT) of retinal pigment epithelium shares commonalities with malignancy-associated EMT
Possible reference: Sripathi, SR. et al. (2021) Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities With Malignancy-Associated EMT., Mol Cell Proteomics, PMID 34455105

PXD019572 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative data-independent acquisition glycoproteomics of sparkling wine
Possible reference: Pegg, CL. et al. (2021) Quantitative Data-Independent Acquisition Glycoproteomics of Sparkling Wine., Mol Cell Proteomics, PMID 32938748

PXD019564 Dataset with its publication pending (from PRIDE)
Dataset title: S-glutathionylation proteome profiling of Streptococcus mutans
Possible reference: Li, Z. et al. (2020) S-glutathionylation proteome profiling reveals a crucial role of a thioredoxin-like protein in interspecies competition and cariogenecity of Streptococcus mutans., PLoS Pathog, PMID 32716974

PXD019556 Dataset with its publication pending (from PRIDE)
Dataset title: iTRAQ-based quantitative proteomic analysis of heat stress-induced mechanisms in pepper seedlings
Possible reference: Wang, J. et al. (2021) iTRAQ-based quantitative proteomic analysis of heat stress-induced mechanisms in pepper seedlings., PeerJ, PMID 34141478

PXD019549 Dataset with its publication pending (from PRIDE)
Dataset title: SWATH-MS based proteomic profiling of Pancreatic Ductal Adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways
Possible reference: Nweke, EE. et al. (2020) SWATH-MS based proteomic profiling of pancreatic ductal adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways., PLoS One, PMID 33048956

PXD019515 Dataset with its publication pending (from PRIDE)
Dataset title: FAIMS single cellUltrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell
Possible reference: Cong, Y. et al. (2020) Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell., Chem Sci, PMID 34163866

PXD019499 Dataset with its publication pending (from PRIDE)
Dataset title: CRYPTOCHROMES promote daily proteome homeostasis
Possible reference: Wong, DCS. et al. (2022) CRYPTOCHROMES promote daily protein homeostasis., EMBO J, PMID 34842284

PXD019497 Dataset with its publication pending (from jPOST)
Dataset title: Improved host cell protein analysis in monoclonal antibody products through ProteoMiner
Possible reference: Chen, IH. et al. (2020) Improved host cell protein analysis in monoclonal antibody products through ProteoMiner., Anal Biochem, PMID 32979367

PXD019486 Dataset with its publication pending (from PRIDE)
Dataset title: Long noncoding RNA (lncRNA), smORF encoded polypeptides (SEPs), NONCODE database, enrichment, mass spectrometry
Possible reference: Zhang, Q. et al. (2021) Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs., Mol Cell Proteomics, PMID 34129944

PXD019484 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial protein interaction landscape of SS-31
Possible reference: Chavez, JD. et al. (2020) Mitochondrial protein interaction landscape of SS-31., Proc Natl Acad Sci U S A, PMID 32554501

PXD019482 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of blood serum and lung about pulmonary hypertension with old anterior myocardial infarction
Possible reference: Wu, X. et al. (2020) Serum biomarker analysis at the protein level on pulmonary hypertension secondary to old anterior myocardial infarction., Pulm Circ, PMID 33282196

PXD019469 Dataset with its publication pending (from PRIDE)
Dataset title: A head and neck cancer protein interaction map reveals PIK3CA mutant drug sensitivity
Possible reference: Swaney, DL. et al. (2021) A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity., Science, PMID 34591642

PXD019465 Dataset with its publication pending (from PRIDE)
Dataset title: ZAP-70 promotes microenvironment interactions and increases protein-translation in chronic lymphocytic leukemia
Possible reference: Chen, J. et al. (2021) ZAP-70 constitutively regulates gene expression and protein synthesis in chronic lymphocytic leukemia., Blood, PMID 33619528

PXD019463 Dataset with its publication pending (from PRIDE)
Dataset title: Bacterial response to glyphosate-based herbicide Roundup stress
Possible reference: P�ppe, J. et al. (2020) Selection for Resistance to a Glyphosate-Containing Herbicide in Salmonella enterica Does Not Result in a Sustained Activation of the Tolerance Response or Increased Cross-Tolerance and Cross-Resistance to Clinically Important Antibiotics., Appl Environ Microbiol, PMID 33008821

PXD019455 no publication (from MassIVE)
Dataset title: Hepatitis C virus NS3-4A protease regulates the lipid environment for RNA replication by cleaving host enzyme 24-dehydrocholesterol reductase
Possible reference: Tallorin, L. et al. (2020) Hepatitis C virus NS3-4A protease regulates the lipid environment for RNA replication by cleaving host enzyme 24-dehydrocholesterol reductase., J Biol Chem, PMID 32641492

PXD019432 no publication (from MassIVE)
Dataset title: Membrane-Based Affinity Purification to Identify Target Proteins of a Small-Molecule Drug
Possible reference: Yang, L. et al. (2020) Membrane-Based Affinity Purification to Identify Target Proteins of a Small-Molecule Drug., Anal Chem, PMID 32867494

PXD019419 no publication (from MassIVE)
Dataset title: Proteomic Analysis of the Air-way Fluid in Lung Cancer. Detection of Periostin in Bronchoalveolar Lavage (BAL).
Possible reference: Zhou, Y. et al. (2020) Proteomic Analysis of the Air-Way Fluid in Lung Cancer. Detection of Periostin in Bronchoalveolar Lavage (BAL)., Front Oncol, PMID 32719746

PXD019413 Dataset with its publication pending (from PRIDE)
Dataset title: Progressive proteome changes in the myocardium of a pig model for Duchenne muscular dystrophy
Possible reference: Tamiyakul, H. et al. (2020) Progressive Proteome Changes in the Myocardium of a Pig Model for Duchenne Muscular Dystrophy., iScience, PMID 32927262

PXD019387 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Profiling of Serum Exosomes from Patients with Metastatic Gastric Cancer
Possible reference: Ding, XQ. et al. (2020) Proteomic Profiling of Serum Exosomes From Patients With Metastatic Gastric Cancer., Front Oncol, PMID 32754443

PXD019371 Dataset with its publication pending (from PRIDE)
Dataset title: The iron-regulated surface determinant B (IsdB) protein from Staphylococcus aureus acts as a vitronectin receptor
Possible reference: Pietrocola, G. et al. (2020) The iron-regulated surface determinant B (IsdB) protein from Staphylococcus aureus acts as a receptor for the host protein vitronectin., J Biol Chem, PMID 32499371

PXD019362 Dataset with its publication pending (from PRIDE)
Dataset title: Towards understandingTissue Mϕ heterogeneity and functions using quantitative proteomics
Possible reference: Hadizadeh Esfahani, A. et al. (2018) A systematic atlas of chaperome deregulation topologies across the human cancer landscape., PLoS Comput Biol, PMID 29293508

PXD019358 Dataset with its publication pending (from PRIDE)
Dataset title: Global Proteomic Analysis of Lysine crotonylation in The Plant Pathogen Botrytis cinerea
Possible reference: Zhang, N. et al. (2020) Global Proteomic Analysis of Lysine Crotonylation in the Plant Pathogen Botrytis cinerea., Front Microbiol, PMID 33193151

PXD019348 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome-Wide Effects of Naphthalene-Derived Secondary Organic Aerosol in BEAS-2B Cells Are Caused by Short-Lived Unsaturated Carbonyls
Possible reference: Han, J. et al. (2020) Proteome-wide effects of naphthalene-derived secondary organic aerosol in BEAS-2B cells are caused by short-lived unsaturated carbonyls., Proc Natl Acad Sci U S A, PMID 32989125

PXD019345 Dataset with its publication pending (from PRIDE)
Dataset title: MPP8 is essential for sustaining self-renewal of ground-state pluripotent stem cells
Possible reference: M�ller, I. et al. (2021) MPP8 is essential for sustaining self-renewal of ground-state pluripotent stem cells., Nat Commun, PMID 34031396

PXD019305 Dataset with its publication pending (from PRIDE)
Dataset title: Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery
Possible reference: Pinheiro, MJ. et al. (2020) Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery., Front Bioeng Biotechnol, PMID 32974324

PXD019293 Dataset with its publication pending (from PRIDE)
Dataset title: Caspofungin induced cell wall changes of Candida species influences macrophage interactions
Possible reference: Walker, LA. et al. (2020) Caspofungin Induced Cell Wall Changes of Candida Species Influences Macrophage Interactions., Front Cell Infect Microbiol, PMID 32528900

PXD019288 Dataset with its publication pending (from PRIDE)
Dataset title: COPPER INDUCES PROTEIN AGGREGATION, A TOXIC PROCESS COMPENSATED BY MOLECULAR CHAPERONES.
Possible reference: Zuily, L. et al. (2022) Copper Induces Protein Aggregation, a Toxic Process Compensated by Molecular Chaperones., mBio, PMID 35289645

PXD019285 Dataset with its publication pending (from PRIDE)
Dataset title: Interferon-induced degradation of the hepatitis B virus persistence form, cccDNA, depends on ISG20
Possible reference: Stadler, D. et al. (2021) Interferon-induced degradation of the persistent hepatitis B virus cccDNA form depends on ISG20., EMBO Rep, PMID 33969602

PXD019282 Dataset with its publication pending (from iProX)
Dataset title: N-glycosites and O-glycosites on Spike glycoprotein of SARS-CoV-2
Possible reference: Bagdonaite, I. et al. (2021) Site-Specific O-Glycosylation Analysis of SARS-CoV-2 Spike Protein Produced in Insect and Human Cells., Viruses, PMID 33806155

PXD019280 no publication (from MassIVE)
Dataset title: Precise temporal regulation of post-transcriptional repressors is required for an orderly Drosophila maternal-to-zygotic transition
Possible reference: Cao, WX. et al. (2020) Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition., Cell Rep, PMID 32579915

PXD019273 Dataset with its publication pending (from PRIDE)
Dataset title: Posttranslational modification of the RHO of plants protein RACB by phosphorylation and cross-kingdom conserved ubiquitination
Possible reference: Wei�, L. et al. (2022) Posttranslational modification of the RHO of plants protein RACB by phosphorylation and cross-kingdom conserved ubiquitination., PLoS One, PMID 35333858

PXD019260 Dataset with its publication pending (from PRIDE)
Dataset title: Cholesterol sensing by CD81 is important for hepatitis C virus entry
Possible reference: Palor, M. et al. (2020) Cholesterol sensing by CD81 is important for hepatitis C virus entry., J Biol Chem, PMID 32900848

PXD019255 Dataset with its publication pending (from PRIDE)
Dataset title: Uncovering tumor-stroma inter-relationships using quantitative MALDI-Mass spectrometry imaging
Possible reference: Boyle, ST. et al. (2020) Uncovering Tumor-Stroma Inter-relationships Using MALDI Mass Spectrometry Imaging., J Proteome Res, PMID 32870688

PXD019246 no publication (from MassIVE)
Dataset title: Oligodendrocyte-derived extracellular vesicles as antigen-specific therapy for autoimmune neuroinflammation
Possible reference: Casella, G. et al. (2020) Oligodendrocyte-derived extracellular vesicles as antigen-specific therapy for autoimmune neuroinflammation in mice., Sci Transl Med, PMID 33148622

PXD019230 no publication (from MassIVE)
Dataset title: EDF1 coordinates cellular responses to ribosome collisions
Possible reference: Sinha, NK. et al. (2020) EDF1 coordinates cellular responses to ribosome collisions., Elife, PMID 32744497

PXD019226 no publication (from MassIVE)
Dataset title: EDF1 coordinates cellular responses to ribosome collisions
Possible reference: Sinha, NK. et al. (2020) EDF1 coordinates cellular responses to ribosome collisions., Elife, PMID 32744497

PXD019224 no publication (from MassIVE)
Dataset title: EDF1 coordinates cellular responses to ribosome collisions
Possible reference: Sinha, NK. et al. (2020) EDF1 coordinates cellular responses to ribosome collisions., Elife, PMID 32744497

PXD019213 no publication (from MassIVE)
Dataset title: Perturbations of hepatic proteome behind the onset of metabolic disorders in mouse offspring developed following assisted reproductive technologies
Possible reference: Zacchini, F. et al. (2021) Perturbations of the hepatic proteome behind the onset of metabolic disorders in mouse offspring developed following embryo manipulation., Theriogenology, PMID 34052779

PXD019199 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping the CCL8:P672 interface using HDX-MS
Possible reference: Darlot, B. et al. (2020) Engineered anti-inflammatory peptides inspired by mapping an evasin-chemokine interaction., J Biol Chem, PMID 32471866

PXD019186 Dataset with its publication pending (from PRIDE)
Dataset title: Adipocytes disrupt the translational programme of Acute Lymphoblastic Leukaemia to favour tumour survival and persistence
Possible reference: Heydt, Q. et al. (2021) Adipocytes disrupt the translational programme of acute lymphoblastic leukaemia to favour tumour survival and persistence., Nat Commun, PMID 34535653

PXD019159 Dataset with its publication pending (from PRIDE)
Dataset title: Protein composition of the subretinal fluid suggest selective diffusion of vitreous proteins in retinal detachment
Possible reference: Poulsen, ET. et al. (2020) Protein Composition of the Subretinal Fluid Suggests Selective Diffusion of Vitreous Proteins in Retinal Detachment., Transl Vis Sci Technol, PMID 33117608

PXD019149 Dataset with its publication pending (from PRIDE)
Dataset title: Extensive transfer of genes for edible seaweed digestion from marine to human gut bacteria
Possible reference: Pudlo, NA. et al. (2022) Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria., Cell Host Microbe, PMID 35240043

PXD019141 Dataset with its publication pending (from PRIDE)
Dataset title: Stress-induced translation inhibition through displacement of scanning initiation factors
Possible reference: Bresson, S. et al. (2020) Stress-Induced Translation Inhibition through Rapid Displacement of Scanning Initiation Factors., Mol Cell, PMID 33053322

PXD019132 no publication (from MassIVE)
Dataset title: A carotenoid-deficient mutant of the plant-associated microbe Pantoea sp. YR343 displays an altered membrane proteome
Possible reference: Vijaya Kumar, S. et al. (2020) A carotenoid-deficient mutant of the plant-associated microbe Pantoea sp. YR343 displays an altered membrane proteome., Sci Rep, PMID 32917935

PXD019127 Dataset with its publication pending (from PRIDE)
Dataset title: PhosR enables processing and functional analysis of phosphoproteomic data
Possible reference: Kim, HJ. et al. (2021) PhosR enables processing and functional analysis of phosphoproteomic data., Cell Rep, PMID 33626354

PXD019102 Dataset with its publication pending (from PRIDE)
Dataset title: Screen Identifies DYRK1B Network as Mediator of Transcription Repression on Damaged Chromatin
Possible reference: Dong, C. et al. (2020) Screen identifies DYRK1B network as mediator of transcription repression on damaged chromatin., Proc Natl Acad Sci U S A, PMID 32611815

PXD019098 Dataset with its publication pending (from PRIDE)
Dataset title: A systems approach delivers a functional 1 microRNA catalog and expanded targets for seizure suppression in temporal lobe epilepsy
Possible reference: Ven�, MT. et al. (2020) A systems approach delivers a functional microRNA catalog and expanded targets for seizure suppression in temporal lobe epilepsy., Proc Natl Acad Sci U S A, PMID 32581127

PXD019093 Dataset with its publication pending (from PRIDE)
Dataset title: Human DICER helicase domain recruits PKR and dsRNA binding proteins during viral infection
Possible reference: Montavon, TC. et al. (2021) Human DICER helicase domain recruits PKR and modulates its antiviral activity., PLoS Pathog, PMID 33984068

PXD019054 Dataset with its publication pending (from PRIDE)
Dataset title: Early cleavage of preimplantation embryos is regulated by tRNAGln-TTG-derived small RNAs present in mature spermatozoa
Possible reference: Chen, X. et al. (2020) Early cleavage of preimplantation embryos is regulated by tRNAGln-TTG-derived small RNAs present in mature spermatozoa., J Biol Chem, PMID 32487749

PXD019045 Dataset with its publication pending (from PRIDE)
Dataset title: Human HCC sample, phosphosites occupancy
Possible reference: Wang, Y. et al. (2020) A New Workflow for the Analysis of Phosphosite Occupancy in Paired Samples by Integration of Proteomics and Phosphoproteomics Data Sets., J Proteome Res, PMID 32786891

PXD019034 Dataset with its publication pending (from PRIDE)
Dataset title: Assembly defects of the human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia
Possible reference: Sekulovski, S. et al. (2021) Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia., Nat Commun, PMID 34584079

PXD019032 Dataset with its publication pending (from PRIDE)
Dataset title: A Cytoskeletal Protein Complex is Essential for Division of Intracellular Amastigotes of Leishmania mexicana (LAND-483 and LAND-536)
Possible reference: Kelly, FD. et al. (2020) A cytoskeletal protein complex is essential for division of intracellular amastigotes of Leishmania mexicana., J Biol Chem, PMID 32719012

PXD019031 Dataset with its publication pending (from PRIDE)
Dataset title: A Cytoskeletal Protein Complex is Essential for Division of Intracellular Amastigotes of Leishmania mexicana (LAN1416)
Possible reference: Kelly, FD. et al. (2020) A cytoskeletal protein complex is essential for division of intracellular amastigotes of Leishmania mexicana., J Biol Chem, PMID 32719012

PXD019020 Dataset with its publication pending (from PRIDE)
Dataset title: Systematic analysis of IL-17 receptor signalosome reveals a robust regulatory feedback loop
Possible reference: Draberova, H. et al. (2020) Systematic analysis of the IL-17 receptor signalosome reveals a robust regulatory feedback loop., EMBO J, PMID 32696476

PXD019013 Dataset with its publication pending (from iProX)
Dataset title: iTRAQ proteomic analysis of I. multifiliis
Possible reference: Yao, JY. et al. (2017) Proteomic analysis of differentially expressed proteins in the two developmental stages of Ichthyophthirius multifiliis., Parasitol Res, PMID 27864673

PXD019012 Dataset with its publication pending (from PRIDE)
Dataset title: Genome-wide effects of the antimicrobial peptide apidaecin on translation termination
Possible reference: Mangano, K. et al. (2020) Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria., Elife, PMID 33031031

PXD018998 no publication (from MassIVE)
Dataset title: Enabling Routine MHC-II Associated Peptide ProteomicS (MAPPs) for Risk Assessment of Drug-Induced Immunogenicity
Possible reference: Steiner, G. et al. (2020) Enabling Routine MHC-II-Associated Peptide Proteomics for Risk Assessment of Drug-Induced Immunogenicity., J Proteome Res, PMID 32786679

PXD018995 Dataset with its publication pending (from PRIDE)
Dataset title: SIRT3 interactions and mitochondrial proteome during HCMV infection
Possible reference: Sheng, X. et al. (2021) The antiviral sirtuin 3 bridges protein acetylation to mitochondrial integrity and metabolism during human cytomegalovirus infection., PLoS Pathog, PMID 33857259

PXD018987 Dataset with its publication pending (from PRIDE)
Dataset title: Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo
Possible reference: M�teignier, LV. et al. (2021) Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo., Nucleic Acids Res, PMID 33398331

PXD018986 no publication (from MassIVE)
Dataset title: The effect of pathogen inactivation on cryoprecipitate: A functional and quantitative evaluation
Possible reference: Kamyszek, RW. et al. (2020) The effect of pathogen inactivation on cryoprecipitate: a functional and quantitative evaluation., Blood Transfus, PMID 33000752

PXD018981 Dataset with its publication pending (from PRIDE)
Dataset title: Structure of the full kinetoplastids mitoribosome and insight on its large subunit maturation
Possible reference: Soufari, H. et al. (2020) Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis., Proc Natl Acad Sci U S A, PMID 33168716

PXD018967 Dataset with its publication pending (from PRIDE)
Dataset title: CreA phosphorylation sites are important for the regulation of carbon catabolite repression in filamentous fungi
Possible reference: de Assis, LJ. et al. (2021) Carbon Catabolite Repression in Filamentous Fungi Is Regulated by Phosphorylation of the Transcription Factor CreA., mBio, PMID 33402538

PXD018964 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated analysis of sialotranscriptome and sialoproteome of the brown dog tick Rhipicephalus sanguineus (s.l.): insights into gene expression during blood feeding
Possible reference: Tirloni, L. et al. (2020) Integrated analysis of sialotranscriptome and sialoproteome of the brown dog tick Rhipicephalus sanguineus (s.l.): Insights into gene expression during blood feeding., J Proteomics, PMID 32673754

PXD018959 Dataset with its publication pending (from jPOST)
Dataset title: A mass spectrometry-based antibody free approach enables the quantification of D-dimer in plasma
Possible reference: Zhang, N. et al. (2020) A Mass-Spectrometry-Based Antibody-Free Approach Enables the Quantification of D-Dimer in Plasma., J Proteome Res, PMID 32519545

PXD018958 no publication (from MassIVE)
Dataset title: Blood circulation of soft nanomaterials is governed by dynamic remodeling of protein opsonins at nanobiointerface
Possible reference: Abbina, S. et al. (2020) Blood circulation of soft nanomaterials is governed by dynamic remodeling of protein opsonins at nano-biointerface., Nat Commun, PMID 32546688

PXD018953 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analyses of the early stage of interaction between Caballeronia mineralivorans PML1(12) and mineral
Possible reference: Uroz, S. et al. (2020) Dual transcriptomics and proteomics analyses of the early stage of interaction between Caballeronia mineralivorans PML1(12) and mineral., Environ Microbiol, PMID 32656915

PXD018943 Dataset with its publication pending (from PRIDE)
Dataset title: Chromosome-level de novo assembly and annotation of pig-tailed (macaca nemestrina) macaque genome
Possible reference: Roodgar, M. et al. (2020) Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding., Gigascience, PMID 32649757

PXD018933 Dataset with its publication pending (from PRIDE)
Dataset title: Protein sequence comparison of human and non-human primate tooth proteomes
Possible reference: Froment, C. et al. (2021) Protein sequence comparison of human and non-human primate tooth proteomes., J Proteomics, PMID 33189847

PXD018915 Dataset with its publication pending (from PRIDE)
Dataset title: Heat-induced proteomes in tomato pollen mother cells
Possible reference: Thapa, P. et al. (2025) Cell-Type-Specific Heat-Induced Changes in the Proteomes of Pollen Mother Cells and Microspores Provide New Insights into Tomato Pollen Production Under Elevated Temperature., Proteomes, PMID 40265418

PXD018910 Dataset with its publication pending (from PRIDE)
Dataset title: Structure of the helicase core of Werner Helicase, a key target in microsatellite instability cancers
Possible reference: Newman, JA. et al. (2021) Structure of the helicase core of Werner helicase, a key target in microsatellite instability cancers., Life Sci Alliance, PMID 33199508

PXD018905 Dataset with its publication pending (from PRIDE)
Dataset title: Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs
Possible reference: Nováček, V. et al. (2020) Accurate prediction of kinase-substrate networks using knowledge graphs., PLoS Comput Biol, PMID 33270624

PXD018894 Dataset with its publication pending (from PRIDE)
Dataset title: CALCOCO1 acts with VAMP-Associated Proteins to mediate ER-phagy
Possible reference: Nthiga, TM. et al. (2020) CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy., EMBO J, PMID 32525583

PXD018873 Dataset with its publication pending (from PRIDE)
Dataset title: eEF2K activity determines synergy to PI3K and MEK inhibitors in combination in cancer cells
Possible reference: Hijazi, M. et al. (2022) eEF2K Activity Determines Synergy to Cotreatment of Cancer Cells With PI3K and MEK Inhibitors., Mol Cell Proteomics, PMID 35513296

PXD018865 Dataset with its publication pending (from PRIDE)
Dataset title: Mouse Muscle Stem Cell Proteome during Activation and CPEB1 Dependent Proteome in Mouse Muscle Stem Cell
Possible reference: Zeng, W. et al. (2022) CPEB1 directs muscle stem cell activation by reprogramming the translational landscape., Nat Commun, PMID 35177647

PXD018854 Dataset with its publication pending (from PRIDE)
Dataset title: Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae
Possible reference: Deng, L. et al. (2021) Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae., J Chromatogr B Analyt Technol Biomed Life Sci, PMID 33279813

PXD018848 Dataset with its publication pending (from PRIDE)
Dataset title: Systematic Analysis of the Lysine Crotonylome and multiple PTM analysis (acetylation, succinylation and crotonylation) in Candida albicans
Possible reference: Zhou, X. et al. (2021) Systematic Analysis of the Lysine Crotonylome and Multiple Posttranslational Modification Analysis (Acetylation, Succinylation, and Crotonylation) in Candida albicans., mSystems, PMID 33500332

PXD018812 Dataset with its publication pending (from PRIDE)
Dataset title: A cell competition-based drug screen identifies a novel compound that induces dual c-Myc degradation and p53 activation
Possible reference: Tadele, DS. et al. (2021) A cell competition-based small molecule screen identifies a novel compound that induces dual c-Myc depletion and p53 activation., J Biol Chem, PMID 33303632

PXD018797 Dataset with its publication pending (from iProX)
Dataset title: Signaling and Metabolic Pathways and Risk Scores of Protein Biomarkers in Pulmonary Arterial Hypertension - Integrated Multi-Omics Studies
Possible reference: Kheyfets, VO. et al. (2024) Identification of candidate biomarkers and molecular networks associated with Pulmonary Arterial Hypertension using machine learning and plasma multi-Omics analysis., medRxiv, PMID 39763543

PXD018785 Dataset with its publication pending (from PRIDE)
Dataset title: Modelling Plasticity and Dysplasia of Pancreatic Ductal Organoids Derived from Human Pluripotent Stem Cells
Possible reference: Breunig, M. et al. (2021) Modeling plasticity and dysplasia of pancreatic ductal organoids derived from human pluripotent stem cells., Cell Stem Cell, PMID 33915078

PXD018781 Dataset with its publication pending (from PRIDE)
Dataset title: Divergent features of the coenzyme Q:cytochrome c oxidoreductase complex in Toxoplasma gondii parasites
Possible reference: Hayward, JA. et al. (2021) Divergent features of the coenzyme Q:cytochrome c oxidoreductase complex in Toxoplasma gondii parasites., PLoS Pathog, PMID 33524071

PXD018759 no publication (from MassIVE)
Dataset title: Partial catalytic Cys oxidation of human GAPDH purified from human epithelial kidney cells
Possible reference: Lia, A. et al. (2020) Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid., Wellcome Open Res, PMID 32802964

PXD018754 Dataset with its publication pending (from PRIDE)
Dataset title: A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
Possible reference: Venturini, E. et al. (2020) A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence., Microlife, PMID 37223003

PXD018690 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding
Possible reference: Skrajna, A. et al. (2020) Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding., Nucleic Acids Res, PMID 32658293

PXD018676 no publication (from MassIVE)
Dataset title: TBL1XR1 MUTATIONS DRIVE EXTRANODAL LYMPHOMA BY INDUCING A PRO-TUMORIGENIC MEMORY FATE
Possible reference: Venturutti, L. et al. (2020) TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate., Cell, PMID 32619424

PXD018662 Dataset with its publication pending (from PRIDE)
Dataset title: USP9X controls the resolution of stalled ribosomes
Possible reference: Clancy, A. et al. (2021) The deubiquitylase USP9X controls ribosomal stalling., J Cell Biol, PMID 33507233

PXD018638 Dataset with its publication pending (from PRIDE)
Dataset title: AIM2 in regulatory T (Treg) cells restrains autoimmune diseases
Possible reference: Chou, WC. et al. (2021) AIM2 in regulatory T cells restrains autoimmune diseases., Nature, PMID 33505023

PXD018618 no publication (from MassIVE)
Dataset title: Functional proteome analysis of placenta membrane associated with preterm birth
Possible reference: Parry, S. et al. (2014) Maternal serum serpin B7 is associated with early spontaneous preterm birth., Am J Obstet Gynecol, PMID 24954659

PXD018605 no publication (from MassIVE)
Dataset title: Proteomic and transcriptomic patterns during lipid accumulation in the microalga Nannochloropsis gaditana
Possible reference: Hulatt, CJ. et al. (2020) Proteomic and Transcriptomic Patterns during Lipid Remodeling in Nannochloropsis gaditana., Int J Mol Sci, PMID 32971781

PXD018587 Dataset with its publication pending (from PRIDE)
Dataset title: Open database searching enables the identification and comparison of glycoproteomes without defining glycan compositions prior to searching
Possible reference: Ahmad Izaham, AR. et al. (2020) Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching., Mol Cell Proteomics, PMID 32576591

PXD018582 no publication (from MassIVE)
Dataset title: AXL CONFERS CELL MIGRATION AND INVASION BY HIJACKING A PEAK1-REGULATED FOCAL ADHESION PROTEIN NETWORK
Possible reference: Abu-Thuraia, A. et al. (2020) AXL confers cell migration and invasion by hijacking a PEAK1-regulated focal adhesion protein network., Nat Commun, PMID 32681075

PXD018580 Dataset with its publication pending (from PRIDE)
Dataset title: Tranylcypromine specificity for monoamine oxidase is limited by promiscuous protein labelling and lysosomal trapping
Possible reference: Drechsel, J. et al. (2020) Tranylcypromine specificity for monoamine oxidase is limited by promiscuous protein labelling and lysosomal trapping., RSC Chem Biol, PMID 34458760

PXD018566 Dataset with its publication pending (from PRIDE)
Dataset title: Rewiring of B cell receptor signaling by Epstein-Barr virus LMP2A
Possible reference: Fish, K. et al. (2020) Rewiring of B cell receptor signaling by Epstein-Barr virus LMP2A., Proc Natl Acad Sci U S A, PMID 33020271

PXD018530 Dataset with its publication pending (from PRIDE)
Dataset title: The PII protein-protein interaction network in Azospirillum brasilense reveals a novel role of PII in the control of c-di-GMP homeostasis
Possible reference: Gerhardt, ECM. et al. (2020) The Protein-Protein Interaction Network Reveals a Novel Role of the Signal Transduction Protein PII in the Control of c-di-GMP Homeostasis in Azospirillum brasilense., mSystems, PMID 33144311

PXD018528 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic changes of Klebsiella pneumoniae in response to colistin treatment and crrB mutation-mediated colistin resistance
Possible reference: Sun, L. et al. (2020) Proteomic Changes of Klebsiella pneumoniae in Response to Colistin Treatment and crrB Mutation-Mediated Colistin Resistance., Antimicrob Agents Chemother, PMID 32229491

PXD018460 Dataset with its publication pending (from PRIDE)
Dataset title: Peptidylarginine Deiminase inhibition abolishes the production of large extracellular vesicles from Giardia intestinalis, affecting host-pathogen interactions by hindering adhesion to host cells
Possible reference: Gavinho, B. et al. (2020) Peptidylarginine Deiminase Inhibition Abolishes the Production of Large Extracellular Vesicles From Giardia intestinalis, Affecting Host-Pathogen Interactions by Hindering Adhesion to Host Cells., Front Cell Infect Microbiol, PMID 33072615

PXD018433 no publication (from MassIVE)
Dataset title: Calsyntenin-3 directly interacts with both alpha- and beta-neurexins
Possible reference: Kim, H. et al. (2020) Calsyntenin-3 interacts with both α- and β-neurexins in the regulation of excitatory synaptic innervation in specific Schaffer collateral pathways., J Biol Chem, PMID 32434929

PXD018415 no publication (from MassIVE)
Dataset title: Essential roles for deubiquitination in Leishmania life cycle progression
Possible reference: Damianou, A. et al. (2020) Essential roles for deubiquitination in Leishmania life cycle progression., PLoS Pathog, PMID 32544189

PXD018411 Dataset with its publication pending (from PRIDE)
Dataset title: FLEXIQuant-LF: Robust Regression to quantify protein modification extent in label-free proteomics data
Possible reference: Schlaffner, CN. et al. (2020) FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data., Elife, PMID 33284109

PXD018382 Dataset with its publication pending (from PRIDE)
Dataset title: Mycobacteria tolerate carbon monoxide by remodelling their respiratory chain
Possible reference: Bayly, K. et al. (2021) Mycobacteria Tolerate Carbon Monoxide by Remodeling Their Respiratory Chain., mSystems, PMID 33975973

PXD018375 Dataset with its publication pending (from PRIDE)
Dataset title: Global mapping of Salmonella enterica-host protein-protein interactions during infection
Possible reference: Walch, P. et al. (2021) Global mapping of Salmonella enterica-host protein-protein interactions during infection., Cell Host Microbe, PMID 34237247

PXD018356 no publication (from MassIVE)
Dataset title: Phosphopeptides identified on SPEG
Possible reference: Guo, H. et al. (2017) Exercise-responsive phosphoproteins in the heart., J Mol Cell Cardiol, PMID 28826663

PXD018353 Dataset with its publication pending (from PRIDE)
Dataset title: Altered N-glycan composition impacts flagella mediated adhesion in Chlamydomonas reinhardtii
Possible reference: Xu, N. et al. (2020) Altered N-glycan composition impacts flagella-mediated adhesion in Chlamydomonas reinhardtii., Elife, PMID 33300874

PXD018352 Dataset with its publication pending (from PRIDE)
Dataset title: Niche stiffening compromises stem cell potential during aging by reducing chromatin accessibility at bivalent promoters
Possible reference: Koester, J. et al. (2021) Niche stiffening compromises hair follicle stem cell potential during ageing by reducing bivalent promoter accessibility., Nat Cell Biol, PMID 34239060

PXD018341 no publication (from MassIVE)
Dataset title: whole-organ mucosal profile of human bladder
Possible reference: Lee, S. et al. (2025) Dysregulated mitochondrial energy metabolism drives the progression of mucosal field effects to invasive bladder cancer., J Pathol, PMID 40996337

PXD018335 no publication (from MassIVE)
Dataset title: Integrative analysis of proteome and transcriptome dynamics during Bacillus subtilis spore revival
Possible reference: Swarge, B. et al. (2020) Integrative Analysis of Proteome and Transcriptome Dynamics during Bacillus subtilis Spore Revival., mSphere, PMID 32759332

PXD018306 Dataset with its publication pending (from PRIDE)
Dataset title: Cardiac organoids reveal mechanisms of human cardiogenesis
Possible reference: Rufaihah, AJ. et al. (2021) Mending a broken heart: In vitro, in vivo and in silico models of congenital heart disease., Dis Model Mech, PMID 33787508

PXD018295 Dataset with its publication pending (from PRIDE)
Dataset title: Improvements on the quantitative analysis of Trypanosoma cruzi histone post translational modifications
Possible reference: de Lima, LP. et al. (2020) Improvements on the quantitative analysis of Trypanosoma cruzi histone post translational modifications: Study of changes in epigenetic marks through the parasite's metacyclogenesis and life cycle., J Proteomics, PMID 32480077

PXD018243 Dataset with its publication pending (from iProX)
Dataset title: Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment
Possible reference: Liu, J. et al. (2020) Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment., Sci Rep, PMID 32913333

PXD018229 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of coagulation factor IX in bioreactor cell culture media predicts yield and quality of purified product
Possible reference: Zacchi, LF. et al. (2021) Coagulation factor IX analysis in bioreactor cell culture supernatant predicts quality of the purified product., Commun Biol, PMID 33758337

PXD018198 Dataset with its publication pending (from jPOST)
Dataset title: Proteome of rice plasma membrane in leaf sheath
Possible reference: Iwasaki, Y. et al. (2020) Proteomics Analysis of Plasma Membrane Fractions of the Root, Leaf, and Flower of Rice., Int J Mol Sci, PMID 32977500

PXD018194 Dataset with its publication pending (from PRIDE)
Dataset title: Mouse mitochondrial CLPP substrate identification
Possible reference: Hofsetz, E. et al. (2020) The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis., Mol Cell Proteomics, PMID 32467259

PXD018190 Dataset with its publication pending (from PRIDE)
Dataset title: BRAF mutations disrupt the hypothalamo-pituitary axis leading to hypopituitarism in mouse and humans
Possible reference: Gualtieri, A. et al. (2021) Activating�mutations in BRAF�disrupt the hypothalamo-pituitary axis leading to hypopituitarism in mice and humans., Nat Commun, PMID 33795686

PXD018179 Dataset with its publication pending (from PRIDE)
Dataset title: Differential expression pattern of the proteome in response to cadmium stress based on proteomics analysis of wheat roots
Possible reference: Jian, M. et al. (2020) Differential expression pattern of the proteome in response to cadmium stress based on proteomics analysis of wheat roots., BMC Genomics, PMID 32380942

PXD018153 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome dynamics in persisting and resuscitating bacterial cells
Possible reference: Mishra, A. et al. (2018) Proteomic analysis of hydroxyl radical-induced resuscitation of hypoxia-induced dormant mycobacterial cells., Int J Mycobacteriol, PMID 29516880

PXD018101 no publication (from MassIVE)
Dataset title: Proteomic Mapping of multifunctional complexes in triatomine Saliva
Possible reference: Santiago, PB. et al. (2020) Proteomic Mapping of Multifunctional Complexes Within Triatomine Saliva., Front Cell Infect Microbiol, PMID 32984079

PXD018081 Dataset with its publication pending (from jPOST)
Dataset title: Metaproteomics of microbial community in the fermented rice for melanogenesis inhibitor synthesis
Possible reference: Sangkaew, O. et al. (2020) Metaproteomic investigation of functional insight into special defined microbial starter on production of fermented rice with melanogenesis inhibition activity., PLoS One, PMID 33147601

PXD018029 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome mapping of human gingival tissue in health and disease
Possible reference: Bao, K. et al. (2020) Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease., Front Cell Infect Microbiol, PMID 33117738

PXD018015 Dataset with its publication pending (from PRIDE)
Dataset title: A unique cell wall synthetic response evoked by glucosamine determines pathogenicity-associated fungal cellular differentiation
Possible reference: Hu, P. et al. (2021) A unique cell wall synthetic response evoked by glucosamine determines pathogenicity-associated fungal cellular differentiation., PLoS Genet, PMID 34624015

PXD017980 no publication (from MassIVE)
Dataset title: Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins
Possible reference: Lee, C. et al. (2020) Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins., Elife, PMID 33263282

PXD017976 Dataset with its publication pending (from PRIDE)
Dataset title: Platelets fuel the inflammasome activation of innate immune cells
Possible reference: Rolfes, V. et al. (2020) Platelets Fuel the Inflammasome Activation of Innate Immune Cells., Cell Rep, PMID 32402278

PXD017971 Dataset with its publication pending (from PRIDE)
Dataset title: The lytic polysaccharide monooxygenase of Pseudomonas aeruginosa promotes bacterial survival during systemic infection
Possible reference: Askarian, F. et al. (2021) The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection., Nat Commun, PMID 33623002

PXD017966 Dataset with its publication pending (from PRIDE)
Dataset title: Carbon source dependent reprograming of anaerobic metabolism in Staphylococcus aureus
Possible reference: Troitzsch, A. et al. (2021) Carbon Source-Dependent Reprogramming of Anaerobic Metabolism in Staphylococcus aureus., J Bacteriol, PMID 33526614

PXD017962 Dataset with its publication pending (from PRIDE)
Dataset title: The gain-of-function allele bamAE470K bypasses the essential requirement for BamD in Î²-barrel outer membrane protein assembly
Possible reference: Hart, EM. et al. (2020) The gain-of-function allele bamAE470K bypasses the essential requirement for BamD in β-barrel outer membrane protein assembly., Proc Natl Acad Sci U S A, PMID 32675245

PXD017952 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omics profiling of paired primary and recurrent glioblastoma patient tissues
Possible reference: Dekker, LJM. et al. (2020) Multiomics profiling of paired primary and recurrent glioblastoma patient tissues., Neurooncol Adv, PMID 32793885

PXD017951 Dataset with its publication pending (from PRIDE)
Dataset title: PrimPol primase mediates replication traverse of DNA interstrand crosslinks
Possible reference: Gonz�lez-Acosta, D. et al. (2021) PrimPol-mediated repriming facilitates replication traverse of DNA interstrand crosslinks., EMBO J, PMID 34128550

PXD017932 Dataset with its publication pending (from PRIDE)
Dataset title: Identification and quantification of small proteins and peptides in Staphylococcus aureus
Possible reference: Blankenburg, S. et al. (2019) Improving Proteome Coverage for Small Sample Amounts: An Advanced Method for Proteomics Approaches with Low Bacterial Cell Numbers., Proteomics, PMID 31532911

PXD017911 no publication (from MassIVE)
Dataset title: Dental calculus from archaeological sites in Africa
Possible reference: Buckley, S. et al. (2014) Dental calculus reveals unique insights into food items, cooking and plant processing in prehistoric central Sudan., PLoS One, PMID 25028938

PXD017891 Dataset with its publication pending (from PRIDE)
Dataset title: Optimization of skeletal protein preparation for LC-MS/MS sequencing yields additional coral skeletal proteins in Stylophora pistillata
Possible reference: Peled, Y. et al. (2020) Optimization of skeletal protein preparation for LC-MS/MS sequencing yields additional coral skeletal proteins in Stylophora pistillata., BMC Mater, PMID 32724895

PXD017883 no publication (from MassIVE)
Dataset title: S-nitrosylation in zebra fish tissue regeneration
Possible reference: Matrone, G. et al. (2021) Nuclear S-nitrosylation impacts tissue regeneration in zebrafish., Nat Commun, PMID 34725362

PXD017875 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of X-linked genes that drive sex differences in murine embryonic stem cells
Possible reference: Genolet, O. et al. (2021) Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach., Genome Biol, PMID 33863351

PXD017870 Dataset with its publication pending (from PRIDE)
Dataset title: Membrane proteome of L. amazonensis PH8 and LV79 strains
Possible reference: Tano, FT. et al. (2022) Proteome and morphological analysis show unexpected differences between promastigotes of Leishmania amazonensis PH8 and LV79 strains., PLoS One, PMID 35998173

PXD017848 Dataset with its publication pending (from PRIDE)
Dataset title: Pilot evaluation of two Fasciola hepatica biomarkers for supporting TCBZ efficacy diagnostics
Possible reference: Collett, CF. et al. (2020) Pilot Evaluation of Two Fasciola hepatica Biomarkers for Supporting Triclabendazole (TCBZ) Efficacy Diagnostics., Molecules, PMID 32751696

PXD017835 Dataset with its publication pending (from PRIDE)
Dataset title: Antioxidant mechanism of glutaredoxins and their role in symbiotic nitrogen fixation in Rhizobium leguminosarum bv. viciae 3841
Possible reference: Zou, Q. et al. (2021) Antioxidant ability of glutaredoxins and their role in symbiotic nitrogen fixation in Rhizobium leguminosarum bv. viciae 3841., Appl Environ Microbiol, PMID 33277272

PXD017825 Dataset with its publication pending (from PRIDE)
Dataset title: Peptidomics of sorted enteroendocrine cells from human organoids
Possible reference: Alcaino, C. et al. (2025) Mechanisms of Activation and Serotonin Release From Human Enterochromaffin Cells., Cell Mol Gastroenterol Hepatol, PMID 40812684

PXD017734 Dataset with its publication pending (from PRIDE)
Dataset title: Histoplasma capsulatum lipid map
Possible reference: Huang, JH. et al. (2015) CR3 and Dectin-1 Collaborate in Macrophage Cytokine Response through Association on Lipid Rafts and Activation of Syk-JNK-AP-1 Pathway., PLoS Pathog, PMID 26132276

PXD017721 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics profiling of KAIMRC1 in comparison to MDA-MB231 and MCF-7
Possible reference: Alghanem, B. et al. (2020) Proteomics Profiling of KAIMRC1 in Comparison to MDA-MB231 and MCF-7., Int J Mol Sci, PMID 32570693

PXD017720 Dataset with its publication pending (from PRIDE)
Dataset title: High-throughput proteotyping based on microplate paramagnetic beads and phylopeptidomics
Possible reference: Hayoun, K. et al. (2020) High-throughput proteotyping of bacterial isolates by double barrel chromatography-tandem mass spectrometry based on microplate paramagnetic beads and phylopeptidomics., J Proteomics, PMID 32619772

PXD017715 Dataset with its publication pending (from PRIDE)
Dataset title: Long-term effects on the transcriptome and proteome in Sprague Dawley rat thyroid and plasma after internal low dose 131I exposure
Possible reference: Larsson, M. et al. (2020) Long-term transcriptomic and proteomic effects in Sprague Dawley rat thyroid and plasma after internal low dose 131I exposure., PLoS One, PMID 33382739

PXD017709 Dataset with its publication pending (from PRIDE)
Dataset title: Anaerobic sulfur oxidation underlies adaptation of a chemosynthetic symbiont to oxic-anoxic interfaces
Possible reference: Paredes, GF. et al. (2021) Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces., mSystems, PMID 34058098

PXD017708 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics reveals rapid divergence in the postmating response of female reproductive tracts among sibling species
Possible reference: McCullough, EL. et al. (2020) Quantitative proteomics reveals rapid divergence in the postmating response of female reproductive tracts among sibling species., Proc Biol Sci, PMID 32576111

PXD017699 Dataset with its publication pending (from PRIDE)
Dataset title: Cul4b promotes CD4 T cell expansion by aiding the repair of damaged DNA
Possible reference: Dar, AA. et al. (2021) The E3 ubiquitin ligase Cul4b promotes CD4+ T cell expansion by aiding the repair of damaged DNA., PLoS Biol, PMID 33524014

PXD017658 Dataset with its publication pending (from PRIDE)
Dataset title: MAX-mutant small cell lung cancers exhibit impaired activities of MGA-dependent ncPRC1.6.
Possible reference: Llabata, P. et al. (2021) MAX mutant small-cell lung cancers exhibit impaired activities of MGA-dependent noncanonical polycomb repressive complex., Proc Natl Acad Sci U S A, PMID 34493659

PXD017639 Dataset with its publication pending (from PRIDE)
Dataset title: Isolation window optimization using predicted libraries for deep and accurate proteome profiling by data-independent acquisition
Possible reference: Doellinger, J. et al. (2020) Isolation Window Optimization of Data-Independent Acquisition Using Predicted Libraries for Deep and Accurate Proteome Profiling., Anal Chem, PMID 32840101

PXD017622 Dataset with its publication pending (from PRIDE)
Dataset title: A divergent cyclin/cyclin-dependent kinase complex controls the atypical replication of Plasmodium berghei during gametogony and parasite transmission.
Possible reference: Balestra, AC. et al. (2020) A divergent cyclin/cyclin-dependent kinase complex controls the atypical replication of a malaria parasite during gametogony and transmission., Elife, PMID 32568069

PXD017618 Dataset with its publication pending (from PRIDE)
Dataset title: ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment
Possible reference: Lima, DB. et al. (2021) ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment., Bioinformatics, PMID 33165572

PXD017599 no publication (from MassIVE)
Dataset title: Age-induced methylmalonic acid accumulation promotes cancer aggressiveness and metastatic disease
Possible reference: Gomes, AP. et al. (2020) Age-induced accumulation of methylmalonic acid promotes tumour progression., Nature, PMID 32814897

PXD017542 Dataset with its publication pending (from PRIDE)
Dataset title: Production and application of recombinant extracellular vesicles for method development, data normalization and assessment of pre-analytical variables
Possible reference: Geeurickx, E. et al. (2021) Recombinant extracellular vesicles as biological reference material for method development, data normalization and assessment of (pre-)analytical variables., Nat Protoc, PMID 33452501

PXD017517 Dataset with its publication pending (from PRIDE)
Dataset title: Inhibitor of Differentiation 4 (ID4) represses myoepithelial differentiation of mammary stem cells through its interaction with HEB
Possible reference: Holliday, H. et al. (2021) Inhibitor of Differentiation 4 (ID4) represses mammary myoepithelial differentiation via inhibition of HEB., iScience, PMID 33554073

PXD017489 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics support the threespine stickleback egg coat as a protective oocyte envelope
Possible reference: Killingbeck, EE. et al. (2021) Proteomics support the threespine stickleback egg coat as a protective oocyte envelope., Mol Reprod Dev, PMID 34148267

PXD017488 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics support the threespine stickleback egg coat as a protective oocyte envelope
Possible reference: Killingbeck, EE. et al. (2021) Proteomics support the threespine stickleback egg coat as a protective oocyte envelope., Mol Reprod Dev, PMID 34148267

PXD017475 Dataset with its publication pending (from PRIDE)
Dataset title: The lncRNA MIR31HG regulates the senescence associated secretory phenotype
Possible reference: Montes, M. et al. (2021) The long non-coding RNA MIR31HG regulates the senescence associated secretory phenotype., Nat Commun, PMID 33911076

PXD017445 Dataset with its publication pending (from PRIDE)
Dataset title: A chemical screen reveals a connection between lipid metabolism and protein translation
Possible reference: Touchette, MH. et al. (2017) A Screen for Protein-Protein Interactions in Live Mycobacteria Reveals a Functional Link between the Virulence-Associated Lipid Transporter LprG and the Mycolyltransferase Antigen 85A., ACS Infect Dis, PMID 28276676

PXD017435 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of the promotive effect of plant-derived smoke on soybean
Possible reference: Zhong, Z. et al. (2020) Plant-derived smoke enhances plant growth through ornithine-synthesis pathway and ubiquitin-proteasome pathway in soybean., J Proteomics, PMID 32294531

PXD017419 Dataset with its publication pending (from PRIDE)
Dataset title: Thermal proteome profiling on zebrafish using napabucasin
Possible reference: Leijten, NM. et al. (2021) Thermal Proteome Profiling in Zebrafish Reveals Effects of Napabucasin on Retinoic Acid Metabolism., Mol Cell Proteomics, PMID 33594990

PXD017388 Tong Zhang, Matthew J. Gaffrey, Dennis G. Thomas, Thomas J. Weber, Becky M. Hess, Karl K.Weitz, Paul D. Piehowski, Vladislav A. Petyuk, Ronald J. Moore, Wei-Jun Qian, and Brian D. Thrall. A proteome-wide assessment of the oxidative stress paradigm for met (from MassIVE)
Dataset title: Reproducible label-free quantitative proteomics profiling cellular responses to engineered nanomaterials
Possible reference: Zhang, T. et al. (2020) Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling., J Proteome Res, PMID 32407631

PXD017387 no publication (from MassIVE)
Dataset title: Enhancing Intracellular Concentration and Target Engagement of PROTACs with Reversible Covalent Chemistry
Possible reference: Rigby, E. et al. (2026) Inducing TRIB2-targeted protein degradation to reverse chemoresistance in acute myeloid leukaemia., Biochem J, PMID 41823345

PXD017379 Dataset with its publication pending (from PRIDE)
Dataset title: New insights into the architecture of the human SMC5/6 complex
Possible reference: Bonato, A. et al. (2025) Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search., Nucleic Acids Res, PMID 40744502

PXD017374 Dataset with its publication pending (from PRIDE)
Dataset title: Differential expressed proteins between Mycoplasma bovis different strains
Possible reference: Khan, FA. et al. (2018) Proteomics identification and characterization of MbovP730 as a potential DIVA antigen of Mycoplasma bovis., Oncotarget, PMID 29983863

PXD017350 Dataset with its publication pending (from PRIDE)
Dataset title: Changes in bovine Lymphocyte proteome after stimulation with pokeweed mitogen
Possible reference: Kleinwort, KJH. et al. (2022) Bovine Peripheral Blood Derived Lymphocyte Proteome and Secretome Show Divergent Reaction of Bovine Immune Phenotypes after Stimulation with Pokeweed Mitogen., Proteomes, PMID 35225986

PXD017344 Dataset with its publication pending (from PRIDE)
Dataset title: Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation
Possible reference: Barnes, CE. et al. (2022) Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation., Mol Omics, PMID 34709266

PXD017343 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of CD5 signalosome in primary T cells
Possible reference: Voisinne, G. et al. (2016) Co-recruitment analysis of the CBL and CBLB signalosomes in primary T cells identifies CD5 as a key regulator of TCR-induced ubiquitylation., Mol Syst Biol, PMID 27474268

PXD017298 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of gene fusion events in Mycobacterium tuberculosis that encode novel chimeric proteins
Possible reference: Gallant, J. et al. (2020) Identification of gene fusion events in Mycobacterium tuberculosis that encode chimeric proteins., NAR Genom Bioinform, PMID 33575588

PXD017295 no publication (from MassIVE)
Dataset title: Mitophagy effector FUNDC1 controls mitochondrial reprogramming and cellular plasticity
Possible reference: Li, J. et al. (2020) The mitophagy effector FUNDC1 controls mitochondrial reprogramming and cellular plasticity in cancer cells., Sci Signal, PMID 32723812

PXD017292 Dataset with its publication pending (from PRIDE)
Dataset title: B-cell-specific MYD88 L252P expression causes a premalignant gammopathy resembling IgM MGUS
Possible reference: Schmidt, K. et al. (2020) B-Cell-Specific Myd88 L252P Expression Causes a Premalignant Gammopathy Resembling IgM MGUS., Front Immunol, PMID 33343574

PXD017277 Dataset with its publication pending (from PRIDE)
Dataset title: Succession of Bifidobacterium longum strains in response to a changing early life nutritional environment reveals dietary substrate adaptations
Possible reference: Kujawska, M. et al. (2020) Succession of Bifidobacterium longum Strains in Response to a Changing Early Life Nutritional Environment Reveals Dietary Substrate Adaptations., iScience, PMID 32721872

PXD017275 Dataset with its publication pending (from PRIDE)
Dataset title: Eudiplozoon nipponicum (Monogenea) - tissue specific proteome of parasitic worm
Possible reference: Roudnick�, P. et al. (2020) Laser capture microdissection in combination with mass spectrometry: Approach to characterization of tissue-specific proteomes of Eudiplozoon nipponicum (Monogenea, Polyopisthocotylea)., PLoS One, PMID 32555742

PXD017261 Dataset with its publication pending (from PRIDE)
Dataset title: DIFFERENTIATION-DEPENDENT SUSCEPTIBILITY OF HUMAN MUSCLE CELLS TO ZIKA VIRUS INFECTION
Possible reference: Legros, V. et al. (2020) Differentiation-dependent susceptibility of human muscle cells to Zika virus infection., PLoS Negl Trop Dis, PMID 32817655

PXD017256 no publication (from MassIVE)
Dataset title: Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling
Possible reference: Amar, M. et al. (2021) Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling., Mol Psychiatry, PMID 33727673

PXD017249 Dataset with its publication pending (from jPOST)
Dataset title: Comparative proteomic analysis of protein methylation provides insight into the resistance of hepatocellular carcinoma to 5-fluorouracil
Possible reference: Liu, Z. et al. (2020) Comparative proteomic analysis of protein methylation provides insight into the resistance of hepatocellular carcinoma to 5-fluorouracil., J Proteomics, PMID 32198070

PXD017219 Dataset with its publication pending (from PRIDE)
Dataset title: Protein Tyrosine Phosphatase SHP2 Controls Interleukin-8 Expression in Breast Cancer Cells
Possible reference: Amante, RJ. et al. (2022) Protein Tyrosine Phosphatase SHP2 Controls Interleukin-8 Expression in Breast Cancer Cells., J Mammary Gland Biol Neoplasia, PMID 35739379

PXD017199 Dataset with its publication pending (from PRIDE)
Dataset title: DECIPHERING THE SIGNALING NETWORK LANDSCAPE OF BREAST CANCER IMPROVES DRUG SENSITIVITY PREDICTION
Possible reference: Tognetti, M. et al. (2021) Deciphering the signaling network of breast cancer improves drug sensitivity prediction., Cell Syst, PMID 33932331

PXD017198 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation of protein purification techniques and effects of storage duration on LC-MS/MS analysis of archived FFPE human CRC tissues
Possible reference: Rossouw, SC. et al. (2021) Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues., Pathol Oncol Res, PMID 34257588

PXD017170 Dataset with its publication pending (from PRIDE)
Dataset title: Hepatocyte-specific knockout of Nicotinamide phosphoribosyltransferase increases susceptibility for liver fibrosis in mice
Possible reference: Dall, M. et al. (2021) Hepatocyte-specific perturbation of NAD+ biosynthetic pathways in mice induces reversible nonalcoholic steatohepatitis-like phenotypes., J Biol Chem, PMID 34762911

PXD017159 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamics in protein translation sustaining T cell preparedness
Possible reference: Wolf, T. et al. (2020) Dynamics in protein translation sustaining T cell preparedness., Nat Immunol, PMID 32632289

PXD017129 Dataset with its publication pending (from PRIDE)
Dataset title: Serum proteome profiling in canine chronic valve disease using TMT-based quantitative proteomics
Possible reference: Kuleš, J. et al. (2020) Serum proteome profiling in canine chronic valve disease using a TMT-based quantitative proteomics approach., J Proteomics, PMID 32422277

PXD017088 Dataset with its publication pending (from PRIDE)
Dataset title: The integrin linked kinase is required for chemokine-triggered high affinity conformation of the leukocyte Î²2-integrin LFA-1The integrin linked kinase is required for chemokine-triggered high affinity conformation of the leukocyte Î²2-integrin LFA-1
Possible reference: Margraf, A. et al. (2020) The integrin-linked kinase is required for chemokine-triggered high-affinity conformation of the neutrophil β2-integrin LFA-1., Blood, PMID 32730588

PXD017074 Dataset with its publication pending (from iProX)
Dataset title: protein partners of novel shell matrix proteins of Mytilus coruscus
Possible reference: Jiang, Y. et al. (2020) Molecular characterization of a whirlin-like protein with biomineralization-related functions from the shell of Mytilus coruscus., PLoS One, PMID 32267882

PXD017067 Dataset with its publication pending (from PRIDE)
Dataset title: The dynamic surface proteome of allergenic fungal conidia
Possible reference: Blango, MG. et al. (2020) Dynamic Surface Proteomes of Allergenic Fungal Conidia., J Proteome Res, PMID 32233371

PXD017066 Dataset with its publication pending (from PRIDE)
Dataset title: Improving identification of in-organello protein-protein interactions using an affinity-enrichable, isotopically-coded, and mass spectrometry-cleavable chemical crosslinker
Possible reference: Makepeace, KAT. et al. (2020) Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker., Mol Cell Proteomics, PMID 32051233

PXD016995 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Analysis of Proteins Downstream of Autism-Associated Gene DIXDC1
Possible reference: Kwan, V. et al. (2021) Proteomic Analysis Reveals Autism-Associated Gene DIXDC1 Regulates Proteins Associated with Mitochondrial Organization and Function., J Proteome Res, PMID 33337894

PXD016976 Dataset with its publication pending (from PanoramaPublic)
Dataset title: Mass Spectrometry-GUided Immunoassay DEvelopment (MS-GUIDE)
Possible reference: Goetze, S. et al. (2022) Use of MS-GUIDE for identification of protein biomarkers for risk stratification of patients with prostate cancer., Clin Proteomics, PMID 35477343

PXD016962 Dataset with its publication pending (from PRIDE)
Dataset title: Genome-scale transcription-translation mapping reveals features of Zymomonas mobilis transcription units and promoters
Possible reference: Vera, JM. et al. (2020) Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters., mSystems, PMID 32694125

PXD016952 no publication (from MassIVE)
Dataset title: Exoproteome of Parascedosporium putredinis NO1 during on wheat straw
Possible reference: Leadbeater, DR. et al. (2025) Comparative exo-proteomics of solid and submerged state fermentation using the lignocellulose degrading Ascomycete Parascedosporium putredinis NO1., Bioresour Technol, PMID 40550366

PXD016943 Dataset with its publication pending (from PRIDE)
Dataset title: Nematostella toxins expression under stress
Possible reference: Nicosia, A. et al. (2014) Characterization of small HSPs from Anemonia viridis reveals insights into molecular evolution of alpha crystallin genes among cnidarians., PLoS One, PMID 25251681

PXD016925 Dataset with its publication pending (from PRIDE)
Dataset title: Sarcoptes scabiei ES proteomics
Possible reference: Randall, TA. et al. (2017) Proteases of Dermatophagoides pteronyssinus., Int J Mol Sci, PMID 28587273

PXD016914 Dataset with its publication pending (from PRIDE)
Dataset title: Design and experimental evaluation of a minimal, innocuous watermarking strategy to distinguish near-identical DNA and RNA sequences
Possible reference: Boonekamp, FJ. et al. (2020) Design and Experimental Evaluation of a Minimal, Innocuous Watermarking Strategy to Distinguish Near-Identical DNA and RNA Sequences., ACS Synth Biol, PMID 32413257

PXD016907 Dataset with its publication pending (from jPOST)
Dataset title: Limited impact of cytoplasmic mRNA recapping on proteome complexity
Possible reference: Agana, BA. et al. (2020) Cytoplasmic mRNA recapping has limited impact on proteome complexity., Open Biol, PMID 33234072

PXD016905 no publication (from MassIVE)
Dataset title: Noise exposures causing hearing loss generate proteotoxic stress and activate the proteostasis network
Possible reference: Jongkamonwiwat, N. et al. (2020) Noise Exposures Causing Hearing Loss Generate Proteotoxic Stress and Activate the Proteostasis Network., Cell Rep, PMID 33238128

PXD016894 Dataset with its publication pending (from jPOST)
Dataset title: Comparative phosphoproteomic analysis of raf36raf22 in Arabidopsis
Possible reference: Kamiyama, Y. et al. (2021) Arabidopsis group C Raf-like protein kinases negatively regulate abscisic acid signaling and are direct substrates of SnRK2., Proc Natl Acad Sci U S A, PMID 34282011

PXD016890 no publication (from MassIVE)
Dataset title: Effects of mobile phone electromagnetic radiation on rat hippocampus proteome
Possible reference: Singh, KV. et al. (2022) Effects of mobile phone electromagnetic radiation on rat hippocampus proteome., Environ Toxicol, PMID 34984797

PXD016863 Dataset with its publication pending (from PRIDE)
Dataset title: Encystation deep proteome of Giardia duodenalis
Possible reference: Balan, B. et al. (2021) Multimodal regulation of encystation in Giardia duodenalis revealed by deep proteomics., Int J Parasitol, PMID 34331939

PXD016861 Dataset with its publication pending (from PRIDE)
Dataset title: Role of Specialized Composition of SWI/SNF Complexes in Prostate Cancer Lineage Plasticity
Possible reference: Cyrta, J. et al. (2020) Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity., Nat Commun, PMID 33144576

PXD016855 no publication (from MassIVE)
Dataset title: Cerebral organoids model neocortical development disrupted by 16p11.2 CNV in autism
Possible reference: Urresti, J. et al. (2021) Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism., Mol Psychiatry, PMID 34433918

PXD016790 Dataset with its publication pending (from PRIDE)
Dataset title: MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) Human HCC proteomics
Possible reference: Wang, H. et al. (2021) An Integrated Transcriptomics and Proteomics Analysis Implicates lncRNA MALAT1 in the Regulation of Lipid Metabolism., Mol Cell Proteomics, PMID 34478876

PXD016776 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin
Possible reference: Saei, AA. et al. (2020) Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin., Redox Biol, PMID 32199331

PXD016772 Dataset with its publication pending (from PRIDE)
Dataset title: Npl3 stabilizes R-loops at telomeres to prevent accelerated replicative senescence
Possible reference: P�rez-Mart�nez, L. et al. (2020) Npl3 stabilizes R-loops at telomeres to prevent accelerated replicative senescence., EMBO Rep, PMID 32026548

PXD016770 no publication (from MassIVE)
Dataset title: Generation of aggregates of alpha-lactalbumin by UV-B light exposure
Possible reference: Zhao, Z. et al. (2020) Generation of Aggregates of α-Lactalbumin by UV-B Light Exposure., J Agric Food Chem, PMID 32396720

PXD016766 Dataset with its publication pending (from PRIDE)
Dataset title: Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics
Possible reference: Yu, Q. et al. (2020) Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics., Anal Chem, PMID 32250601

PXD016752 no publication (from MassIVE)
Dataset title: Cross-linking modifications of HDL apoproteins by oxidized phospholipids: Structural characterization, in vivo detection, and functional implications
Possible reference: Gao, D. et al. (2020) Cross-linking modifications of HDL apoproteins by oxidized phospholipids: structural characterization, in vivo detection, and functional implications., J Biol Chem, PMID 31907281

PXD016714 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of KARS knockout zebrafish larvae
Possible reference: Wang, J. et al. (2025) Proteomic profiling of kars knockout zebrafish larvae., Gene, PMID 40032059

PXD016664 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of bronchoalveolar lavage fluid during invasive pulmonary aspergillosis in mice and humans
Possible reference: Machata, S. et al. (2020) Proteome analysis of bronchoalveolar lavage fluids reveals host and fungal proteins highly expressed during invasive pulmonary aspergillosis in mice and humans., Virulence, PMID 33043780

PXD016638 Dataset with its publication pending (from PRIDE)
Dataset title: Dissecting the mechanism of signaling-triggered nuclear export of newly synthesized influenza virus ribonucleoprotein complexes
Possible reference: Schreiber, A. et al. (2020) Dissecting the mechanism of signaling-triggered nuclear export of newly synthesized influenza virus ribonucleoprotein complexes., Proc Natl Acad Sci U S A, PMID 32601201

PXD016630 Dataset with its publication pending (from PRIDE)
Dataset title: HIF-1Î± and HIF-2Î± differently regulate tumour development, metabolism and inflammation of clear cell renal cell carcinoma in mice
Possible reference: Hoefflin, R. et al. (2020) HIF-1α and HIF-2α differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice., Nat Commun, PMID 32807776

PXD016608 no publication (from MassIVE)
Dataset title: The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors
Possible reference: Gebregiworgis, T. et al. (2021) The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors., Nat Commun, PMID 34725361

PXD016591 Dataset with its publication pending (from PRIDE)
Dataset title: Functional Analysis of the Francisella Lysine Decarboxylase
Possible reference: Felix, J. et al. (2021) Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance., Sci Rep, PMID 33441661

PXD016590 Dataset with its publication pending (from PRIDE)
Dataset title: Desulfoluna protein expression analysis
Possible reference: Liu, J. et al. (2020) Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor., Appl Environ Microbiol, PMID 31836581

PXD016558 no publication (from MassIVE)
Dataset title: EGFR inhibition triggers an adaptive response by co-opting antiviral signaling pathways in lung cancer
Possible reference: Gong, K. et al. (2020) EGFR inhibition triggers an adaptive response by co-opting antiviral signaling pathways in lung cancer., Nat Cancer, PMID 33269343

PXD016536 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes
Possible reference: Song, T. et al. (2020) Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes., PeerJ, PMID 33384895

PXD016523 Dataset with its publication pending (from PRIDE)
Dataset title: Precise temporal regulation of post-transcriptional repressors is required for an orderly Drosophila maternal-to-zygotic transition
Possible reference: Cao, WX. et al. (2020) Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition., Cell Rep, PMID 32579915

PXD016487 Dataset with its publication pending (from PRIDE)
Dataset title: ESCRT complexes in Giardia intestinalis (CHMP7)
Possible reference: Pipaliya, SV. et al. (2021) Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata., BMC Biol, PMID 34446013

PXD016448 Dataset with its publication pending (from PRIDE)
Dataset title: ESCRT complexes in Giardia intestinalis (VPS25)
Possible reference: Pipaliya, SV. et al. (2021) Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata., BMC Biol, PMID 34446013

PXD016444 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Analysis Reveals Key Proteins Involved in Ethylene-Induced Adventitious Root Development in Cucumber (Cucumis sativus L.)
Possible reference: Lyu, J. et al. (2021) Proteomic analysis reveals key proteins involved in ethylene-induced adventitious root development in cucumber (Cucumis sativus L.)., PeerJ, PMID 33868797

PXD016409 Dataset with its publication pending (from jPOST)
Dataset title: An identification of kinases which phosphorylates Ebola virus VP30 protein
Possible reference: Takamatsu, Y. et al. (2020) Serine-Arginine Protein Kinase 1 Regulates Ebola Virus Transcription., mBio, PMID 32098814

PXD016394 Dataset with its publication pending (from PRIDE)
Dataset title: The GTPase Rab39a matures phagosomes into MHC-I antigen-presenting compartments.
Possible reference: Cruz, FM. et al. (2020) The GTPase Rab39a promotes phagosome maturation into MHC-I antigen-presenting compartments., EMBO J, PMID 31821587

PXD016376 Dataset with its publication pending (from PRIDE)
Dataset title: The Aspartic Protease Ddi1 Contributes to DNA-Protein Crosslink Repair in Yeast
Possible reference: Serbyn, N. et al. (2020) The Aspartic Protease Ddi1 Contributes to DNA-Protein Crosslink Repair in Yeast., Mol Cell, PMID 31902667

PXD016352 no publication (from MassIVE)
Dataset title: Quantitative Proteomic Comparison of Myofibroblasts Derived from Bone Marrow and Cornea
Possible reference: Saikia, P. et al. (2020) Quantitative proteomic comparison of myofibroblasts derived from bone marrow and cornea., Sci Rep, PMID 33028893

PXD016304 Dataset with its publication pending (from PRIDE)
Dataset title: Towards the molecular architecture of the peroxisomal receptor docking complex
Possible reference: Lill, P. et al. (2020) Towards the molecular architecture of the peroxisomal receptor docking complex., Proc Natl Acad Sci U S A, PMID 33323485

PXD016215 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling of a high mannose-type N-glycosylated lipase using hydrophilic interaction chromatography-mass spectrometry
Possible reference: Gargano, AFG. et al. (2020) Profiling of a high mannose-type N-glycosylated lipase using hydrophilic interaction chromatography-mass spectrometry., Anal Chim Acta, PMID 32252907

PXD016212 no publication (from MassIVE)
Dataset title: Long-lived Metabolic Enzymes in the Crystallin Lens Identified by Pulse-labeling of Mice and Mass Spectrometry
Possible reference: Liu, P. et al. (2019) Long-lived metabolic enzymes in the crystalline lens identified by pulse-labeling of mice and mass spectrometry., Elife, PMID 31820737

PXD016194 Dataset with its publication pending (from jPOST)
Dataset title: Improved host cell protein analysis in monoclonal antibody products through molecular weight cutoff enrichment
Possible reference: Chen, IH. et al. (2020) Improved Host Cell Protein Analysis in Monoclonal Antibody Products through Molecular Weight Cutoff Enrichment., Anal Chem, PMID 31999105

PXD016177 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics analysis of the second-generation merozoites of Eimeria tenella under Nitromezuril and Ethanamizuril stress
Possible reference: Li, XY. et al. (2019) Proteomic analysis of the second-generation merozoites of Eimeria tenella under nitromezuril and ethanamizuril stress., Parasit Vectors, PMID 31852494

PXD016122 Dataset with its publication pending (from PRIDE)
Dataset title: Influenza virus infection leads to global proteome remodeling of Streptococcus pneumoniae
Possible reference: Platt, MP. et al. (2022) A multiomics analysis of direct interkingdom dynamics between influenza A virus and Streptococcus pneumoniae uncovers host-independent changes to bacterial virulence fitness., PLoS Pathog, PMID 36542660

PXD016114 D. Salvach�a, A.Z. Werner, I. Pardo, M. Michalska, B.A. Black, B.S. Donohoe, S. Haugen, R. Katahira, S. Notonier, K.J. Ramirez, S.O. Purvine, E.M. Zink, Paul Abraham, R.J. Giannone, S. Poudel, P. Laible, R.L. Hettich, G.T. Beckham. Outer membrane vesicles (from MassIVE)
Dataset title: Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440
Possible reference: Salvach�a, D. et al. (2020) Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440., Proc Natl Acad Sci U S A, PMID 32245809

PXD016080 Dataset with its publication pending (from PRIDE)
Dataset title: Genomic rewiring of Sox2 chromatin interaction network during differentiation of ESCs to postmitotic neurons
Possible reference: Bunina, D. et al. (2020) Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons., Cell Syst, PMID 32553182

PXD016079 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative Differential Cuproproteomes of Rhodobacter capsulatus
Possible reference: Selamoglu, N. et al. (2020) Comparative differential cuproproteomes of Rhodobacter capsulatus reveal novel copper homeostasis related proteins., Metallomics, PMID 32149296

PXD016053 Dataset with its publication pending (from PRIDE)
Dataset title: The M-phase regulatory phosphatase PP2A-B55Î´ opposes protein kinase A on Arpp19 to initiate meiotic division
Possible reference: Lemonnier, T. et al. (2021) The M-phase regulatory phosphatase PP2A-B55δ opposes protein kinase A on Arpp19 to initiate meiotic division., Nat Commun, PMID 33758202

PXD016030 Dataset with its publication pending (from iProX)
Dataset title: Peptidomic Analysis Reveals Potential Contribution of the Placenta to Preeclampsia
Possible reference: Shangguan, Y. et al. (2021) Systematic proteomics analysis of lysine acetylation reveals critical features of placental proteins in pregnant women with preeclampsia., J Cell Mol Med, PMID 34697885

PXD015996 Dataset with its publication pending (from PRIDE)
Dataset title: Aberrant astrocyte protein secretion contributes to altered neuronal development in diverse disorders
Possible reference: Caldwell, ALM. et al. (2022) Aberrant astrocyte protein secretion contributes to altered neuronal development in multiple models of neurodevelopmental disorders., Nat Neurosci, PMID 36042312

PXD015973 no publication (from MassIVE)
Dataset title: Development of an updated genome-scale metabolic model of Clostridium thermocellum and its application for integration of multi-omics datasets
Possible reference: Garcia, S. et al. (2020) Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design., Front Bioeng Biotechnol, PMID 32974289

PXD015971 no publication (from MassIVE)
Dataset title: Mapping microbial bile acid transformations along the murine gut
Possible reference: Marion, S. et al. (2020) Biogeography of microbial bile acid transformations along the murine gut., J Lipid Res, PMID 32661017

PXD015918 no publication (from MassIVE)
Dataset title: Mapping the proximity interaction network of the RHO-family GTPases reveals signalling pathways and regulatory mechanisms
Possible reference: Bagci, H. et al. (2020) Mapping the proximity interaction network of the Rho-family GTPases reveals signalling pathways and regulatory mechanisms., Nat Cell Biol, PMID 31871319

PXD015915 no publication (from MassIVE)
Dataset title: Mass spectrometry-based proteomics reveals potential roles of NEK9 and MAP2K4 in resistance to PI3K inhibitors in triple negative breast cancer
Possible reference: Mundt, F. et al. (2018) Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers., Cancer Res, PMID 29472518

PXD015911 no publication (from MassIVE)
Dataset title: Proteogenomic Integration Reveals Therapeutic Targets in Breast Cancer Xenografts
Possible reference: Huang, KL. et al. (2017) Proteogenomic integration reveals therapeutic targets in breast cancer xenografts., Nat Commun, PMID 28348404

PXD015910 no publication (from MassIVE)
Dataset title: Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer
Possible reference: Mertins, P. et al. (2016) Proteogenomics connects somatic mutations to signalling in breast cancer., Nature, PMID 27251275

PXD015909 no publication (from MassIVE)
Dataset title: Integrated bottom-up and top-down proteomics of patient-derived breast tumor xenografts
Possible reference: Ntai, I. et al. (2016) Integrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts., Mol Cell Proteomics, PMID 26503891

PXD015877 Dataset with its publication pending (from PRIDE)
Dataset title: The length of a ubiquitin chain is a general determinant for selective recognition by ubiquitin-binding proteins.
Possible reference: Lutz, J. et al. (2020) The Length of a Ubiquitin Chain: A General Factor for Selective Recognition by Ubiquitin-Binding Proteins., Angew Chem Int Ed Engl, PMID 32301549

PXD015794 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of chloroplast envelope proteins with critical importance for cold acclimation
Possible reference: Trentmann, O. et al. (2020) Identification of Chloroplast Envelope Proteins with Critical Importance for Cold Acclimation., Plant Physiol, PMID 31932409

PXD015767 Dataset with its publication pending (from PRIDE)
Dataset title: SMOC1 as a therapeutic target for type 2 diabetes
Possible reference: Montgomery, MK. et al. (2020) SMOC1 is a glucose-responsive hepatokine and therapeutic target for glycemic control., Sci Transl Med, PMID 32878981

PXD015727 Dataset with its publication pending (from PRIDE)
Dataset title: Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage
Possible reference: Goulielmaki, E. et al. (2020) Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage., Nat Commun, PMID 31896748

PXD015657 Dataset with its publication pending (from PRIDE)
Dataset title: Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor
Possible reference: Struk, S. et al. (2021) Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor., Mol Cell Proteomics, PMID 33372050

PXD015619 Dataset with its publication pending (from PRIDE)
Dataset title: Cerebrospinal fluid ecto-GPR37 in Parkinson’s disease
Possible reference: Morat�, X. et al. (2021) Ecto-GPR37: a potential biomarker for Parkinson's disease., Transl Neurodegener, PMID 33637132

PXD015584 no publication (from MassIVE)
Dataset title: Quantitative Analysis of Global Protein Stability Rates in Tissues
Possible reference: McClatchy, DB. et al. (2020) Quantitative analysis of global protein stability rates in tissues., Sci Rep, PMID 32994440

PXD015579 Dataset with its publication pending (from PRIDE)
Dataset title: The cytosolic DNA sensor cGAS recognizes Neutrophil Extracellular Traps
Possible reference: Apel, F. et al. (2021) The cytosolic DNA sensor cGAS recognizes neutrophil extracellular traps., Sci Signal, PMID 33688080

PXD015525 Dataset with its publication pending (from PRIDE)
Dataset title: HipBA toxin-antitoxin system Caulobacter crescentus.
Possible reference: Huang, CY. et al. (2020) hipBA toxin-antitoxin systems mediate persistence in Caulobacter crescentus., Sci Rep, PMID 32071324

PXD015506 Dataset with its publication pending (from PRIDE)
Dataset title: In vitro expanded and activated polyclonal Î³Î´ memory T cells for treatment of cancer
Possible reference: Polito, VA. et al. (2019) Universal Ready-to-Use Immunotherapeutic Approach for the Treatment of Cancer: Expanded and Activated Polyclonal γδ Memory T Cells., Front Immunol, PMID 31824502

PXD015488 Dataset with its publication pending (from PRIDE)
Dataset title: Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription
Possible reference: Kollenstart, L. et al. (2019) Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription., J Biol Chem, PMID 31699900

PXD015469 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics Analysis of the Mechanism of AMP-17 against Candida albicans
Possible reference: Yang, LB. et al. (2022) TMT-based quantitative proteomic analysis of the effects of novel antimicrobial peptide AMP-17 against Candida albicans., J Proteomics, PMID 34606990

PXD015456 Dataset with its publication pending (from PRIDE)
Dataset title: Stress signaling and cellular proliferation reverse the effects of mitochondrial mistranslation
Possible reference: Ferreira, N. et al. (2019) Stress signaling and cellular proliferation reverse the effects of mitochondrial mistranslation., EMBO J, PMID 31721250

PXD015453 Dataset with its publication pending (from PRIDE)
Dataset title: CDK13 cooperates with CDK12 to control global RNA polymerase II processivity
Possible reference: Fan, Z. et al. (2020) CDK13 cooperates with CDK12 to control global RNA polymerase II processivity., Sci Adv, PMID 32917631

PXD015442 Dataset with its publication pending (from PRIDE)
Dataset title: Rat plasma proteomics using single-shot proteomics
Possible reference: Gaun, A. et al. (2021) Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice., J Proteome Res, PMID 33499602

PXD015434 Dataset with its publication pending (from PRIDE)
Dataset title: PROTEOMIC RESPONSE OF EARLY JUVENILE PACIFIC OYSTERS TO TEMPERATURE
Possible reference: Crandall, G. et al. (2022) Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature., PeerJ, PMID 36262416

PXD015375 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicles from human plasma and serum are carriers of extravesicular cargo - implications for biomarker discovery
Possible reference: Palviainen, M. et al. (2020) Extracellular vesicles from human plasma and serum are carriers of extravesicular cargo-Implications for biomarker discovery., PLoS One, PMID 32813744

PXD015364 Dataset with its publication pending (from PRIDE)
Dataset title: A label-free shotgun proteomics analysis of macadamia nut
Possible reference: Rost, J. et al. (2020) A label-free shotgun proteomics analysis of macadamia nut., Food Res Int, PMID 32036921

PXD015333 no publication (from MassIVE)
Dataset title: The anti-MRSA compound KCR inhibits protein synthesis in Staphylococcus aureus
Possible reference: Carruthers, NJ. et al. (2020) The anti-MRSA compound 3-O-alpha-L-(2″,3″-di-p-coumaroyl)rhamnoside (KCR) inhibits protein synthesis in Staphylococcus aureus., J Proteomics, PMID 31629958

PXD015320 Dataset with its publication pending (from PRIDE)
Dataset title: Proteostasis network alteration in lysosomal storage disorders: insights from the mouse model of Krabbe diseaseProteostasis network alteration in lysosomal storage disorders: insights from the mouse model of Krabbe diseaseProteostasis network alteration i
Possible reference: Landi, C. et al. (2020) Proteostasis network alteration in lysosomal storage disorders: Insights from the mouse model of Krabbe disease., J Neurosci Res, PMID 31797419

PXD015319 Dataset with its publication pending (from PRIDE)
Dataset title: Peptide-based quorum sensing systems in Paenibacillus polymyxa
Possible reference: Voichek, M. et al. (2020) Peptide-based quorum sensing systems in Paenibacillus polymyxa., Life Sci Alliance, PMID 32764104

PXD015314 Dataset with its publication pending (from iProX)
Dataset title: DPHL: A pan-human protein mass spectrometry library for robust biomarker discovery using Data-Independent Acquisition and Parallel Reaction Monitoring
Possible reference: Zhu, T. et al. (2020) DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery., Genomics Proteomics Bioinformatics, PMID 32795611

PXD015291 no publication (from MassIVE)
Dataset title: Comprehensive spectral library from the pathogenic bacterium Streptococcus pneumoniae with focus on phosphoproteins
Possible reference: Hentschker, C. et al. (2020) Comprehensive Spectral Library from the Pathogenic Bacterium Streptococcus pneumoniae with Focus on Phosphoproteins., J Proteome Res, PMID 32154730

PXD015262 no publication (from MassIVE)
Dataset title: ClpX, activated by SSB, is required for DNA replication in Mycobacterium tuberculosis
Possible reference: Kester, JC. et al. (2021) ClpX Is Essential and Activated by Single-Strand DNA Binding Protein in Mycobacteria., J Bacteriol, PMID 33229461

PXD015257 no publication (from MassIVE)
Dataset title: A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments
Possible reference: Paulo, JA. et al. (2016) A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments., J Am Soc Mass Spectrom, PMID 27400695

PXD015207 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery of a Small Molecule Degrader that Sustains pan-AKT Degradation and Downstream Signaling Effects
Possible reference: You, I. et al. (2020) Discovery of an AKT Degrader with Prolonged Inhibition of Downstream Signaling., Cell Chem Biol, PMID 31859249

PXD015200 Dataset with its publication pending (from PRIDE)
Dataset title: N-terminomics/TAILS profiling of macrophages after chemical inhibition of legumain
Possible reference: Anderson, BM. et al. (2020) N-Terminomics/TAILS Profiling of Macrophages after Chemical Inhibition of Legumain., Biochemistry, PMID 31774660

PXD015150 no publication (from MassIVE)
Dataset title: Induced Systemic Effects of Engineering the Cell Membrane Composition in Bacillus subtilis
Possible reference: Nickels, JD. et al. (2020) Impact of Fatty-Acid Labeling of Bacillus subtilis Membranes on the Cellular Lipidome and Proteome., Front Microbiol, PMID 32499768

PXD015148 Dataset with its publication pending (from PRIDE)
Dataset title: Rescuing over-activated microglia by acetaminophen treatment restores cognitive performance in the Dp(16) mouse model of Down Syndrome.
Possible reference: Pinto, B. et al. (2020) Rescuing Over-activated Microglia Restores Cognitive Performance in Juvenile Animals of the Dp(16) Mouse Model of Down Syndrome., Neuron, PMID 33027640

PXD015113 Dataset with its publication pending (from PRIDE)
Dataset title: Rescuing over-activated microglia by acetaminophen treatment restores cognitive performance in the Dp(16) mouse model of Down Syndrome.
Possible reference: Pinto, B. et al. (2020) Rescuing Over-activated Microglia Restores Cognitive Performance in Juvenile Animals of the Dp(16) Mouse Model of Down Syndrome., Neuron, PMID 33027640

PXD015050 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic and phosphoproteomic analyses of protein PKA catalytic-alpha-null mpkCCD cells and PKA catalytic-beta-null mpkCCD cells.
Possible reference: Limbutara, K. et al. (2019) Phosphorylation Changes in Response to Kinase Inhibitor H89 in PKA-Null Cells., Sci Rep, PMID 30808967

PXD015037 Dataset with its publication pending (from PRIDE)
Dataset title: Development of Photocrosslinking Probes Based on Huwentoxin-IV to Map the Site of Interaction on Nav1.7
Possible reference: Tzakoniati, F. et al. (2020) Development of Photocrosslinking Probes Based on Huwentoxin-IV to Map the Site of Interaction on Nav1.7., Cell Chem Biol, PMID 31732432

PXD015016 no publication (from MassIVE)
Dataset title: Dynamic incorporation of histone H3 variants into chromatin is essential for acquisition of aggressive traits and metastatic colonization
Possible reference: Gomes, AP. et al. (2019) Dynamic Incorporation of Histone H3 Variants into Chromatin Is Essential for Acquisition of Aggressive Traits and Metastatic Colonization., Cancer Cell, PMID 31564638

PXD015015 Dataset with its publication pending (from PRIDE)
Dataset title: Down-regulation of collagen hydroxylation in colorectal liver metastasis
Possible reference: van Huizen, NA. et al. (2020) Down-Regulation of Collagen Hydroxylation in Colorectal Liver Metastasis., Front Oncol, PMID 33117689

PXD014995 Dataset with its publication pending (from PRIDE)
Dataset title: The Function of Ectopic ATP Synthase in Extracellular Vesicles.
Possible reference: Dong, Z. et al. (2022) Exosomal miR-181a-2-3p derived from citreoviridin-treated hepatocytes activates hepatic stellate cells trough inducing mitochondrial calcium overload., Chem Biol Interact, PMID 35305974

PXD014988 Dataset with its publication pending (from PRIDE)
Dataset title: Long non-coding RNA HOTTIP promotes CCL3 expression and induces cartilage degradation by sponging miR-455-3p
Possible reference: Mao, G. et al. (2019) Long Non-coding RNA HOTTIP Promotes CCL3 Expression and Induces Cartilage Degradation by Sponging miR-455-3p., Front Cell Dev Biol, PMID 31508417

PXD014983 Dataset with its publication pending (from iProX)
Dataset title: A technology to capture DNA binding proteins based on biolistic transformation
Possible reference: Wang, Z. et al. (2023) A DNA-binding protein capture technology that purifies proteins by directly isolating the target DNA., Plant Sci, PMID 37467789

PXD014966 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative and dynamic catalogs of proteins released during apoptotic and necroptotic cell death
Possible reference: Tanzer, MC. et al. (2020) Quantitative and Dynamic Catalogs of Proteins Released during Apoptotic and Necroptotic Cell Death., Cell Rep, PMID 31995763

PXD014965 no publication (from MassIVE)
Dataset title: Proteomic and metabolomic analyses of Mahonia bealei under UV-B and dark treatments
Possible reference: Zhu, W. et al. (2021) Combined ultraviolet and darkness regulation of medicinal metabolites in Mahonia bealei revealed by proteomics and metabolomics., J Proteomics, PMID 33352312

PXD014964 no publication (from MassIVE)
Dataset title: Proteomic profiling of Mycobacterium tuberculosis culture filtrate identifies novel O-glycosylated proteins
Possible reference: Tucci, P. et al. (2020) Integrative proteomic and glycoproteomic profiling of Mycobacterium tuberculosis culture filtrate., PLoS One, PMID 32126063

PXD014963 no publication (from MassIVE)
Dataset title: The Mitochondrial Protease, Neurolysin, Regulates Respiratory Chain Supercomplex Formation and is Necessary for AML Viability
Possible reference: Mirali, S. et al. (2020) The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplex formation and is necessary for AML viability., Sci Transl Med, PMID 32269163

PXD014958 Dataset with its publication pending (from PRIDE)
Dataset title: Slow growing behavior in African trypanosomes during adipose tissue colonization
Possible reference: Trindade, S. et al. (2022) Slow growing behavior in African trypanosomes during adipose tissue colonization., Nat Commun, PMID 36481558

PXD014948 Dataset with its publication pending (from PRIDE)
Dataset title: From coarse to fine: The absolute Escherichia coli proteome under diverse growth conditions
Possible reference: Mori, M. et al. (2021) From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions., Mol Syst Biol, PMID 34032011

PXD014886 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial reprogramming using dCas9 boosts glia-to-neuron conversion
Possible reference: Russo, GL. et al. (2021) CRISPR-Mediated Induction of Neuron-Enriched Mitochondrial Proteins Boosts Direct Glia-to-Neuron Conversion., Cell Stem Cell, PMID 33202244

PXD014826 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of donor and cardiomyopathy pre-mortem human hearts
Possible reference: Hunter, B. et al. (2024) Proteomic and metabolomic analyses of the human adult myocardium reveal ventricle-specific regulation in end-stage cardiomyopathies., Commun Biol, PMID 39702518

PXD014823 Dataset with its publication pending (from PRIDE)
Dataset title: Global proteomic profiling of meningioma cohort
Possible reference: Papaioannou, MD. et al. (2019) Proteomic analysis of meningiomas reveals clinically distinct molecular patterns., Neuro Oncol, PMID 31077268

PXD014817 Dataset with its publication pending (from iProX)
Dataset title: TRIB3 Supports Breast Cancer Stemness by Suppressing FOXO1 Degradation and Enhancing SOX2 Transcription
Possible reference: Yu, JM. et al. (2019) TRIB3 supports breast cancer stemness by suppressing FOXO1 degradation and enhancing SOX2 transcription., Nat Commun, PMID 31844113

PXD014805 no publication (from MassIVE)
Dataset title: Extended snake venomics on the newly discovered subspecies Vipera anatolica senliki
Possible reference: Hempel, BF. et al. (2020) Extended Snake Venomics by Top-Down In-Source Decay: Investigating the Newly Discovered Anatolian Meadow Viper Subspecies, Vipera anatolica senliki., J Proteome Res, PMID 32073270

PXD014798 Dataset with its publication pending (from PRIDE)
Dataset title: Epigenetic reprogramming shapes the cellular landscape of schwannoma
Possible reference: Liu, SJ. et al. (2024) Epigenetic reprogramming shapes the cellular landscape of schwannoma., Nat Commun, PMID 38216587

PXD014791 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic cellular signatures of kinase inhibitor-induced cardiotoxicity
Possible reference: Xiong, Y. et al. (2022) Proteomic cellular signatures of kinase inhibitor-induced cardiotoxicity., Sci Data, PMID 35058449

PXD014787 Dataset with its publication pending (from PRIDE)
Dataset title: Gene regulatory networks of kiwifruit response to Pseudomonas syringae pv. actinidiae
Possible reference: Wang, Z. et al. (2017) Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes., Sci Rep, PMID 28687784

PXD014775 no publication (from MassIVE)
Dataset title: Extracellular matrix hydrogel derived from decellularized tissues enables endodermal organoid culture
Possible reference: Giobbe, GG. et al. (2019) Extracellular matrix hydrogel derived from decellularized tissues enables endodermal organoid culture., Nat Commun, PMID 31827102

PXD014764 Dataset with its publication pending (from PRIDE)
Dataset title: eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5’UTR.
Possible reference: Wilczynska, A. et al. (2019) eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5'UTR., Genome Biol, PMID 31791371

PXD014724 no publication (from MassIVE)
Dataset title: Molecular and immunological interrogation of a live-attenuated enterotoxigenic Escherichia coli vaccine highlights features unique to wild type infection
Possible reference: Chakraborty, S. et al. (2019) Interrogation of a live-attenuated enterotoxigenic Escherichia coli vaccine highlights features unique to wild-type infection., NPJ Vaccines, PMID 31482013

PXD014713 Dataset with its publication pending (from PRIDE)
Dataset title: Chemical labeling for fine mapping of IgG N-glycosylation by ETD-MS
Possible reference: Yang, L. et al. (2019) Chemical labeling for fine mapping of IgG N-glycosylation by ETD-MS., Chem Sci, PMID 32110292

PXD014694 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of extracellular vesicles derived from platelet concentrates treated with Mirasol� identifies biomarkers of platelet storage lesion
Possible reference: Hermida-Nogueira, L. et al. (2020) Proteomic analysis of extracellular vesicles derived from platelet concentrates treated with Mirasol� identifies biomarkers of platelet storage lesion., J Proteomics, PMID 31605789

PXD014666 Dataset with its publication pending (from PRIDE)
Dataset title: Decoding the genomic basis of osteoarthritis
Possible reference: Rahmioglu, N. et al. (2023) The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions., Nat Genet, PMID 36914876

PXD014652 Dataset with its publication pending (from PRIDE)
Dataset title: Multifunctional temozolomide-loaded lipid superparamagnetic nanovectors: dual targeting and disintegration of glioblastoma spheroids by synergic chemotherapy and hyperthermia treatment
Possible reference: Marino, A. et al. (2019) Multifunctional temozolomide-loaded lipid superparamagnetic nanovectors: dual targeting and disintegration of glioblastoma spheroids by synergic chemotherapy and hyperthermia treatment., Nanoscale, PMID 31663592

PXD014644 Dataset with its publication pending (from PRIDE)
Dataset title: Role for ribosomal quality control in sampling proteins for MHC class I-mediated antigen presentation
Possible reference: Trentini, DB. et al. (2020) Role for ribosome-associated quality control in sampling proteins for MHC class I-mediated antigen presentation., Proc Natl Acad Sci U S A, PMID 32047030

PXD014579 Dataset with its publication pending (from PRIDE)
Dataset title: Cell-derived extracellular vesicles can be used as a biomarker reservoir for glioblastoma tumor subtyping
Possible reference: Lane, R. et al. (2019) Cell-derived extracellular vesicles can be used as a biomarker reservoir for glioblastoma tumor subtyping., Commun Biol, PMID 31453379

PXD014476 no publication (from MassIVE)
Dataset title: A reference map of the human proinsulin biosynthetic interaction network
Possible reference: Tran, DT. et al. (2020) Unbiased Profiling of the Human Proinsulin Biosynthetic Interaction Network Reveals a Role for Peroxiredoxin 4 in Proinsulin Folding., Diabetes, PMID 32457219

PXD014463 no publication (from MassIVE)
Dataset title: Defining how Pak1 regulates cell polarity and cell division in fission yeast
Possible reference: Magliozzi, JO. et al. (2020) Fission yeast Pak1 phosphorylates anillin-like Mid1 for spatial control of cytokinesis., J Cell Biol, PMID 32421151

PXD014453 no publication (from MassIVE)
Dataset title: Revealing dynamic protein acetylation across subcellular compartments
Possible reference: Baeza, J. et al. (2020) Revealing Dynamic Protein Acetylation across Subcellular Compartments., J Proteome Res, PMID 32290654

PXD014368 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery of TBC1D7 as a potential driver for melanoma cell invasion.
Possible reference: Qi, TF. et al. (2020) Discovery of TBC1D7 as a Potential Driver for Melanoma Cell Invasion., Proteomics, PMID 32510182

PXD014323 Dataset with its publication pending (from PRIDE)
Dataset title: Host cholesterol modulates the generation and enrichment of persister population during Mycobacterium tuberculosis infection.
Possible reference: Talwar, S. et al. (2020) Role of VapBC12 Toxin-Antitoxin Locus in Cholesterol-Induced Mycobacterial Persistence., mSystems, PMID 33323416

PXD014315 Dataset with its publication pending (from PRIDE)
Dataset title: Active thrombin is produced by intestinal epithelium to control mucosal biofilm
Possible reference: Motta, JP. et al. (2019) Active thrombin produced by the intestinal epithelium controls mucosal biofilms., Nat Commun, PMID 31324782

PXD014306 Dataset with its publication pending (from iProX)
Dataset title: Proteome Analysis of the antivenom for Jellyfish Nemopilema nomurai
Possible reference: Lv, B. et al. (2025) Purification, characterization and the hemolytic mechanism of the hemolysin NnTX-45 from the jellyfish Nemopilema nomurai., Toxicon, PMID 40784661

PXD014280 no publication (from MassIVE)
Dataset title: Profiling the surfaceome identifies therapeutic targets for cells with hyperactive mTORC1 signaling
Possible reference: Wei, J. et al. (2020) Profiling the Surfaceome Identifies Therapeutic Targets for Cells with Hyperactive mTORC1 Signaling., Mol Cell Proteomics, PMID 31792071

PXD014210 no publication (from MassIVE)
Dataset title: Proteomic analysis reveals that topoisomerase 2A is associated with defective sperm head morphology
Possible reference: Netherton, J. et al. (2020) Proteomic Analysis Reveals that Topoisomerase 2A is Associated with Defective Sperm Head Morphology., Mol Cell Proteomics, PMID 31848259

PXD014206 Dataset with its publication pending (from jPOST)
Dataset title: In-gel digestion protocol to analyze proteome of Medaka after acute ionizing radiation exposure
Possible reference: P�rez-G�lvez, Y. et al. (2019) An Effective Protocol for Proteome Analysis of Medaka (Oryzias latipes) after Acute Exposure to Ionizing Radiation., Methods Protoc, PMID 31366181

PXD014181 no publication (from MassIVE)
Dataset title: HSV1_Quantitative_Proteomic_Analysis
Possible reference: Cui, YH. et al. (2019) Quantitative proteomic analysis of human corneal epithelial cells infected with HSV-1., Exp Eye Res, PMID 31085182

PXD014162 no publication (from MassIVE)
Dataset title: The purine biosynthesis regulator PurR moonlights as a virulence regulator in Staphylococcus aureus
Possible reference: Sause, WE. et al. (2019) The purine biosynthesis regulator PurR moonlights as a virulence regulator in Staphylococcus aureus., Proc Natl Acad Sci U S A, PMID 31217288

PXD014156 Dataset with its publication pending (from PRIDE)
Dataset title: Using Proteomics for an Insight into the Performance of Activated Sludge
Possible reference: Xing, M. et al. (2016) Highlighting earthworm contribution in uplifting biochemical response for organic matter decomposition during vermifiltration processing sewage sludge: Insights from proteomics., Bioresour Technol, PMID 27287202

PXD014128 no publication (from MassIVE)
Dataset title: High fat diet response metaproteomics
Possible reference: Clavel, T. et al. (2014) Intestinal microbiota in metabolic diseases: from bacterial community structure and functions to species of pathophysiological relevance., Gut Microbes, PMID 25003516

PXD014127 no publication (from MassIVE)
Dataset title: Primary human natural killer cells retain proinflammatory IgG1 at the cell surface and express CD16a glycoforms with donor-dependent variability
Possible reference: Patel, KR. et al. (2019) Primary Human Natural Killer Cells Retain Proinflammatory IgG1 at the Cell Surface and Express CD16a Glycoforms with Donor-dependent Variability., Mol Cell Proteomics, PMID 31467031

PXD014106 no publication (from MassIVE)
Dataset title: Data files for Various HMGB1 proteases
Possible reference: Ning, W. et al. (2021) Shared Molecular Mechanisms between Atherosclerosis and Periodontitis by Analyzing the Transcriptomic Alterations of Peripheral Blood Monocytes., Comput Math Methods Med, PMID 34899963

PXD014055 Dataset with its publication pending (from PRIDE)
Dataset title: Improving identification of in-organello protein-protein interactions using an affinity-enrichable, isotopically-coded, and mass spectrometry-cleavable chemical crosslinker
Possible reference: Makepeace, KAT. et al. (2020) Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker., Mol Cell Proteomics, PMID 32051233

PXD014034 Dataset with its publication pending (from PRIDE)
Dataset title: mTOR-regulated phosphorylation of electrogenic sodium bicarbonate cotransporter 1, NBCe1, at S255-257 regulates NBCe1 functional expression in mouse cortical astrocyte
Possible reference: Khakipoor, S. et al. (2019) Functional expression of electrogenic sodium bicarbonate cotransporter 1 (NBCe1) in mouse cortical astrocytes is dependent on S255-257 and regulated by mTOR., Glia, PMID 31318482

PXD013979 Dataset with its publication pending (from PRIDE)
Dataset title: Rapid and culture free identification of Francisella in hare carcasses by high-resolution mass spectrometry
Possible reference: Witt, N. et al. (2020) Rapid and Culture Free Identification of Francisella in Hare Carcasses by High-Resolution Tandem Mass Spectrometry Proteotyping., Front Microbiol, PMID 32457701

PXD013922 Dataset with its publication pending (from PRIDE)
Dataset title: Proteogenomic Network Analysis of Context-Specific KRAS Signaling In Mouse-to-Human Cross-Species Translation
Possible reference: Brubaker, DK. et al. (2019) Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation., Cell Syst, PMID 31521603

PXD013917 no publication (from MassIVE)
Dataset title: GBS Choroid Plexus Infection Proteomics
Possible reference: Campeau, A. et al. (2020) Multidimensional Proteome Profiling of Blood-Brain Barrier Perturbation by Group B Streptococcus., mSystems, PMID 32843537

PXD013907 Dataset with its publication pending (from PRIDE)
Dataset title: The dynamic configuration and phosphorylation of the C-terminal HEAT domain of huntingtin modulates its function
Possible reference: Jung, T. et al. (2020) The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain., Structure, PMID 32668197

PXD013905 Dataset with its publication pending (from jPOST)
Dataset title: The Correlation among Serum Proteomics and Clinical Profiles in Fibromyalgia Women
Possible reference: Han, CL. et al. (2020) Serum proteome profiles revealed dysregulated proteins and mechanisms associated with fibromyalgia syndrome in women., Sci Rep, PMID 32704114

PXD013894 Dataset with its publication pending (from PRIDE)
Dataset title: The ER protein translocation channel subunit Sbh1 controls virulence of Cryptococcus neoformans
Possible reference: Santiago-Tirado, FH. et al. (2023) The ER Protein Translocation Channel Subunit Sbh1 Controls Virulence of Cryptococcus neoformans., mBio, PMID 36749043

PXD013893 Dataset with its publication pending (from PRIDE)
Dataset title: Sequential phosphoproteomics and N-glycoproteomics of plasma-derived extracellular vesicles
Possible reference: Andaluz Aguilar, H. et al. (2020) Sequential phosphoproteomics and N-glycoproteomics of plasma-derived extracellular vesicles., Nat Protoc, PMID 31863077

PXD013886 no publication (from MassIVE)
Dataset title: A dynamic charge:charge interaction modulates PP2A:B56 interactions
Possible reference: Wang, X. et al. (2020) A dynamic charge-charge interaction modulates PP2A:B56 substrate recruitment., Elife, PMID 32195664

PXD013858 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics analysis of Volvariella volvacea after cold treatment
Possible reference: Gong, M. et al. (2020) Chilling stress reduced protein translation by the ubiquitination of ribosomal proteins in Volvariella volvacea., J Proteomics, PMID 31982547

PXD013852 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative comparative analysis of human erythrocyte surface proteins between individuals from two genetically distinct populations
Possible reference: Ravenhill, BJ. et al. (2019) Quantitative comparative analysis of human erythrocyte surface proteins between individuals from two genetically distinct populations., Commun Biol, PMID 31552303

PXD013806 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of lactate grown Eubacterium limosum ATCC 8486
Possible reference: Picking, JW. et al. (2019) MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation., J Biol Chem, PMID 31341018

PXD013800 Dataset with its publication pending (from PRIDE)
Dataset title: LARGE2 mediates O-glycosylation in HT-29 colorectal cancer cells
Possible reference: Dietinger, V. et al. (2020) Wnt-driven LARGE2 mediates laminin-adhesive O-glycosylation in human colonic epithelial cells and colorectal cancer., Cell Commun Signal, PMID 32586342

PXD013791 Dataset with its publication pending (from PRIDE)
Dataset title: Adaptation of Dinoroseobacter shibae to different kinds of oxidative stress
Possible reference: Beier, N. et al. (2021) Adaptation of Dinoroseobacter shibae to oxidative stress and the specific role of RirA., PLoS One, PMID 33780465

PXD013760 no publication (from MassIVE)
Dataset title: A Proteomic Atlas for the Heterogeneous Senescence Associated Secretory Phenotype
Possible reference: Salvato, I. et al. (2023) Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation., Front Immunol, PMID 37483631

PXD013727 Dataset with its publication pending (from PRIDE)
Dataset title: ��Identifying the cellular interactome of Epstein-Barr virus lytic regulator Zta reveals cellular targets contributing to viral replication.
Possible reference: Zhou, Y. et al. (2020) Identifying the Cellular Interactome of Epstein-Barr Virus Lytic Regulator Zta Reveals Cellular Targets Contributing to Viral Replication., J Virol, PMID 31694936

PXD013697 no publication (from MassIVE)
Dataset title: Oxygen-dependent interaction between FBXL5 and CIA targeting complex regulates iron homeostasis
Possible reference: Mayank, AK. et al. (2019) An Oxygen-Dependent Interaction between FBXL5 and the CIA-Targeting Complex Regulates Iron Homeostasis., Mol Cell, PMID 31229404

PXD013689 Dataset with its publication pending (from PRIDE)
Dataset title: Brain adiponectin signaling controls peripheral insulin response in Drosophila
Possible reference: Arquier, N. et al. (2021) Brain adiponectin signaling controls peripheral insulin response in Drosophila., Nat Commun, PMID 34561451

PXD013645 Dataset with its publication pending (from PRIDE)
Dataset title: The O-GlcNAc transferase interaction network regulates the stress response
Possible reference: Martinez, M. et al. (2021) Quantitative Proteomics Reveals that the OGT Interactome Is Remodeled in Response to Oxidative Stress., Mol Cell Proteomics, PMID 33716169

PXD013602 Dataset with its publication pending (from PRIDE)
Dataset title: Prochlorococcus extracellular vesicles: molecular composition and adsorption to diverse microbes
Possible reference: Biller, SJ. et al. (2022) Prochlorococcus extracellular vesicles: molecular composition and adsorption to diverse microbes., Environ Microbiol, PMID 34766712

PXD013540 Dataset with its publication pending (from jPOST)
Dataset title: Anti-Influenza Activity of the Ribonuclease Binase in A549 cells
Possible reference: Ulyanova, V. et al. (2020) Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics., Int J Mol Sci, PMID 33167434

PXD013527 no publication (from MassIVE)
Dataset title: Wigington_calcineurinphosphatasesignaling_2019
Possible reference: Wigington, CJ. et al. (2019) Tracking Public Health Workforce Retention: Observations From CDC's Public Health Associate Program., Am J Public Health, PMID 31318602

PXD013410 Dataset with its publication pending (from jPOST)
Dataset title: Age-associated mouse brown adipose tissue mitochondrial proteome
Possible reference: Tajima, K. et al. (2019) Mitochondrial lipoylation integrates age-associated decline in brown fat thermogenesis., Nat Metab, PMID 32313871

PXD013316 Dataset with its publication pending (from PRIDE)
Dataset title: Cyclin-dependent-like kinase 5 is required for pain signalling in both human neurons and mouse models
Possible reference: La Montanara, P. et al. (2020) Cyclin-dependent-like kinase 5 is required for pain signaling in human sensory neurons and mouse models., Sci Transl Med, PMID 32641489

PXD013266 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of differentially expressed proteins in two Trypanosoma vivax strains with different patterns of virulence and pathogenicity in sheep.
Possible reference: Ramirez-Barrios, R. et al. (2019) Trypanosoma vivax infection in sheep: Different patterns of virulence and pathogenicity associated with differentially expressed proteomes., Vet Parasitol, PMID 34311938

PXD013257 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic analysis of pepper (Capsicum annuum L.) seedlings under selenium stress
Possible reference: Zhang, C. et al. (2019) Comparative proteomic analysis of pepper (Capsicum annuum L.) seedlings under selenium stress., PeerJ, PMID 31799069

PXD013215 Dataset with its publication pending (from PRIDE)
Dataset title: APEX2-mediated proximity labeling of mitochondrial matrix and chromatin in budding yeast
Possible reference: Singer-Kr�ger, B. et al. (2020) APEX2-mediated proximity labeling resolves protein networks in Saccharomyces�cerevisiae cells., FEBS J, PMID 31323700

PXD013199 no publication (from MassIVE)
Dataset title: Analysis of brain and cerebrospinal fluid from mouse models of the three major forms of neuronal ceroid lipofuscinosis reveals changes in the lysosomal proteome.
Possible reference: Sleat, DE. et al. (2019) Analysis of Brain and Cerebrospinal Fluid from Mouse Models of the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Changes in the Lysosomal Proteome., Mol Cell Proteomics, PMID 31501224

PXD013185 Dataset with its publication pending (from jPOST)
Dataset title: Species-specific quantitative proteomics profiles of sarcoma patient-derived models closely reflect their primary tumors　
Possible reference: Shiozawa, K. et al. (2019) Species-Specific Quantitative Proteomics Profiles of Sarcoma Patient-Derived Models Closely Reflect Their Primary Tumors., Proteomics Clin Appl, PMID 31419061

PXD013131 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring the virulence gene interactome with CRISPR/dCas9 in the human malaria parasite
Possible reference: Bryant, JM. et al. (2020) Exploring the virulence gene interactome with CRISPR/dCas9 in the human malaria parasite., Mol Syst Biol, PMID 32816370

PXD013111 Dataset with its publication pending (from PRIDE)
Dataset title: The Urinary Peptidome Identifies Prognostic Biomarkers for Small Renal Masses
Possible reference: Di Meo, A. et al. (2020) Searching for prognostic biomarkers for small renal masses in the urinary proteome., Int J Cancer, PMID 31465112

PXD013046 Dataset with its publication pending (from jPOST)
Dataset title: Global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii
Possible reference: Cerletti, M. et al. (2015) Global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii., J Proteomics, PMID 25829260

PXD013043 no publication (from MassIVE)
Dataset title: Proteomic analysis of synovial fluid identifies periostin as a biomarker for anterior cruciate ligament injury
Possible reference: Brophy, RH. et al. (2019) Proteomic analysis of synovial fluid identifies periostin as a biomarker for anterior cruciate ligament injury., Osteoarthritis Cartilage, PMID 31430535

PXD012999 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics and proteogenomics analysis of sweet potato (Ipomoea batatas) leaf and root
Possible reference: Al-Mohanna, T. et al. (2019) Proteomics and Proteogenomics Analysis of Sweetpotato ( Ipomoea batatas) Leaf and Root., J Proteome Res, PMID 31117636

PXD012939 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative photo-crosslinking mass spectrometry reveals protein structure response to environmental changes
Possible reference: M�ller, F. et al. (2019) Quantitative Photo-crosslinking Mass Spectrometry Revealing Protein Structure Response to Environmental Changes., Anal Chem, PMID 31274288

PXD012925 Dataset with its publication pending (from PRIDE)
Dataset title: DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate the emergence of 2C-like cells and zygotic transcriptional program
Possible reference: Yan, YL. et al. (2019) DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program., PLoS Biol, PMID 31226106

PXD012919 no publication (from MassIVE)
Dataset title: Analysis of mitochondrial N termini by HUNTER (High-efficiency Undecanal-based N Termini EnRichment)
Possible reference: Weng, SSH. et al. (2019) Sensitive Determination of Proteolytic Proteoforms in Limited Microscale Proteome Samples., Mol Cell Proteomics, PMID 31471496

PXD012860 Dataset with its publication pending (from PRIDE)
Dataset title: Cdc14 and PP2A Phosphatases Cooperate to Shape Phosphoproteome Dynamics during Mitotic Exit
Possible reference: Touati, SA. et al. (2019) Cdc14 and PP2A Phosphatases Cooperate to Shape Phosphoproteome Dynamics during Mitotic Exit., Cell Rep, PMID 31722221

PXD012798 Dataset with its publication pending (from PRIDE)
Dataset title: Variability in exosomal protein cargo of human lung adenocarcinoma cells
Possible reference: Tiruvayipati, S. et al. (2020) Variability in protein cargo detection in technical and biological replicates of exosome-enriched extracellular vesicles., PLoS One, PMID 32119684

PXD012759 Dataset with its publication pending (from PRIDE)
Dataset title: Crosslinking Proteomics Indicates Effects of Simvastatin on the TLR2 interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade
Possible reference: Kamal, AHM. et al. (2019) Cross-linking Proteomics Indicates Effects of Simvastatin on the TLR2 Interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade., Mol Cell Proteomics, PMID 31221720

PXD012718 no publication (from MassIVE)
Dataset title: RIT1 oncoproteins escape LZTR1-mediated proteolysis
Possible reference: Castel, P. et al. (2019) RIT1 oncoproteins escape LZTR1-mediated proteolysis., Science, PMID 30872527

PXD012696 no publication (from MassIVE)
Dataset title: Sirtuin 5 regulates proximal tubule fatty acid oxidation to protect against acute kidney injury
Possible reference: Chiba, T. et al. (2019) Sirtuin 5 Regulates Proximal Tubule Fatty Acid Oxidation to Protect against AKI., J Am Soc Nephrol, PMID 31575700

PXD012601 Dataset with its publication pending (from jPOST)
Dataset title: A Label Free Mass Spectrometry Method to Predict Endogenous Protein Complex Composition
Possible reference: McBride, Z. et al. (2019) A Label-free Mass Spectrometry Method to Predict Endogenous Protein Complex Composition., Mol Cell Proteomics, PMID 31186290

PXD012576 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of different types of immunity in potato
Possible reference: Burra, DD. et al. (2018) Comparative Membrane-Associated Proteomics of Three Different Immune Reactions in Potato., Int J Mol Sci, PMID 29439444

PXD012569 Venkataraman YR, Timmins-Schiffman E, Horwith MJ, Lowe AT, Nunn B, Vadopalas B, Spencer LH, Roberts SB. Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences. Marine Ecology Progress Series. 2019 Feb (from PanoramaPublic)
Dataset title: Characterization of Pacific oyster (Crassostrea gigas) proteomic response to natural environmental differences
Possible reference: Simon, A. et al. (2025) Microgeographic variation in gene expression plasticity under osmotic stress in wild eastern oyster juveniles (Crassostrea virginica)., Comp Biochem Physiol Part D Genomics Proteomics, PMID 40669247

PXD012542 no publication (from MassIVE)
Dataset title: Proteome profiling of triple negative breast cancer cells overexpressing NOD1 and NOD2 receptors unveils molecular signatures of malignant cell proliferation
Possible reference: Velloso, FJ. et al. (2019) Proteome profiling of triple negative breast cancer cells overexpressing NOD1 and NOD2 receptors unveils molecular signatures of malignant cell proliferation., BMC Genomics, PMID 30791886

PXD012540 Dataset with its publication pending (from jPOST)
Dataset title: HDAC2 regulates site-specific acetylation of MDM2 and its ubiquitination signaling in tumor suppression
Possible reference: Patel, N. et al. (2019) HDAC2 Regulates Site-Specific Acetylation of MDM2 and Its Ubiquitination Signaling in Tumor Suppression., iScience, PMID 30818224

PXD012336 Dataset with its publication pending (from PRIDE)
Dataset title: Bermudagrass stolon and shoot comparative proteomics
Possible reference: Zhang, B. et al. (2019) Comparative proteomic analysis provides new insights into the specialization of shoots and stolons in bermudagrass (Cynodon dactylon L.)., BMC Genomics, PMID 31510936

PXD012268 Dataset with its publication pending (from jPOST)
Dataset title: One-step SH2 superbinder based approach for sensitive analysis of tyrosine phosphoproteome
Possible reference: Yao, Y. et al. (2019) One-Step SH2 Superbinder-Based Approach for Sensitive Analysis of Tyrosine Phosphoproteome., J Proteome Res, PMID 30875230

PXD012205 no publication (from MassIVE)
Dataset title: Quantitative Proteomics by SWATH-MS of Maternal Plasma Exosome Determine Pathways Associated with Term and Preterm Birth
Possible reference: Menon, R. et al. (2019) Quantitative Proteomics by SWATH-MS of Maternal Plasma Exosomes Determine Pathways Associated With Term and Preterm Birth., Endocrinology, PMID 30668697

PXD012198 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of glomerular organoid extracellular matrix
Possible reference: Morais, MRPT. et al. (2022) Kidney organoids recapitulate human basement membrane assembly in health and disease., Elife, PMID 35076391

PXD012177 Dataset with its publication pending (from PRIDE)
Dataset title: Cassiopea xamachana: Cassiosomes
Possible reference: Ames, CL. et al. (2020) Cassiosomes are stinging-cell structures in the mucus of the upside-down jellyfish Cassiopea xamachana., Commun Biol, PMID 32054971

PXD012157 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic proximity mapping by rapamycin-dependent targeting of APEX2 to tail-anchored membrane proteins
Possible reference: James, C. et al. (2019) Proteomic mapping by rapamycin-dependent targeting of APEX2 identifies binding partners of VAPB at the inner nuclear membrane., J Biol Chem, PMID 31519755

PXD012103 Dataset with its publication pending (from PRIDE)
Dataset title: Toxoplasma HCE1 Immunoprecipitations
Possible reference: Panas, MW. et al. (2019) Toxoplasma Controls Host Cyclin E Expression through the Use of a Novel MYR1-Dependent Effector Protein, HCE1., mBio, PMID 31040242

PXD011996 Dataset with its publication pending (from PRIDE)
Dataset title: Depletion of high molecular mass proteins for the identification of small proteins and small open reading frame encoded peptides in cellular proteomes
Possible reference: Cassidy, L. et al. (2019) Depletion of High-Molecular-Mass Proteins for the Identification of Small Proteins and Short Open Reading Frame Encoded Peptides in Cellular Proteomes., J Proteome Res, PMID 30779583

PXD011981 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics analysis of behavioral adaptation in zebrafish larvae
Possible reference: Huang, KT. et al. (2023) Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox responses in larval fish., Nat Protoc, PMID 37020146

PXD011945 no publication (from MassIVE)
Dataset title: Xcc Pan Proteome
Possible reference: T�vora, FTPK. et al. (2019) Pan Proteome of Xanthomonas campestris pv. campestris Isolates Contrasting in Virulence., Proteomics, PMID 31050381

PXD011858 no publication (from MassIVE)
Dataset title: Chemical Derivatization of Streptavidin Provides Protection from Tryptic Proteolysis
Possible reference: Barshop, WD. et al. (2019) Chemical Derivatization of Affinity Matrices Provides Protection from Tryptic Proteolysis., J Proteome Res, PMID 31498634

PXD011769 Dataset with its publication pending (from PRIDE)
Dataset title: Acetylome analysis of Thermus thermophilus HB27
Possible reference: Masui, R. et al. (2014) Structural insights of post-translational modification sites in the proteome of Thermus thermophilus., J Struct Funct Genomics, PMID 24407378

PXD011749 Dataset with its publication pending (from PRIDE)
Dataset title: Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies
Possible reference: Geyer, PE. et al. (2019) Plasma Proteome Profiling to detect and avoid sample-related biases in biomarker studies., EMBO Mol Med, PMID 31566909

PXD011748 Chen A, Franks, A & Slavov, N. DART-ID increases single-cell proteome coverage. (submitted).; Chen A, Franks A & Slavov N. DART-ID increases single-cell proteome coverage. biorXiv, DOI: 10.1101/399121. PLOS Comp Bio (submitted). (from MassIVE)
Dataset title: DART-ID increases single-cell proteome coverage
Possible reference: Chen, AT. et al. (2019) DART-ID increases single-cell proteome coverage., PLoS Comput Biol, PMID 31260443

PXD011737 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omics of the rhizosphere communities of Arabidopsis
Possible reference: Secomandi, E. et al. (2025) Waterlogging alone and combined with other abiotic stresses provides unique metabolic signatures at the plant-rhizosphere interface: A multi-omics perspective on root metabolome, root exudation and rhizomicrobiome., Plant Physiol Biochem, PMID 39965412

PXD011726 Dataset with its publication pending (from PRIDE)
Dataset title: E. coli BW25113 proteomics in nutrient-rich and minimal medium
Possible reference: Maser, A. et al. (2020) Amino acids are key substrates to Escherichia coli BW25113 for achieving high specific growth rate., Res Microbiol, PMID 32057959

PXD011725 Dataset with its publication pending (from PRIDE)
Dataset title: Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae
Possible reference: S�nchez, BJ. et al. (2021) Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae., Proteomics, PMID 33452728

PXD011717 Dataset with its publication pending (from PRIDE)
Dataset title: A Qualitative Proteome-wide Lysine Succinylation Profiling of Tea Revealed Its Involvement in Primary Metabolism
Possible reference: Qiu, C. et al. (2020) [A Qualitative Proteome-Wide Lysine Succinylation Profiling of Tea Revealed its Involvement in Primary Metabolism]., Mol Biol (Mosk), PMID 32163400

PXD011713 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of frontal cortex area 8 in frontotemporal lobar degeneration with c9orf72 mutation
Possible reference: Andr�s-Benito, P. et al. (2019) Combined Transcriptomics and Proteomics in Frontal Cortex Area 8 in Frontotemporal Lobar Degeneration Linked to C9ORF72 Expansion., J Alzheimers Dis, PMID 30909235

PXD011703 Dataset with its publication pending (from PRIDE)
Dataset title: A chemical probe for Tudor domain protein SPIN1 to investigate chromatin functions
Possible reference: Fagan, V. et al. (2019) A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function., J Med Chem, PMID 31550156

PXD011693 Dataset with its publication pending (from PRIDE)
Dataset title: Shotgun Proteomic Analysis of ESBL and non ESBL Producing Klebsiella Pneumoniae Clinical Isolates
Possible reference: Enany, S. et al. (2020) Shotgun proteomic analysis of ESBL-producing and non-ESBL-producing Klebsiella Pneumoniae clinical isolates., Microbiol Res, PMID 32078895

PXD011667 Dataset with its publication pending (from PRIDE)
Dataset title: Dirhodium (II) Complex Interferes with Iron-Transport System to Exert Antibacterial Action against Streptococcus pneumoniae
Possible reference: Yang, XY. et al. (2019) Dirhodium (II) complex interferes with iron-transport system to exert antibacterial action against Streptococcus pneumoniae., J Proteomics, PMID 30521977

PXD011637 no publication (from MassIVE)
Dataset title: Spatial and proteomic profiling reveals centrosome-independent features of centriolar satellites
Possible reference: Gheiratmand, L. et al. (2019) Spatial and proteomic profiling reveals centrosome-independent features of centriolar satellites., EMBO J, PMID 31304627

PXD011630 Dataset with its publication pending (from PRIDE)
Dataset title: Integrative analysis identifies key molecular signatures underlying neurodevelopmental deficits in fragile X syndrome
Possible reference: Utami, KH. et al. (2020) Integrative Analysis Identifies Key Molecular Signatures Underlying Neurodevelopmental Deficits in Fragile X Syndrome., Biol Psychiatry, PMID 32653109

PXD011611 Dataset with its publication pending (from PRIDE)
Dataset title: Lipopolysaccharide-regulated secretion of soluble and vesicle-based colorectal cancer cell proteins
Possible reference: Garcia de Durango, CR. et al. (2021) Lipopolysaccharide-regulated secretion of soluble and vesicle-based proteins from a panel of colorectal cancer cell lines., Proteomics Clin Appl, PMID 33587312

PXD011560 Dataset with its publication pending (from PRIDE)
Dataset title: Emiliania Huxleyi exposed to 4 treatments of HHQ
Possible reference: Garrett, O. et al. (2023) A bacterial quorum sensing signal is a potent inhibitor of de novo pyrimidine biosynthesis in the globally abundant Emiliania huxleyi., Front Microbiol, PMID 37869665

PXD011558 Dataset with its publication pending (from PRIDE)
Dataset title: Shotgun Proteomic Analysis of ESBL and non ESBL Producing Klebsiella Pneumoniae Clinical Isolates
Possible reference: Enany, S. et al. (2020) Shotgun proteomic analysis of ESBL-producing and non-ESBL-producing Klebsiella Pneumoniae clinical isolates., Microbiol Res, PMID 32078895

PXD011544 no publication (from MassIVE)
Dataset title: Sequential Windowed Acquisition of Reporter Masses for Quantitation-First Proteomics
Possible reference: Barshop, WD. et al. (2019) Sequential Windowed Acquisition of Reporter Masses for Quantitation-First Proteomics., J Proteome Res, PMID 30781952

PXD011534 Dataset with its publication pending (from PRIDE)
Dataset title: Deacetylation inhibition reverses PABPN1-dependent muscle wasting
Possible reference: Olie, CS. et al. (2019) Deacetylation Inhibition Reverses PABPN1-Dependent Muscle Wasting., iScience, PMID 30739015

PXD011476 no publication (from MassIVE)
Dataset title: Extended sialylated O-glycan repertoire of human urinary glycoproteins discovered and characterized using EThcD
Possible reference: Darula, Z. et al. (2019) Extended Sialylated O-Glycan Repertoire of Human Urinary Glycoproteins Discovered and Characterized Using Electron-Transfer/Higher-Energy Collision Dissociation., J Proteome Res, PMID 30407017

PXD011475 Dataset with its publication pending (from PRIDE)
Dataset title: espB deletion mutant of Mycobacterium tuberculosis
Possible reference: Soler-Arnedo, P. et al. (2020) Polarly Localized EccE1 Is Required for ESX-1 Function and Stabilization of ESX-1 Membrane Proteins in Mycobacterium tuberculosis., J Bacteriol, PMID 31843799

PXD011459 Dataset with its publication pending (from PRIDE)
Dataset title: Sequential digestion with Trypsin and Elastase in cross-linking/mass spectrometry
Possible reference: Dau, T. et al. (2019) Sequential Digestion with Trypsin and Elastase in Cross-Linking Mass Spectrometry., Anal Chem, PMID 30817130

PXD011338 Dataset with its publication pending (from jPOST)
Dataset title: Degradation of OPG by HtrA1
Possible reference: Ochiai, N. et al. (2019) Murine osteoclasts secrete serine protease HtrA1 capable of degrading osteoprotegerin in the bone microenvironment., Commun Biol, PMID 30854478

PXD011323 Dataset with its publication pending (from PRIDE)
Dataset title: On-chip AP-MS: Interaction proteomics on a microfluidics platform
Possible reference: Furlan, C. et al. (2019) Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements., Nat Commun, PMID 30948724

PXD011298 no publication (from MassIVE)
Dataset title: Multi-omics of azacitidine-treated AML cells reveals variable and convergent targets that remodel the cell surface proteome
Possible reference: Leung, KK. et al. (2019) Multiomics of azacitidine-treated AML cells reveals variable and convergent targets that remodel the cell-surface proteome., Proc Natl Acad Sci U S A, PMID 30584089

PXD011281 Dataset with its publication pending (from PRIDE)
Dataset title: proteogenomic and metabolic adaptations of Staphylococcus aureus
Possible reference: Busche, T. et al. (2018) Comparative Secretome Analyses of Human and Zoonotic Staphylococcus aureus Isolates CC8, CC22, and CC398., Mol Cell Proteomics, PMID 30201737

PXD011260 no publication (from MassIVE)
Dataset title: Excreted-Secreted Proteins from activated infective junveiles of the entomopathogenic nematode Steinernema feltiae
Possible reference: Chang, DZ. et al. (2019) A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema., PLoS Pathog, PMID 31042778

PXD011251 Dataset with its publication pending (from PRIDE)
Dataset title: AML1-ETO induced leukemia stem cell self-renewal depends on Plcg1
Possible reference: Schnoeder, TM. et al. (2022) PLCG1 is required for AML1-ETO leukemia stem cell self-renewal., Blood, PMID 34695195

PXD011232 Dataset with its publication pending (from jPOST)
Dataset title: Comparative phosphoproteomic analysis of barley grains during imbibition
Possible reference: Ishikawa, S. et al. (2019) Comparative Phosphoproteomic Analysis of Barley Embryos with Different Dormancy during Imbibition., Int J Mol Sci, PMID 30669653

PXD011223 Dataset with its publication pending (from PRIDE)
Dataset title: Gen� organ engagement in lipid metabolism revealed by a combined transcriptomic and proteomic approach
Possible reference: Xavier, MA. et al. (2019) Tick Gen�'s organ engagement in lipid metabolism revealed by a combined transcriptomic and proteomic approach., Ticks Tick Borne Dis, PMID 30904537

PXD011221 Dataset with its publication pending (from PRIDE)
Dataset title: Improved SILAC Method for Double Labeling of Bacterial Proteome
Possible reference: Han, J. et al. (2019) Improved SILAC method for double labeling of bacterial proteome., J Proteomics, PMID 30553074

PXD011211 Dataset with its publication pending (from PRIDE)
Dataset title: Chaperonin CCT Checkpoint Function in Basal Transcription Factor TFIID Assembly
Possible reference: Antonova, SV. et al. (2018) Chaperonin CCT checkpoint function in basal transcription factor TFIID assembly., Nat Struct Mol Biol, PMID 30510221

PXD011209 Dataset with its publication pending (from PRIDE)
Dataset title: Two of a kind: Transmissible Schwann cell cancers in the endangered Tasmanian devil.
Possible reference: Patchett, AL. et al. (2020) Two of a kind: transmissible Schwann cell cancers in the endangered Tasmanian devil (Sarcophilus harrisii)., Cell Mol Life Sci, PMID 31375869

PXD011151 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial proteome analysis from LC-MS/MS glioblastoma cell lines
Possible reference: Gómez-Caudillo, L. et al. (2020) Principal component analysis on LC‑MS/MS and 2DE‑MALDI‑TOF in glioblastoma cell lines reveals that mitochondria act as organelle sensors of the metabolic state in glioblastoma., Oncol Rep, PMID 32468038

PXD011143 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome Profiling of PBMC-originated, iPSC-derived Lentoid Bodies at differentiation day 25
Possible reference: Ali, M. et al. (2020) Generation and proteome profiling of PBMC-originated, iPSC-derived lentoid bodies., Stem Cell Res, PMID 32474394

PXD011039 Dataset with its publication pending (from PRIDE)
Dataset title: Microautophagy of storage proteins in maize aleurone cells.
Possible reference: Ding, X. et al. (2022) Microautophagy Mediates Vacuolar Delivery of Storage Proteins in Maize Aleurone Cells., Front Plant Sci, PMID 35251104

PXD011023 Dataset with its publication pending (from PRIDE)
Dataset title: Heat and pressure resistance relates to protein folding and aggregation
Possible reference: Li, H. et al. (2020) Heat and Pressure Resistance in Escherichia coli Relates to Protein Folding and Aggregation., Front Microbiol, PMID 32117137

PXD010996 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of Covalent Modifications Regulating Immune Signaling Complex Composition and Phenotype
Possible reference: Frauenstein, A. et al. (2021) Identification of covalent modifications regulating�immune signaling complex composition and phenotype., Mol Syst Biol, PMID 34318608

PXD010901 Dataset with its publication pending (from PRIDE)
Dataset title: Further evidence for sustainable alternatives to replace threatened animal horn based on quantitative proteomic analysis
Possible reference: Liu, R. et al. (2018) Further evidence for sustainable alternatives to replace threatened animal horn based on quantitative proteomic analysis., Electrophoresis, PMID 30192403

PXD010874 Dataset with its publication pending (from PRIDE)
Dataset title: A 6-Month Systems Toxicology Inhalation/Cessation Study in ApoE-/- Mice to Investigate Cardiovascular and Respiratory Exposure Effects of the Modified-Risk Tobacco Products CHTP1.2 and THS2.2 Compared with the Effects of Conventional Cigarettes [Liver iTR
Possible reference: Phillips, B. et al. (2019) A six-month systems toxicology inhalation/cessation study in ApoE-/- mice to investigate cardiovascular and respiratory exposure effects of modified risk tobacco products, CHTP 1.2 and THS 2.2, compared with conventional cigarettes., Food Chem Toxicol, PMID 30763686

PXD010873 Dataset with its publication pending (from PRIDE)
Dataset title: A 6-Month Systems Toxicology Inhalation/Cessation Study in ApoE-/- Mice to Investigate Cardiovascular and Respiratory Exposure Effects of the Modified-Risk Tobacco Products CHTP1.2 and THS2.2 Compared with the Effects of Conventional Cigarettes [Heart iTR
Possible reference: Phillips, B. et al. (2019) A six-month systems toxicology inhalation/cessation study in ApoE-/- mice to investigate cardiovascular and respiratory exposure effects of modified risk tobacco products, CHTP 1.2 and THS 2.2, compared with conventional cigarettes., Food Chem Toxicol, PMID 30763686

PXD010836 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of the cellulose degradation system of Cytophaga hutchinsonii and Sporocytophaga myxococcoides
Possible reference: Taillefer, M. et al. (2018) Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling Bacteroidetes., mSystems, PMID 30505945

PXD010817 Dataset with its publication pending (from PRIDE)
Dataset title: Detergent-resistant microdomains in Saprolegnia parasitica
Possible reference: M�lida, H. et al. (2024) Quantitative proteomic analysis of plasma membranes from the fish pathogen Saprolegnia parasitica reveals promising targets for disease control., Microbiol Spectr, PMID 38888349

PXD010814 no publication (from MassIVE)
Dataset title: Proteomic Manifestations of Genetic Defects in Autosomal Recessive Congenital Ichthyosis
Possible reference: Karim, N. et al. (2019) Proteomic manifestations of genetic defects in autosomal recessive congenital ichthyosis., J Proteomics, PMID 30978464

PXD010805 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamic proteomics reveals unexpected plasticity of cellular proteome
Possible reference: Budzik, JM. et al. (2020) Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages., Elife, PMID 31951200

PXD010803 Dataset with its publication pending (from jPOST)
Dataset title: Ubiquitin receptors are required for substrate-mediated activation of the proteasome's unfolding ability
Possible reference: Cundiff, MD. et al. (2019) Ubiquitin receptors are required for substrate-mediated activation of the proteasome's unfolding ability., Sci Rep, PMID 31601863

PXD010766 no publication (from MassIVE)
Dataset title: Delayed effect of early-life exposure to 17-alpha-ethinylestradiol on brain proteome of adult mangrove rivulus fish
Possible reference: Voisin, AS. et al. (2019) Early-life exposure to the endocrine disruptor 17-α-ethinylestradiol induces delayed effects in adult brain, liver and ovotestis proteomes of a self-fertilizing fish., J Proteomics, PMID 30550985

PXD010765 no publication (from MassIVE)
Dataset title: Delayed effect of early-life exposure to 17-alpha-ethinylestradiol on brain proteome of adult mangrove rivulus fish
Possible reference: Voisin, AS. et al. (2019) Early-life exposure to the endocrine disruptor 17-α-ethinylestradiol induces delayed effects in adult brain, liver and ovotestis proteomes of a self-fertilizing fish., J Proteomics, PMID 30550985

PXD010764 no publication (from MassIVE)
Dataset title: Delayed effect of early-life exposure to 17-alpha-ethinylestradiol on brain proteome of adult mangrove rivulus fish
Possible reference: Voisin, AS. et al. (2019) Early-life exposure to the endocrine disruptor 17-α-ethinylestradiol induces delayed effects in adult brain, liver and ovotestis proteomes of a self-fertilizing fish., J Proteomics, PMID 30550985

PXD010754 Dataset with its publication pending (from jPOST)
Dataset title: human feces metaproteome from 81 persons
Possible reference: Ferrer, M. et al. (2013) Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure., Environ Microbiol, PMID 22891823

PXD010753 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of Asrij perturbed Drosophila lymph glands as a resource for identification of new regulators of hematopoiesis
Possible reference: Sinha, S. et al. (2019) Proteomics of Asrij Perturbation in Drosophila Lymph Glands for Identification of New Regulators of Hematopoiesis., Mol Cell Proteomics, PMID 30923041

PXD010718 no publication (from MassIVE)
Dataset title: A cross-linking-aided PRM mass spectrometry for EGFR proteome
Possible reference: Chen, Y. et al. (2019) A Cross-Linking-Aided Immunoprecipitation/Mass Spectrometry Workflow Reveals Extensive Intracellular Trafficking in Time-Resolved, Signal-Dependent Epidermal Growth Factor Receptor Proteome., J Proteome Res, PMID 31442056

PXD010717 no publication (from MassIVE)
Dataset title: A cross-linking-aided mass spectrometry workflow reveals extensive intracellular trafficking in time-resolved, signal-dependent EGFR proteome
Possible reference: Chen, Y. et al. (2019) A Cross-Linking-Aided Immunoprecipitation/Mass Spectrometry Workflow Reveals Extensive Intracellular Trafficking in Time-Resolved, Signal-Dependent Epidermal Growth Factor Receptor Proteome., J Proteome Res, PMID 31442056

PXD010716 Dataset with its publication pending (from jPOST)
Dataset title: Isolated peroxisome-division machinery
Possible reference: Imoto, Y. et al. (2013) Single-membrane-bounded peroxisome division revealed by isolation of dynamin-based machinery., Proc Natl Acad Sci U S A, PMID 23696667

PXD010706 no publication (from MassIVE)
Dataset title: Venomics of the horned desert Viper (Cerastes Cerastes) and the mangrove pit viper (Cryptelytrops purpureomaculatus)
Possible reference: Ozverel, CS. et al. (2019) Investigating the cytotoxic effects of the venom proteome of two species of the Viperidae family (Cerastes cerastes and Cryptelytrops purpureomaculatus) from various habitats., Comp Biochem Physiol C Toxicol Pharmacol, PMID 30825636

PXD010682 Dataset with its publication pending (from jPOST)
Dataset title: Total proteome of Andrographis paniculata
Possible reference: Talei, D. et al. (2015) Salt stress-induced protein pattern associated with photosynthetic parameters and andrographolide content in Andrographis paniculata Nees., Biosci Biotechnol Biochem, PMID 25384250

PXD010681 Dataset with its publication pending (from jPOST)
Dataset title: Shotgun proteomics of Mn (II)-oxidizing Serratia marcescens
Possible reference: Queiroz, PS. et al. (2018) Alterations in the proteomic composition of Serratia marcescens in response to manganese (II)., BMC Biotechnol, PMID 30594179

PXD010628 Dataset with its publication pending (from PRIDE)
Dataset title: Nitric oxide modulates metabolic remodelling and immunometabolism in inflammatory murine macrophages
Possible reference: Bailey, JD. et al. (2019) Nitric Oxide Modulates Metabolic Remodeling in Inflammatory Macrophages through TCA Cycle Regulation and Itaconate Accumulation., Cell Rep, PMID 31269442

PXD010588 Dataset with its publication pending (from PRIDE)
Dataset title: Discerning strain specific beta-lactam drug resistance of P. aeruginosa
Possible reference: Jorgensen, SCJ. et al. (2018) Meropenem and Vaborbactam: Stepping up the Battle against Carbapenem-resistant Enterobacteriaceae., Pharmacotherapy, PMID 29427523

PXD010484 Mu A, Tak Shun Fung, Arminja N. Kettenbach, Rajarshi Chakrabarti, Henry Higgs. A complex containing lysine-acetylated actin inhibits the formin INF2. . (from MassIVE)
Dataset title: A complex containing lysine-acetylated actin inhibits the formin INF2
Possible reference: A, M. et al. (2019) A complex containing lysine-acetylated actin inhibits the formin INF2., Nat Cell Biol, PMID 30962575

PXD010481 Dataset with its publication pending (from PRIDE)
Dataset title: Cross-Linking/mass spectrometry (CLMS) analysis of RNA polymerase II
Possible reference: Luo, J. et al. (2019) Identification of Cross-linked Peptides Using Isotopomeric Cross-linkers., J Am Soc Mass Spectrom, PMID 31168746

PXD010448 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of soluble and surface-enriched proteins from Acanthamoeba castellanii trophozoites
Possible reference: Maschio, VJ. et al. (2018) Comparative proteomic analysis of soluble and surface-enriched proteins from Acanthamoeba castellanii trophozoites., Mol Biochem Parasitol, PMID 30205118

PXD010381 Dataset with its publication pending (from PRIDE)
Dataset title: Systems-based approaches enable the development of industrial yeast strains with improved phenotypesSystems-based approaches enable the development of industrial yeast strains with improved phenotypes
Possible reference: Varela, C. et al. (2018) Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains., Metab Eng, PMID 30138679

PXD010366 no publication (from MassIVE)
Dataset title: Selective Permeability of Mouse Blood-Aqueous Barrier as Determined by 15N-Heavy Isotope Tracing and Mass Spectrometry
Possible reference: Liu, P. et al. (2018) Selective permeability of mouse blood-aqueous barrier as determined by 15N-heavy isotope tracing and mass spectrometry., Proc Natl Acad Sci U S A, PMID 30127000

PXD010346 no publication (from MassIVE)
Dataset title: Proteomics reveals localization of cuticular proteins in Anopheles gambiae
Possible reference: Zhou, Y. et al. (2019) Proteomics reveals localization of cuticular proteins in Anopheles gambiae., Insect Biochem Mol Biol, PMID 30278207

PXD010328 Dataset with its publication pending (from PRIDE)
Dataset title: Identification and validation of stage-associated serum biomarkers in colorectal cancer_discovery phase C
Possible reference: Mar�n-Vicente, C. et al. (2020) Identification and Validation of Stage-Associated Serum Biomarkers in Colorectal Cancer Using MS-Based Procedures., Proteomics Clin Appl, PMID 31502404

PXD010302 Dataset with its publication pending (from iProX)
Dataset title: Hepatoma-derived growth factor and high mobility group protein HMGI-C upregulated expression promote the papillary thyroid microcarcinoma metastasis
Possible reference: Jin, S. et al. (2019) Proteomic analysis of the papillary thyroid microcarcinoma., Ann Endocrinol (Paris), PMID 31606199

PXD010236 no publication (from MassIVE)
Dataset title: Time-Course Mass Spectrometry Data of Adipose Mesenchymal Stem Cells Acquiring Chondrogenic Phenotype
Possible reference: Janus, JR. et al. (2018) Time-course mass spectrometry data of adipose mesenchymal stem cells acquiring chondrogenic phenotype., BMC Res Notes, PMID 30208918

PXD010185 Dataset with its publication pending (from PRIDE)
Dataset title: Metaproteomic analysis of glacial ecosystem
Possible reference: Martinez-Alonso, E. et al. (2019) Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica., Sci Rep, PMID 31434915

PXD010170 Dataset with its publication pending (from jPOST)
Dataset title: Comparative phosphoproteomic analysis of barley grains
Possible reference: Ishikawa, S. et al. (2019) Comparative Phosphoproteomic Analysis of Barley Embryos with Different Dormancy during Imbibition., Int J Mol Sci, PMID 30669653

PXD010151 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of candidate Desulfatiglans TRIP_1 and identification of enzymes involved in anaerobic degradation of phenanthrene
Possible reference: Kraiselburd, I. et al. (2019) Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation., Environ Microbiol, PMID 30680888

PXD010135 Dataset with its publication pending (from PRIDE)
Dataset title: In vitro - in vivo correlation of gut microbiome response to metformin
Possible reference: Li, L. et al. (2019) An in vitro model maintaining taxon-specific functional activities of the gut microbiome., Nat Commun, PMID 31515476

PXD010134 Dataset with its publication pending (from PRIDE)
Dataset title: In vitro evaluation of MiPro cultuturing model
Possible reference: Huang, Z. et al. (2025) Saccharomyces boulardii CNCM I-745 mitigates antibiotic-induced gut microbiome functional alterations independently of the host., Gut Microbes, PMID 41200858

PXD010123 Dataset with its publication pending (from PRIDE)
Dataset title: Drosophila BAF complex crosslinking (
Possible reference: Mashtalir, N. et al. (2018) Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes., Cell, PMID 30343899

PXD010063 no publication (from MassIVE)
Dataset title: USP7 Regulates Cytokinesis through FBXO38 and KIF20B
Possible reference: Georges, A. et al. (2019) USP7 Regulates Cytokinesis through FBXO38 and KIF20B., Sci Rep, PMID 30804394

PXD010060 Dataset with its publication pending (from PRIDE)
Dataset title: Metaproteomic analysis of glacial ecosystem
Possible reference: Martinez-Alonso, E. et al. (2019) Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica., Sci Rep, PMID 31434915

PXD010050 Dataset with its publication pending (from jPOST)
Dataset title: In presence Manganese of Meyerozyma guilliermondii
Possible reference: Ruas, FAD. et al. (2019) Manganese alters expression of proteins involved in the oxidative stress of Meyerozyma guilliermondii., J Proteomics, PMID 30414513

PXD010026 no publication (from MassIVE)
Dataset title: Classification of Single Particles from Human Cell Extract Reveals Distinct Structures
Possible reference: Verbeke, EJ. et al. (2018) Classification of Single Particles from Human Cell Extract Reveals Distinct Structures., Cell Rep, PMID 29972786

PXD009990 Dataset with its publication pending (from PRIDE)
Dataset title: Direct proteome labelling in fruit flies with SILAF reveals differential phosphorylation of mitochondrial proteins upon loss of OXPHOS subunits
Possible reference: Rosenberger, FA. et al. (2021) Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits., Mol Cell Proteomics, PMID 33640490

PXD009985 no publication (from MassIVE)
Dataset title: MYC dephosphorylation by the PP1/PNUTS phosphatase complex regulates chromatin binding and protein stability
Possible reference: Dingar, D. et al. (2018) MYC dephosphorylation by the PP1/PNUTS phosphatase complex regulates chromatin binding and protein stability., Nat Commun, PMID 30158517

PXD009872 no publication (from MassIVE)
Dataset title: SET1A-mediated mono-methylation at K342 regulates YAP activation by blocking its nuclear export and promotes tumorigenesis
Possible reference: Fang, L. et al. (2018) SET1A-Mediated Mono-Methylation at K342 Regulates YAP Activation by Blocking Its Nuclear Export and Promotes Tumorigenesis., Cancer Cell, PMID 30008322

PXD009653 Dataset with its publication pending (from jPOST)
Dataset title: Histone Middle Down UVPD
Possible reference: Greer, SM. et al. (2018) Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy., Anal Chem, PMID 30063333

PXD009633 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome Profiling of PBMC-originated, iPSC-derived Lentoid Bodies at differentiation day 35
Possible reference: Ali, M. et al. (2020) Generation and proteome profiling of PBMC-originated, iPSC-derived lentoid bodies., Stem Cell Res, PMID 32474394

PXD009547 no publication (from MassIVE)
Dataset title: A novel differential ion mobility interface expands the depth of proteome coverage and the sensitivity of multiplex proteomic measurements
Possible reference: Pfammatter, S. et al. (2018) A Novel Differential Ion Mobility Device Expands the Depth of Proteome Coverage and the Sensitivity of Multiplex Proteomic Measurements., Mol Cell Proteomics, PMID 30007914

PXD009545 no publication (from MassIVE)
Dataset title: Alcohol-driven changes in fetal cerebral artery proteome
Possible reference: Bukiya, AN. et al. (2019) Fetal Cerebral Artery Mitochondrion as Target of Prenatal Alcohol Exposure., Int J Environ Res Public Health, PMID 31067632

PXD009523 Dataset with its publication pending (from PRIDE)
Dataset title: JEV and ZIKV NS5 interactome .
Possible reference: Kovanich, D. et al. (2019) Analysis of the Zika and Japanese Encephalitis Virus NS5 Interactomes., J Proteome Res, PMID 31199156

PXD009486 no publication (from MassIVE)
Dataset title: Hemocyanin facilitates lignocellulose digestion by marine wood-boring crustaceans
Possible reference: Besser, K. et al. (2018) Hemocyanin facilitates lignocellulose digestion by wood-boring marine crustaceans., Nat Commun, PMID 30510200

PXD009474 Dataset with its publication pending (from PRIDE)
Dataset title: Translocase of the Outer Membrane (TOM complex) of hydrogenosomes in Trichomonas vaginalis
Possible reference: Makki, A. et al. (2019) Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis., PLoS Biol, PMID 30608924

PXD009420 Dataset with its publication pending (from PRIDE)
Dataset title: A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae
Possible reference: Garcia-Albornoz, M. et al. (2020) A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae., Mol Omics, PMID 31868867

PXD009386 Dataset with its publication pending (from iProX)
Dataset title: Quantitative S-nitrosylation proteome reveals the susceptibility of translational machinery to oxidized low-density lipoprotein in vascular endothelial cells
Possible reference: Xu, X. et al. (2019) The protein S-nitrosylation of splicing and translational machinery in vascular endothelial cells is susceptible to oxidative stress induced by oxidized low-density lipoprotein., J Proteomics, PMID 30630120

PXD009381 Dataset with its publication pending (from PRIDE)
Dataset title: Chikungunya virus phosphoproteomics
Possible reference: Treffers, EE. et al. (2023) The alphavirus nonstructural protein 2 NTPase induces a host translational shut-off through phosphorylation of eEF2 via cAMP-PKA-eEF2K signaling., PLoS Pathog, PMID 36848386

PXD009359 Dataset with its publication pending (from PRIDE)
Dataset title: Nuclear speckles enable processing of RNA from GC-rich isochores
Possible reference: Małszycki, M. et al. (2026) Nuclear speckles enable processing of RNA from GC-rich isochores., Cell, PMID 41747727

PXD009356 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative platelet releasate proteome profiling of acute coronary syndrome versus stable coronary artery disease
Possible reference: Maguire, PB. et al. (2020) Comparative Platelet Releasate Proteomic Profiling of Acute Coronary Syndrome versus Stable Coronary Artery Disease., Front Cardiovasc Med, PMID 32671099

PXD009347 no publication (from MassIVE)
Dataset title: Proteomics analysis of phage phiR201 infecting Yersinia enterocolitica
Possible reference: Skurnik, M. et al. (2012) Characterization of the genome, proteome, and structure of yersiniophage ϕR1-37., J Virol, PMID 22973030

PXD009313 no publication (from MassIVE)
Dataset title: Noordermeer_Shieldin_2018
Possible reference: Noordermeer, SM. et al. (2018) The shieldin complex mediates 53BP1-dependent DNA repair., Nature, PMID 30022168

PXD009263 no publication (from MassIVE)
Dataset title: (3S)-Lysyl hydroxylation of TRAFAC GTPases is catalyzed by the 1 Jumonji-C oxygenase JMJD7
Possible reference: Markolovic, S. et al. (2018) The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases., Nat Chem Biol, PMID 29915238

PXD009245 Dataset with its publication pending (from jPOST)
Dataset title: TGFÎ²-Induced Proteins in Non-Endocrine Mouse Pituitary Cell Line TtT/GF
Possible reference: Tsukada, T. et al. (2018) TGFβ signaling reinforces pericyte properties of the non-endocrine mouse pituitary cell line TtT/GF., Cell Tissue Res, PMID 29274061

PXD009200 Dataset with its publication pending (from PRIDE)
Dataset title: Global hyperactivation of enhancers stabilizes human and mouse na�ve pluripotency
Possible reference: Lynch, CJ. et al. (2020) Global hyperactivation of enhancers stabilizes human and mouse naive pluripotency through inhibition of CDK8/19 Mediator kinases., Nat Cell Biol, PMID 32989249

PXD009168 no publication (from MassIVE)
Dataset title: Global assessment of Plk1 network dynamics identifies inhibition of PP6 as a mechanism to promote Aurora A activity
Possible reference: Kettenbach, AN. et al. (2018) Global assessment of its network dynamics reveals that the kinase Plk1 inhibits the phosphatase PP6 to promote Aurora A activity., Sci Signal, PMID 29764989

PXD009160 Dataset with its publication pending (from PRIDE)
Dataset title: BXD Mouse Aging Liver Proteomics
Possible reference: Williams, EG. et al. (2018) Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population., Mol Cell Proteomics, PMID 29945935

PXD009152 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphotyrosine profiling of human cerebrospinal fluid
Possible reference: Sathe, G. et al. (2018) Phosphotyrosine profiling of human cerebrospinal fluid., Clin Proteomics, PMID 30220890

PXD009130 Dataset with its publication pending (from jPOST)
Dataset title: Universal plant phosphoproteomics workflow and its application to tomato signaling in response to cold stress
Possible reference: Hsu, CC. et al. (2018) Universal Plant Phosphoproteomics Workflow and Its Application to Tomato Signaling in Response to Cold Stress., Mol Cell Proteomics, PMID 30006488

PXD009124 Dataset with its publication pending (from PRIDE)
Dataset title: Label-free quantitative proteomic approach to investigate the effect of heat stress on Panax ginseng leaves
Possible reference: Kim, SW. et al. (2019) Label-free quantitative proteomic analysis of Panax ginseng leaves upon exposure to heat stress., J Ginseng Res, PMID 30662303

PXD009054 Dataset with its publication pending (from PRIDE)
Dataset title: MitoTAILS: N-terminomics profiling of mitochondrial proteolysis
Possible reference: Araya, LE. et al. (2021) Deorphanizing Caspase-3 and Caspase-9 Substrates In and Out of Apoptosis with Deep Substrate Profiling., ACS Chem Biol, PMID 34553588

PXD009017 Dataset with its publication pending (from PRIDE)
Dataset title: Myristic acid induces proteomic changes in primary murine hepatocytes
Possible reference: Speziali, G. et al. (2018) Myristic acid induces proteomic and secretomic changes associated with steatosis, cytoskeleton remodeling, endoplasmic reticulum stress, protein turnover and exosome release in HepG2 cells., J Proteomics, PMID 29654920

PXD008965 Dataset with its publication pending (from PRIDE)
Dataset title: KMT9 writes the histone mark H4K12me1 and controls metabolism and proliferation of castration-resistant prostate cancer cells
Possible reference: Metzger, E. et al. (2019) KMT9 monomethylates histone H4 lysine 12 and controls proliferation of prostate cancer cells., Nat Struct Mol Biol, PMID 31061526

PXD008927 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Alterations in Multiple Myeloma: A Comprehensive Study Using Bone Marrow Interstitial Fluid and Serum Samples
Possible reference: Chanukuppa, V. et al. (2020) Proteomic Alterations in Multiple Myeloma: A Comprehensive Study Using Bone Marrow Interstitial Fluid and Serum Samples., Front Oncol, PMID 33585190

PXD008921 Dataset with its publication pending (from jPOST)
Dataset title: A new tool to reveal bacterial signaling mechanisms in antibiotic treatment and resistance
Possible reference: Lin, MH. et al. (2018) A New Tool to Reveal Bacterial Signaling Mechanisms in Antibiotic Treatment and Resistance., Mol Cell Proteomics, PMID 30232125

PXD008874 Dataset with its publication pending (from PRIDE)
Dataset title: Eukaryotic translation initiation factor 5A regulates autophagy via translation of ATG3
Possible reference: Frankel, LB. et al. (2018) EIF5A mediates autophagy via translation of ATG3., Autophagy, PMID 29973124

PXD008812 Dataset with its publication pending (from PRIDE)
Dataset title: The formation of a camalexin-biosynthetic metabolon
Possible reference: Mucha, S. et al. (2019) The Formation of a Camalexin Biosynthetic Metabolon., Plant Cell, PMID 31511315

PXD008714 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of CLIC4 overexpressing human pulmonary artery endothelial cells
Possible reference: Abdul-Salam, VB. et al. (2019) CLIC4/Arf6 Pathway., Circ Res, PMID 30582444

PXD008653 Dataset with its publication pending (from PRIDE)
Dataset title: Docosahexaenoic and Arachidonic Free Fatty Acids Exert Different Antitumor Activities on Colorectal Cancer Cells
Possible reference: Ramos-Bueno, RP. et al. (2016) Various Acylglycerols from Common Oils Exert Different Antitumor Activities on Colorectal Cancer Cells., Nutr Cancer, PMID 27007804

PXD008618 no publication (from MassIVE)
Dataset title: Diet-Induced Acetylation and Succinylation
Possible reference: Wang, F. et al. (2020) Diet-induced obesity is associated with altered expression of sperm motility-related genes and testicular post-translational modifications in a mouse model., Theriogenology, PMID 32980686

PXD008560 no publication (from MassIVE)
Dataset title: gpGrouper: A Peptide Grouping and Quantification Algorithm
Possible reference: Saltzman, AB. et al. (2018) gpGrouper: A Peptide Grouping Algorithm for Gene-Centric Inference and Quantitation of Bottom-Up Proteomics Data., Mol Cell Proteomics, PMID 30093420

PXD008557 no publication (from MassIVE)
Dataset title: Quantifying homologous proteins and proteoforms
Possible reference: Enk, VM. et al. (2016) Regulation of highly homologous major urinary proteins in house mice quantified with label-free proteomic methods., Mol Biosyst, PMID 27464909

PXD008489 Dataset with its publication pending (from iProX)
Dataset title: Proteomic profile of ET-1 induced dysfunctional hiPS-C cells
Possible reference: Vignon-Zellweger, N. et al. (2014) Endothelin-1 overexpression and endothelial nitric oxide synthase knock-out induce different pathological responses in the heart of male and female mice., Life Sci, PMID 24355292

PXD008476 Dataset with its publication pending (from PRIDE)
Dataset title: Mutant calreticulin binders analysis
Possible reference: Achyutuni, S. et al. (2021) Hematopoietic expression of a chimeric murine-human CALR oncoprotein allows the assessment of anti-CALR antibody immunotherapies in vivo., Am J Hematol, PMID 33761144

PXD008457 no publication (from MassIVE)
Dataset title: Proteomic and biochemical comparison of the cellular interaction partners of human VPS33A and VPS33B
Possible reference: Hunter, MR. et al. (2018) Proteomic and Biochemical Comparison of the Cellular Interaction Partners of Human VPS33A and VPS33B., J Mol Biol, PMID 29778605

PXD008439 Dataset with its publication pending (from PRIDE)
Dataset title: Changes in the proteome of mediterranean sea urchin Paracentrotus lividus due to activation of its immune system
Possible reference: Inguglia, L. et al. (2020) Changes in the proteome of sea urchin Paracentrotus lividus coelomocytes in response to LPS injection into the body cavity., PLoS One, PMID 32074628

PXD008416 no publication (from MassIVE)
Dataset title: Xiong_NDR1_2017
Possible reference: Xiong, S. et al. (2017) Regulation of Protein Interactions by Mps One Binder (MOB1) Phosphorylation., Mol Cell Proteomics, PMID 28373297

PXD008384 Dataset with its publication pending (from PRIDE)
Dataset title: Micro-metastases regression following primary tumor excision: a critical role for primary tumor secretome
Possible reference: Shaashua, L. et al. (2020) Spontaneous regression of micro-metastases following primary tumor excision: a critical role for primary tumor secretome., BMC Biol, PMID 33158447

PXD008339 Dataset with its publication pending (from PRIDE)
Dataset title: Characterisation of proteome of a novel Escherichia coli strain exhibiting mucoviscous phenotype.
Possible reference: Harris, S. et al. (2018) Variant O89 O-Antigen of E. coli Is Associated With Group 1 Capsule Loci and Multidrug Resistance., Front Microbiol, PMID 30233517

PXD008313 Dataset with its publication pending (from PRIDE)
Dataset title: Absolute quantification of selected photosynthetic electron transfer proteins in Chlamydomonas reinhardtii in the presence and absence of oxygen
Possible reference: Nikolova, D. et al. (2018) Absolute quantification of selected photosynthetic electron transfer proteins in Chlamydomonas reinhardtii in the presence and absence of oxygen., Photosynth Res, PMID 29594952

PXD008295 no publication (from MassIVE)
Dataset title: High throughput and accurate serum proteome profiling by integrated sample preparation technology and single-run data independent mass spectrometry analysis
Possible reference: Lin, L. et al. (2018) High throughput and accurate serum proteome profiling by integrated sample preparation technology and single-run data independent mass spectrometry analysis., J Proteomics, PMID 29278786

PXD008282 Dataset with its publication pending (from jPOST)
Dataset title: HeLa, Orbitrap Fusion Lumos, Parameter optimization
Possible reference: Greguš, M. et al. (2024) Improved Data Acquisition Settings on Q Exactive HF-X and Fusion Lumos Tribrid Orbitrap-Based Mass Spectrometers for Proteomic Analysis of Limited Samples., J Proteome Res, PMID 38690845

PXD008277 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome and phosphoproteome of Wip1-knockout mouse testis
Possible reference: Wei, Y. et al. (2019) Integrative Proteomic and Phosphoproteomic Profiling of Testis from Wip1 Phosphatase-Knockout Mice: Insights into Mechanisms of Reduced Fertility., Mol Cell Proteomics, PMID 30361445

PXD008214 Dataset with its publication pending (from PRIDE)
Dataset title: Host-pathogen dynamics through secretome analysis of stimulated macrophages
Possible reference: Khan, MM. et al. (2018) Host-pathogen dynamics through targeted secretome analysis of stimulated macrophages., J Proteomics, PMID 29572161

PXD008180 no publication (from MassIVE)
Dataset title: The Functions of the COPII Gene Paralogs SEC23A and SEC23B Are Interchangeable In Vivo
Possible reference: Khoriaty, R. et al. (2018) Functions of the COPII gene paralogs SEC23A and SEC23B are interchangeable in vivo., Proc Natl Acad Sci U S A, PMID 30065114

PXD008158 Dataset with its publication pending (from PRIDE)
Dataset title: Large-scale identification and visualization of human Liver N-glycome enriched from LO2 cells
Possible reference: Xiao, K. et al. (2018) Large-scale identification and visualization of human liver N-glycome enriched from LO2 cells., Anal Bioanal Chem, PMID 29725729

PXD008045 no publication (from MassIVE)
Dataset title: Acinetobacter baumannii 17978 growth temperature proteomics analysis
Possible reference: De Silva, PM. et al. (2018) Effect of Incubation Temperature on Antibiotic Resistance and Virulence Factors of Acinetobacter baumannii ATCC 17978., Antimicrob Agents Chemother, PMID 29061747

PXD007997 no publication (from MassIVE)
Dataset title: Proteome of Gastrointestinal Stromal Tumor-Derived Exosomes
Possible reference: Atay, S. et al. (2018) Insights into the Proteome of Gastrointestinal Stromal Tumors-Derived Exosomes Reveals New Potential Diagnostic Biomarkers., Mol Cell Proteomics, PMID 29242380

PXD007974 Dataset with its publication pending (from PRIDE)
Dataset title: Deep Multilayer Tissue Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression
Possible reference: Bai, B. et al. (2020) Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression., Neuron, PMID 31926610

PXD007899 no publication (from MassIVE)
Dataset title: Integrated in vivo quantitative proteomics and nutrient tracing reveals age-related metabolic rewiring of pancreatic B-cell function
Possible reference: Wortham, M. et al. (2018) Integrated In Vivo Quantitative Proteomics and Nutrient Tracing Reveals Age-Related Metabolic Rewiring of Pancreatic β Cell Function., Cell Rep, PMID 30517875

PXD007870 no publication (from MassIVE)
Dataset title: Insights into the evolution of host association through the isolation and characterization of a human periodontal pathogen, Desulfobulbus oralis
Possible reference: Cross, KL. et al. (2018) Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis., mBio, PMID 29535201

PXD007779 Dataset with its publication pending (from PRIDE)
Dataset title: Effect of acadesine and overexpression of the karyopherin Kap123 on nuclear abundance of yeast proteins
Possible reference: Douillet, DC. et al. (2019) Metabolomics and proteomics identify the toxic form and the associated cellular binding targets of the anti-proliferative drug AICAR., J Biol Chem, PMID 30478173

PXD007736 no publication (from MassIVE)
Dataset title: Critical Period Inhibition of NKCC1 Rectifies Synapse Development and Restores Adult Tactile Response Maps in Fragile X Mice
Possible reference: He, Q. et al. (2019) Critical period inhibition of NKCC1 rectifies synapse plasticity in the somatosensory cortex and restores adult tactile response maps in fragile X mice., Mol Psychiatry, PMID 29703945

PXD007670 Dataset with its publication pending (from PRIDE)
Dataset title: Vitis vinifera rhizosphere characterization: a metaproteome approach
Possible reference: Bona, E. et al. (2019) Metaproteomic characterization of theVitis vinifera rhizosphere., FEMS Microbiol Ecol, PMID 30307579

PXD007631 no publication (from MassIVE)
Dataset title: Smith_AF6-RAS_2017
Possible reference: Smith, MJ. et al. (2017) Evolution of AF6-RAS association and its implications in mixed-lineage leukemia., Nat Commun, PMID 29062045

PXD007609 Hempel, B.-F.; Damm, M.; G��men, B.; Karis, M.; Oguz, M.A.; Nalbantsoy, A.; S�ssmuth, R.D. Comparative Venomics of the Vipera ammodytes transcaucasiana and Vipera ammodytes montandoni from Turkey Provides Insights into Kinship. Toxins 2018, 10 (1), 23. do (from MassIVE)
Dataset title: Venomics of Vipera a. transcaucasiana and Vipera a. montandoni
Possible reference: Hempel, BF. et al. (2018) Comparative Venomics of the Vipera ammodytes transcaucasiana and Vipera ammodytes montandoni from Turkey Provides Insights into Kinship., Toxins (Basel), PMID 29301241

PXD007548 Dataset with its publication pending (from jPOST)
Dataset title: Quantitative Proteomic Analysis of Brucella abortus under Multiple Environmental Stresses
Possible reference: Zai, X. et al. (2017) Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses., Front Microbiol, PMID 29238329

PXD007541 no publication (from MassIVE)
Dataset title: Characterization of indole-3-acetic acid biosynthesis and the effects of IAA exposure on the proteome of the plant-associated microbe Pantoea sp. YR343
Possible reference: Estenson, K. et al. (2018) Characterization of Indole-3-acetic Acid Biosynthesis and the Effects of This Phytohormone on the Proteome of the Plant-Associated Microbe Pantoea sp. YR343., J Proteome Res, PMID 29464956

PXD007531 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics based identification and validation of biomarkers for AMD
Possible reference: Kim, HJ. et al. (2016) Proteomics-based identification and validation of novel plasma biomarkers phospholipid transfer protein and mannan-binding lectin serine protease-1 in age-related macular degeneration., Sci Rep, PMID 27605007

PXD007248 no publication (from MassIVE)
Dataset title: Blood from GAS- and mock-infected mice
Possible reference: Almeida-Souza, F. et al. (2016) Morinda citrifolia Linn. Reduces Parasite Load and Modulates Cytokines and Extracellular Matrix Proteins in C57BL/6 Mice Infected with Leishmania (Leishmania) amazonensis., PLoS Negl Trop Dis, PMID 27579922

PXD007213 no publication (from MassIVE)
Dataset title: Defining Host Responses During Systemic Bacterial Infection Through Construction of a Murine Organ Proteome Atlas
Possible reference: Lapek, JD. et al. (2018) Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas., Cell Syst, PMID 29778837

PXD007197 no publication (from MassIVE)
Dataset title: Comparison of genomes and proteomes of whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds
Possible reference: Clark, CG. et al. (2018) Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds., PLoS One, PMID 29293692

PXD007162 Dataset with its publication pending (from PRIDE)
Dataset title: The proteome of germlings from urediniospores of Puccinia triticina
Possible reference: Ozketen, AC. et al. (2026) The proteome study of germinated Puccinia triticina urediniospores reveals a novel effector protein required for virulence., Sci Rep, PMID 41965863

PXD007141 no publication (from MassIVE)
Dataset title: Refinement of synapses without postsynaptic activity: Role for a 4E-BP dependent mechanism
Possible reference: Chong, Y. et al. (2018) Removing 4E-BP Enables Synapses to Refine without Postsynaptic Activity., Cell Rep, PMID 29617653

PXD007047 no publication (from MassIVE)
Dataset title: Proteomic analysis of antigen-specific serum and gut antibodies in celiac disease patients
Possible reference: Iversen, R. et al. (2017) Strong Clonal Relatedness between Serum and Gut IgA despite Different Plasma Cell Origins., Cell Rep, PMID 28877470

PXD006933 Dataset with its publication pending (from PRIDE)
Dataset title: THE PROTEOME SPECIATION OF AN IMMORTALIZED CYSTIC FIBROSIS CELL LINE: NEW PERSPECTIVES ON THE PATHOPHYSIOLOGY OF THE DISEASE.
Possible reference: Puglia, M. et al. (2018) The proteome speciation of an immortalized cystic fibrosis cell line: New perspectives on the pathophysiology of the disease., J Proteomics, PMID 28970102

PXD006925 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of extracellular vesicles from a Plasmodium falciparum Kenyan clinical isolate defines a core parasite secretome
Possible reference: Abdi, A. et al. (2017) Proteomic analysis of extracellular vesicles from a Plasmodium falciparum Kenyan clinical isolate defines a core parasite secretome., Wellcome Open Res, PMID 28944300

PXD006865 Dataset with its publication pending (from PRIDE)
Dataset title: Human osteoblast-derived extracellular matrix with high homology to human bone proteome is osteopromotive for mesenchymal stromal cells
Possible reference: Baroncelli, M. et al. (2018) Human Osteoblast-Derived Extracellular Matrix with High Homology to Bone Proteome Is Osteopromotive., Tissue Eng Part A, PMID 29667532

PXD006794 no publication (from MassIVE)
Dataset title: Profiling of proteins secreted in the bovine oviduct reveals diverse functions of this luminal microenvironment
Possible reference: Pillai, VV. et al. (2017) Profiling of proteins secreted in the bovine oviduct reveals diverse functions of this luminal microenvironment., PLoS One, PMID 29155854

PXD006782 no publication (from MassIVE)
Dataset title: Mechanisms connecting the conserved protein kinases Kin1, Pom1, and Ssp1 in fission yeast cell polarity and division
Possible reference: Lee, ME. et al. (2018) Mechanisms Connecting the Conserved Protein Kinases Ssp1, Kin1, and Pom1 in Fission Yeast Cell Polarity and Division., Curr Biol, PMID 29249658

PXD006721 no publication (from MassIVE)
Dataset title: Mechanisms of subzero growth in the cryophile Planococcus halocryophilus determined through proteomic analysis
Possible reference: Raymond-Bouchard, I. et al. (2017) Mechanisms of subzero growth in the cryophile Planococcus halocryophilus determined through proteomic analysis., Environ Microbiol, PMID 28834033

PXD006681 no publication (from MassIVE)
Dataset title: Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice
Possible reference: Deol, P. et al. (2017) Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice., Sci Rep, PMID 28970503

PXD006680 Dataset with its publication pending (from PRIDE)
Dataset title: Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal Modifications in Cells
Possible reference: Sun, R. et al. (2017) Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal Modifications in Cells., Mol Cell Proteomics, PMID 28814509

PXD006612 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Analyses of Cysteine Redox in High-fat-fed and Fasted Mouse Livers: Implications for Liver Metabolic Homeostasis
Possible reference: Li, Y. et al. (2018) Proteomic Analyses of Cysteine Redox in High-Fat-Fed and Fasted Mouse Livers: Implications for Liver Metabolic Homeostasis., J Proteome Res, PMID 29098862

PXD006586 no publication (from MassIVE)
Dataset title: Blue light and CO2 signals converge to regulate light-induced stomatal opening
Possible reference: Hiyama, A. et al. (2017) Blue light and CO2 signals converge to regulate light-induced stomatal opening., Nat Commun, PMID 29101334

PXD006567 Dataset with its publication pending (from PRIDE)
Dataset title: An Insight into Glyco-microheterogeneity of Plasma von Willebrand Factor (vWF) by Mass Spectrometry
Possible reference: Gashash, EA. et al. (2017) An Insight into Glyco-Microheterogeneity of Plasma von Willebrand Factor by Mass Spectrometry., J Proteome Res, PMID 28696719

PXD006565 Dataset with its publication pending (from jPOST)
Dataset title: CEBPbeta interacting partners identification.
Possible reference: Nishimura, R. et al. (2018) Transcriptional network systems in cartilage development and disease., Histochem Cell Biol, PMID 29308531

PXD006548 Dataset with its publication pending (from PRIDE)
Dataset title: Potential molecular mechanisms of overgrazing-induced plant dwarf of sheepgrass (Leymus chinensis) analyzed using proteome data
Possible reference: Ren, W. et al. (2018) Potential molecular mechanisms of overgrazing-induced dwarfism in sheepgrass (Leymus chinensis) analyzed using proteomic data., BMC Plant Biol, PMID 29739327

PXD006521 no publication (from MassIVE)
Dataset title: Massey Dolin Hepatology 2017 Hepatic matrisome response to injury
Possible reference: Massey, VL. et al. (2017) The hepatic "matrisome" responds dynamically to injury: Characterization of transitional changes to the extracellular matrix in mice., Hepatology, PMID 28035785

PXD006485 no publication (from MassIVE)
Dataset title: CDK7/TFIIH regulates SETD1A/B activity
Possible reference: Ebmeier, CC. et al. (2017) Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications., Cell Rep, PMID 28768201

PXD006452 Dataset with its publication pending (from PRIDE)
Dataset title: CDK5 and GSK3 mediate neuroinflammation-induced neurodegeneration
Possible reference: Reinhardt, L. et al. (2019) Dual Inhibition of GSK3β and CDK5 Protects the Cytoskeleton of Neurons from Neuroinflammatory-Mediated Degeneration In Vitro and In Vivo., Stem Cell Reports, PMID 30773488

PXD006361 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics Reveal Global Regulation of Protein SUMOylation by ATM and ATR Kinases during Replication Stress
Possible reference: Munk, S. et al. (2017) Proteomics Reveals Global Regulation of Protein SUMOylation by ATM and ATR Kinases during Replication Stress., Cell Rep, PMID 29020638

PXD006357 Dataset with its publication pending (from MassIVE)
Dataset title: Cerebrospinal fluid markers to distinguish bacterial meningitis from cerebral malaria in children
Possible reference: Njunge, JM. et al. (2017) Cerebrospinal fluid markers to distinguish bacterial meningitis from cerebral malaria in children., Wellcome Open Res, PMID 29181450

PXD006304 Dataset with its publication pending (from MassIVE)
Dataset title: Analysis of neuronal phosphoproteome reveals PINK1 regulation of BAD function and cell death
Possible reference: Wan, H. et al. (2018) Analysis of neuronal phosphoproteome reveals PINK1 regulation of BAD function and cell death., Cell Death Differ, PMID 29234155

PXD006229 Dataset with its publication pending (from MassIVE)
Dataset title: O-GlcNAcylation of fumarase maintains tumour growth under glucose deficiency
Possible reference: Wang, T. et al. (2017) O-GlcNAcylation of fumarase maintains tumour growth under glucose deficiency., Nat Cell Biol, PMID 28628081

PXD006101 Dataset with its publication pending (from MassIVE)
Dataset title: Chlamydia trachomatis ChxR is a transcriptional regulator of virulence factors that function in in vivo host pathogen interactions
Possible reference: Yang, C. et al. (2017) Chlamydia trachomatis ChxR is a transcriptional regulator of virulence factors that function in in vivo host-pathogen interactions., Pathog Dis, PMID 28369275

PXD006094 no publication (from MassIVE)
Dataset title: C. elegans SUP-46, an HNRNPM family RNA-binding protein that prevents paternally-mediated epigenetic sterility
Possible reference: Johnston, WL. et al. (2017) C. elegans SUP-46, an HNRNPM family RNA-binding protein that prevents paternally-mediated epigenetic sterility., BMC Biol, PMID 28716093

PXD006013 Dataset with its publication pending (from PRIDE)
Dataset title: SILAC analysis of relative protein abundance in nuclei - PRF168 and PRF167
Possible reference: Wang, H. et al. (2012) Chromatin-Associated Proteins Revealed by SILAC-Proteomic Analysis Exhibit a High Likelihood of Requirement for Growth Fitness under DNA Damage Stress., Int J Proteomics, PMID 22900175

PXD005983 Dataset with its publication pending (from MassIVE)
Dataset title: Properties of the Cuticular Proteins of Anopheles Gambiae as Revealed by Serial Extraction of Adults
Possible reference: Zhou, Y. et al. (2017) Properties of the cuticular proteins of Anopheles gambiae as revealed by serial extraction of adults., PLoS One, PMID 28419115

PXD005945 Dataset with its publication pending (from PRIDE)
Dataset title: Deep LC-MS/MS analysis of the proteome from six cell lines
Possible reference: Wu, C. et al. (2026) Target proteomics-based analysis of the deep association between USP30 and prognosis of glioblastoma multiforme., Int J Surg, PMID 41190352

PXD005930 no publication (from MassIVE)
Dataset title: Biomimetic Virulomics
Possible reference: Lapek, JD. et al. (2017) Biomimetic Virulomics for Capture and Identification of Cell-Type Specific Effector Proteins., ACS Nano, PMID 28892626

PXD005830 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome Analysis of Non-Small Cell Lung Cancer Cell Line Secretomes and Patient Sputum Reveals Biofluid Biomarker Candidates for Cisplatin Response Prediction
Possible reference: B�ttger, F. et al. (2019) Proteome analysis of non-small cell lung cancer cell line secretomes and patient sputum reveals biofluid biomarker candidates for cisplatin response prediction., J Proteomics, PMID 30710758

PXD005829 Dataset with its publication pending (from PRIDE)
Dataset title: The 3’-UTR of MYC couples RNA polymerase II function to ribonucleotide levels
Possible reference: Dejure, FR. et al. (2017) The MYC mRNA 3'-UTR couples RNA polymerase II function to glutamine and ribonucleotide levels., EMBO J, PMID 28408437

PXD005811 Dataset with its publication pending (from MassIVE)
Dataset title: Kinobead and single-shot LC-MS profiling identifies selective PKD inhibitors
Possible reference: Golkowski, M. et al. (2017) Kinobead and Single-Shot LC-MS Profiling Identifies Selective PKD Inhibitors., J Proteome Res, PMID 28102076

PXD005797 Dataset with its publication pending (from PRIDE)
Dataset title: Extensive Peptide Fractionation and y1 Ion-based Interference Detection Enable Accurate Quantification by Isobaric Labeling and Mass Spectrometry
Possible reference: Niu, M. et al. (2017) Extensive Peptide Fractionation and y1 Ion-Based Interference Detection Method for Enabling Accurate Quantification by Isobaric Labeling and Mass Spectrometry., Anal Chem, PMID 28194965

PXD005758 Dataset with its publication pending (from PRIDE)
Dataset title: A method for spatially and temporally resolved protein network interrogation in living cells
Possible reference: Lobingier, BT. et al. (2017) An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells., Cell, PMID 28388416

PXD005617 Alexander S. Dowdell, Maxwell D. Murphy, Christina Azodi, Selene K. Swanson , Laurence Florens, Shiyong Chenac & Wolfram R. Z�ckert. Comprehensive Spatial Analysis of the Borrelia burgdorferi Lipoproteome Reveals a Compartmentalization Bias Toward the B (from MassIVE)
Dataset title: Comprehensive Spatial Analysis of the Borrelia burgdorferi Lipoproteome
Possible reference: Dowdell, AS. et al. (2017) Comprehensive Spatial Analysis of the Borrelia burgdorferi Lipoproteome Reveals a Compartmentalization Bias toward the Bacterial Surface., J Bacteriol, PMID 28069820

PXD005608 Dataset with its publication pending (from MassIVE)
Dataset title: Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression
Possible reference: Naba, A. et al. (2017) Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression., Sci Rep, PMID 28071719

PXD005591 no publication (from MassIVE)
Dataset title: Nucleoredoxin Guards against Oxidative Stress by Protecting Antioxidant Enzymes
Possible reference: Kneeshaw, S. et al. (2017) Nucleoredoxin guards against oxidative stress by protecting antioxidant enzymes., Proc Natl Acad Sci U S A, PMID 28724723

PXD005560 no publication (from MassIVE)
Dataset title: Identification of oxidative modifications of hemopexin and their physiological relevance
Possible reference: Hahl, P. et al. (2017) Identification of oxidative modifications of hemopexin and their predicted physiological relevance., J Biol Chem, PMID 28596380

PXD005542 Dataset with its publication pending (from PRIDE)
Dataset title: The papain-like cysteine proteinases NbCysP6 and NbCysP7 are highly processive enzymes with substrate specificities complementary to Nicotiana benthamiana cathepsin B
Possible reference: Paireder, M. et al. (2017) The papain-like cysteine proteinases NbCysP6 and NbCysP7 are highly processive enzymes with substrate specificities complementary to Nicotiana benthamiana cathepsin B., Biochim Biophys Acta Proteins Proteom, PMID 28188928

PXD005474 no publication (from MassIVE)
Dataset title: Proteomic analysis of pemphigus autoantibodies indicates a much larger, more diverse, and dynamic repertoire than determined by B-cell genetics
Possible reference: Chen, J. et al. (2017) Proteomic Analysis of Pemphigus Autoantibodies Indicates a Larger, More Diverse, and More Dynamic Repertoire than Determined by B Cell Genetics., Cell Rep, PMID 28052253

PXD005460 Dataset with its publication pending (from MassIVE)
Dataset title: Ethological principles predict the neuropeptides co-opted to influence parenting
Possible reference: Cunningham, CB. et al. (2017) Ethological principles predict the neuropeptides co-opted to influence parenting., Nat Commun, PMID 28145404

PXD005438 Takashi Nakasuji, Narumi Ogonuki, Tomoki Chiba, Tomomi Kato, Kumiko Shiozawa, Kenji Yamatoya, Hiromitsu Tanaka, Tadashi Kondo, Kenji Miyado, Naoyuki Miyasaka, Toshiro Kubota, Atsuo Ogura, and Hiroshi Asahara. Complementary critical functions of Zfy1 and Z (from MassIVE)
Dataset title: Complementary critical functions of Zfy1 and Zfy2 in mouse spermatogenesis and reproduction
Possible reference: Nakasuji, T. et al. (2017) Complementary Critical Functions of Zfy1 and Zfy2 in Mouse Spermatogenesis and Reproduction., PLoS Genet, PMID 28114340

PXD005279 Dataset with its publication pending (from MassIVE)
Dataset title: macroH2A is a BRCA1 ubiquitin ligase substrate
Possible reference: Kim, BJ. et al. (2017) The Histone Variant MacroH2A1 Is a BRCA1�Ubiquitin Ligase Substrate., Cell Rep, PMID 28564596

PXD005232 Dataset with its publication pending (from PRIDE)
Dataset title: N-GlycositeAtlas, a database resource for mass spectrometry-based human N-linked glycoproteins and glycosylation sites
Possible reference: Sun, S. et al. (2019) N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping., Clin Proteomics, PMID 31516400

PXD005222 Dataset with its publication pending (from PRIDE)
Dataset title: Tapered-tip Capillary Electrophoresis Nano-electrospray Ionization Mass Spectrometry for Ultrasensitive Proteomics: The Mouse Cortex
Possible reference: Choi, SB. et al. (2017) Tapered-Tip Capillary Electrophoresis Nano-Electrospray Ionization Mass Spectrometry for Ultrasensitive Proteomics: the Mouse Cortex., J Am Soc Mass Spectrom, PMID 27853976

PXD005203 Dataset with its publication pending (from MassIVE)
Dataset title: Staphylococcus aureus Secretome Profiling using Label Free Quantitation
Possible reference: Burian, M. et al. (2015) Quantitative proteomics of the human skin secretome reveal a reduction in immune defense mediators in ectodermal dysplasia patients., J Invest Dermatol, PMID 25347115

PXD005181 Dataset with its publication pending (from PRIDE)
Dataset title: Specific mixing facilitates the comparative quantification of phosphorylation sites with significant dysregulations
Possible reference: Liu, J. et al. (2017) Specific mixing facilitates the comparative quantification of phosphorylation sites with significant dysregulations., Anal Chim Acta, PMID 27916117

PXD005147 Dataset with its publication pending (from MassIVE)
Dataset title: proteomic analysis of porcine extracellular vesicles isolated from adipose tissue-derived mesenchymal stem/stromal cells
Possible reference: Eirin, A. et al. (2016) Comparative proteomic analysis of extracellular vesicles isolated from porcine adipose tissue-derived mesenchymal stem/stromal cells., Sci Rep, PMID 27786293

PXD005104 Dataset with its publication pending (from PRIDE)
Dataset title: The CVSC mechanically reinforces HSV-1
Possible reference: Snijder, J. et al. (2017) Vertex-Specific Proteins pUL17 and pUL25 Mechanically Reinforce Herpes Simplex Virus Capsids., J Virol, PMID 28381566

PXD005089 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of brain and testis reveals the diverse changes in ribosome proteins in fmr1 knockout mice
Possible reference: Xu, B. et al. (2018) Proteomic Profiling of Brain and Testis Reveals the Diverse Changes in Ribosomal Proteins in fmr1 Knockout Mice., Neuroscience, PMID 29292077

PXD005037 Dataset with its publication pending (from MassIVE)
Dataset title: Progeroid Syndrome Patients with ZMPSTE24 Deficiency Could Benefit When Treated with Rapamycin and Dimethylsulfoxide
Possible reference: Akinci, B. et al. (2017) Progeroid syndrome patients with ZMPSTE24 deficiency could benefit when treated with rapamycin and dimethylsulfoxide., Cold Spring Harb Mol Case Stud, PMID 28050601

PXD004949 Dataset with its publication pending (from PRIDE)
Dataset title: Proteogenomics of adenosine-to-inosine RNA editing in fruit fly
Possible reference: Kuznetsova, KG. et al. (2018) Proteogenomics of Adenosine-to-Inosine RNA Editing in the Fruit Fly., J Proteome Res, PMID 30298734

PXD004828 Dataset with its publication pending (from PRIDE)
Dataset title: CRL2LRR1 is required for CMG unloading during vertebrate replication termination
Possible reference: Low, E. et al. (2020) The DNA replication fork suppresses CMG unloading from chromatin before termination., Genes Dev, PMID 32943574

PXD004679 Dataset with its publication pending (from PRIDE)
Dataset title: Transcriptome and proteome studies during the development of barnacle amphitrite
Possible reference: Han, Z. et al. (2013) iTRAQ-based proteomic profiling of the barnacle Balanus amphitrite in response to the antifouling compound meleagrin., J Proteome Res, PMID 23540395

PXD004648 Dataset with its publication pending (from PRIDE)
Dataset title: ER-RIME in wt-MCF7 and MCF7-LTED
Possible reference: Ribas, R. et al. (2014) Identification of chemokine receptors as potential modulators of endocrine resistance in oestrogen receptor-positive breast cancers., Breast Cancer Res, PMID 25358600

PXD004643 Dataset with its publication pending (from PRIDE)
Dataset title: PP1 interactome during heart failure development
Possible reference: Chiang, DY. et al. (2016) Regulating the regulator: Insights into the cardiac protein phosphatase 1 interactome., J Mol Cell Cardiol, PMID 27663175

PXD004590 Dataset with its publication pending (from PRIDE)
Dataset title: Characterisation of the human hemostatic O-glycoproteome
Possible reference: King, SL. et al. (2017) Characterizing the O-glycosylation landscape of human plasma, platelets, and endothelial cells., Blood Adv, PMID 29296958

PXD004580 Dataset with its publication pending (from MassIVE)
Dataset title: Proteotranscriptomic profiling of 231-BR breast cancer cells
Possible reference: Dun, MD. et al. (2015) Proteotranscriptomic Profiling of 231-BR Breast Cancer Cells: Identification of Potential Biomarkers and Therapeutic Targets for Brain Metastasis., Mol Cell Proteomics, PMID 26041846

PXD004495 Dataset with its publication pending (from PRIDE)
Dataset title: Detection of Aggressive Prostate Cancer-Associated Glycoproteins in Urine using Glycoproteomics and Mass Spectrometry
Possible reference: Jia, X. et al. (2016) Detection of aggressive prostate cancer associated glycoproteins in urine using glycoproteomics and mass spectrometry., Proteomics, PMID 27749016

PXD004379 Shelly Rozen, et al., CSNAP Is a Stoichiometric Subunit of the COP9Signalosome 2015 13(3):585-598 (from PeptideAtlas)
Dataset title: CSNAP is a novel subunit of the COP9 signalosome
Possible reference: Barth, E. et al. (2016) The Evolution of COP9 Signalosome in Unicellular and Multicellular Organisms., Genome Biol Evol, PMID 27044515

PXD004356 Dataset with its publication pending (from PRIDE)
Dataset title: Defining the interactome of human adenine nucleotide translocases
Possible reference: Lu, YW. et al. (2017) Human adenine nucleotide translocases physically and functionally interact with respirasomes., Mol Biol Cell, PMID 28404750

PXD004290 Dataset with its publication pending (from MassIVE)
Dataset title: Comparing the diagnostic classification accuracy of iTRAQ, peak-area, spectral-counting and emPAI methods for relative quantification in expression proteomics
Possible reference: Dowle, AA. et al. (2016) Comparing the Diagnostic Classification Accuracy of iTRAQ, Peak-Area, Spectral-Counting, and emPAI Methods for Relative Quantification in Expression Proteomics., J Proteome Res, PMID 27546623

PXD004234 79) J.G. Meyer, A.K. D?Souza, D.J. Sorensen, M.J. Rardin, A.J. Wolfe, B.W. Gibson, B. Schilling. Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH). J. Amer. Soc. (from MassIVE)
Dataset title: Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH)
Possible reference: Meyer, JG. et al. (2016) Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH)., J Am Soc Mass Spectrom, PMID 27590315

PXD004224 Dataset with its publication pending (from MassIVE)
Dataset title: The Null-Test for Peptide Identification Algorithm in Shotgun Proteomics
Possible reference: Zhang, SR. et al. (2017) The Null-Test for peptide identification algorithm in Shotgun proteomics., J Proteomics, PMID 28506863

PXD004160 Dataset with its publication pending (from MassIVE)
Dataset title: Top-down venomics Mapping proteoforms and protein complexes from king cobra venom
Possible reference: Melani, RD. et al. (2016) Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics., Mol Cell Proteomics, PMID 27178327

PXD004140 Dataset with its publication pending (from PRIDE)
Dataset title: Chronic p53-independent p21 expression deregulates replication licensing, leading to genomic instability
Possible reference: Galanos, P. et al. (2016) Chronic p53-independent p21 expression causes genomic instability by deregulating replication licensing., Nat Cell Biol, PMID 27323328

PXD004136 Dataset with its publication pending (from MassIVE)
Dataset title: Post-transcriptional program governing the proteome of the green alga Micromonas pusilla
Possible reference: Waltman, PH. et al. (2016) Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla., PLoS One, PMID 27434306

PXD004058 Dataset with its publication pending (from MassIVE)
Dataset title: Cardiotoxocity of Cancer Therapy Biomarkers
Possible reference: Dieci, MV. et al. (2019) Escalation and de-escalation in HER2 positive early breast cancer., Curr Opin Oncol, PMID 30325338

PXD004038 Dataset with its publication pending (from MassIVE)
Dataset title: Lysine acetylation in Mycobacterium abscessus GZ002
Possible reference: Guo, J. et al. (2016) Identification of Lysine Acetylation in Mycobacterium abscessus Using LC-MS/MS after Immunoprecipitation., J Proteome Res, PMID 27323652

PXD003982 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling carbonylated proteins in heart and skeletal muscle mitochondria from trained and untrained mice
Possible reference: Carpentieri, A. et al. (2016) Profiling Carbonylated Proteins in Heart and Skeletal Muscle Mitochondria from Trained and Untrained Mice., J Proteome Res, PMID 27571187

PXD003862 Dataset with its publication pending (from MassIVE)
Dataset title: Top-down venomics of the East African green mamba and the black mamba
Possible reference: Petras, D. et al. (2016) Top-down venomics of the East African green mamba, Dendroaspis angusticeps, and the black mamba, Dendroaspis polylepis, highlight the complexity of their toxin arsenals., J Proteomics, PMID 27318176

PXD003834 Dataset with its publication pending (from PRIDE)
Dataset title: Role of CLRC complex in telomeric assembly of shelterin proteins
Possible reference: Shi, S. et al. (2021) Ccq1-Raf2 interaction mediates CLRC recruitment to establish heterochromatin at telomeres., Life Sci Alliance, PMID 34493579

PXD003681 Dataset with its publication pending (from MassIVE)
Dataset title: Identification of CDK1 substrates in mitosis by quantitative phosphoproteomics
Possible reference: Petrone, A. et al. (2016) Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics., Mol Cell Proteomics, PMID 27134283

PXD003626 Dataset with its publication pending (from MassIVE)
Dataset title: Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis
Possible reference: Wippler, J. et al. (2016) Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis., BMC Genomics, PMID 27871231

PXD003481 Kai-Ting Fan, Aaron K. Rendahl, Wen-Ping Chen, Dana M. Freund, William M. Gray, Jerry D. Cohen, and Adrian D. Hegeman. Proteome scale-protein turnover analysis using high resolution mass spectrometric data from stable-isotope labeled plants. J. Proteome R (from MassIVE)
Dataset title: Proteome turnover of Arabidopsis root soluble fraction
Possible reference: Fan, KT. et al. (2016) Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants., J Proteome Res, PMID 26824330

PXD003460 Dataset with its publication pending (from MassIVE)
Dataset title: Using the ubiquitin-modified proteome to monitor distinct and spatially restricted protein homeostasis dysfunction
Possible reference: Gendron, JM. et al. (2016) Using the Ubiquitin-modified Proteome to Monitor Distinct and Spatially Restricted Protein Homeostasis Dysfunction., Mol Cell Proteomics, PMID 27185884

PXD003436 Dataset with its publication pending (from PRIDE)
Dataset title: FOXE3 Contributes to Peters Anomaly through Transcriptional Regulation of an Autophagy Associated Protein termed DNAJB1
Possible reference: Khan, SY. et al. (2016) FOXE3 contributes to Peters anomaly through transcriptional regulation of an autophagy-associated protein termed DNAJB1., Nat Commun, PMID 27218149

PXD003400 Dataset with its publication pending (from PRIDE)
Dataset title: Filter-aided sample preparation depends on filter unit shape
Possible reference: Lipecka, J. et al. (2016) Sensitivity of mass spectrometry analysis depends on the shape of the filtration unit used for filter aided sample preparation (FASP)., Proteomics, PMID 27219663

PXD003344 Robert T. Lawrence, Brian C. Searle, Ariadna Llovet, Judit Villén. Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry. Nature Methods. 2016 Mar. doi: 10.1038/nmeth.3811. (from MassIVE)
Dataset title: Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry
Possible reference: Lawrence, RT. et al. (2016) Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry., Nat Methods, PMID 27018578

PXD003261 Dataset with its publication pending (from PRIDE)
Dataset title: Vibrio cholerae VesB Analysis-posttranslational modifications
Possible reference: Gadwal, S. et al. (2018) C-terminal processing of GlyGly-CTERM containing proteins by rhombosortase in Vibrio cholerae., PLoS Pathog, PMID 30352106

PXD003184 Dataset with its publication pending (from MassIVE)
Dataset title: Identifying Predictors Of Taxane-Induced Peripheral Neuropathy Using Mass Spectrometry-based Proteomics Technology
Possible reference: Chen, EI. et al. (2015) Identifying Predictors of Taxane-Induced Peripheral Neuropathy Using Mass Spectrometry-Based Proteomics Technology., PLoS One, PMID 26710119

PXD003119 Dataset with its publication pending (from PRIDE)
Dataset title: Protein stable isotope fingerprinting (P-SIF): Chocolate Pots (Yellowstone) biomass
Possible reference: Gonzalez-Nayeck, AC. et al. (2022) Absence of canonical trophic levels in a microbial mat., Geobiology, PMID 35831948

PXD002791 Dataset with its publication pending (from MassIVE)
Dataset title: Ubiquitin-activated interaction traps (UBAITs) identify E3 ligase binding partners
Possible reference: O'Connor, HF. et al. (2015) Ubiquitin-Activated Interaction Traps (UBAITs) identify E3 ligase binding partners., EMBO Rep, PMID 26508657

PXD002764 Dataset with its publication pending (from PRIDE)
Dataset title: A combined proteomic and targeted analysis unravels new toxic mechanisms for zinc oxide nanoparticles in macrophages
Possible reference: Aude-Garcia, C. et al. (2016) A combined proteomic and targeted analysis unravels new toxic mechanisms for zinc oxide nanoparticles in macrophages., J Proteomics, PMID 26710724

PXD002730 Dataset with its publication pending (from MassIVE)
Dataset title: Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens
Possible reference: Elfenbein, JR. et al. (2015) Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens., PLoS Genet, PMID 26367458

PXD002719 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic analysis of duck lung tissue during infection of avian influenza
Possible reference: Ye, Y. et al. (2022) Differential proteome response to H5N1 highly pathogenic avian influenza (HPAI) viruses infection in duck., Front Immunol, PMID 36059479

PXD002609 Dataset with its publication pending (from MassIVE)
Dataset title: Quantitative Phosphoproteomics reveals new roles for PP6 in chromosome condensation and segregation
Possible reference: Rusin, SF. et al. (2015) Quantitative phosphoproteomics reveals new roles for the protein phosphatase PP6 in mitotic cells., Sci Signal, PMID 26462736

PXD002603 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics Analyses of Mycelium and Cysts of Phytophthora capsici
Possible reference: Pang, Z. et al. (2017) Quantitative proteomics links metabolic pathways to specific developmental stages of the plant-pathogenic oomycete Phytophthora capsici., Mol Plant Pathol, PMID 27019332

PXD002408 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative K-GG site analysis
Possible reference: Anania, VG. et al. (2014) Peptide level immunoaffinity enrichment enhances ubiquitination site identification on individual proteins., Mol Cell Proteomics, PMID 24142993

PXD002392 Dataset with its publication pending (from PRIDE)
Dataset title: Dithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions
Possible reference: Zaman, U. et al. (2015) Dithiothreitol (DTT) Acts as a Specific, UV-inducible Cross-linker in Elucidation of Protein-RNA Interactions., Mol Cell Proteomics, PMID 26450613

PXD002112 Dataset with its publication pending (from PRIDE)
Dataset title: Feedback circuitry between miR-218 repression and RTK activation in glioblastoma
Possible reference: Mathew, LK. et al. (2015) Feedback circuitry between miR-218 repression and RTK activation in glioblastoma., Sci Signal, PMID 25943352

PXD002096 Dataset with its publication pending (from PRIDE)
Dataset title: The influence of simulated microgravity on the proteome of Daphnia magna
Possible reference: Trotter, B. et al. (2015) The influence of simulated microgravity on the proteome of Daphnia magna., NPJ Microgravity, PMID 28725717

PXD002027 Dataset with its publication pending (from PRIDE)
Dataset title: Plasma membrane proteomics in the maize primary root elongation zone under water stress conditions
Possible reference: Voothuluru, P. et al. (2016) Plasma membrane proteomics in the maize primary root growth zone: novel insights into root growth adaptation to water stress., Plant Cell Environ, PMID 27341663

PXD002017 Dataset with its publication pending (from MassIVE)
Dataset title: Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging
Possible reference: Rhee, HW. et al. (2013) Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging., Science, PMID 23371551

PXD002008 Dataset with its publication pending (from MassIVE)
Dataset title: MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions
Possible reference: Rardin, MJ. et al. (2015) MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments., Mol Cell Proteomics, PMID 25987414

PXD001887 Dataset with its publication pending (from MassIVE)
Dataset title: Deep, quantitative coverage of the lysine acetylome using novel anti-acetyl-lysine antibodies
Possible reference: Svinkina, T. et al. (2015) Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow., Mol Cell Proteomics, PMID 25953088

PXD001769 Dataset with its publication pending (from PRIDE)
Dataset title: A Circular RNA Controls Ribosomal RNA Maturation and Atherosclerosis in Humans
Possible reference: Holdt, LM. et al. (2016) Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans., Nat Commun, PMID 27539542

PXD001748 no publication (from PeptideAtlas)
Dataset title: Candidate Biomarkers for Invasive Aspergillosis, Verification
Possible reference: Brasier, AR. et al. (2015) Improved Detection of Invasive Pulmonary Aspergillosis Arising during Leukemia Treatment Using a Panel of Host Response Proteins and Fungal Antigens., PLoS One, PMID 26581097

PXD001746 Graaf, et al. (from PeptideAtlas)
Dataset title: Signal transduction reaction monitoring deciphers site-specific PI3K-mTOR/MAPK pathway dynamics
Possible reference: de Graaf, EL. et al. (2015) Signal Transduction Reaction Monitoring Deciphers Site-Specific PI3K-mTOR/MAPK Pathway Dynamics in Oncogene-Induced Senescence., J Proteome Res, PMID 26011226

PXD001711 Dataset with its publication pending (from PRIDE)
Dataset title: Casein kinase 2 (CK2) phosphorylates the deubiquitylase OTUB1 at Ser16 to trigger its nuclear localisation.
Possible reference: Herhaus, L. et al. (2015) Casein kinase 2 (CK2) phosphorylates the deubiquitylase OTUB1 at Ser16 to trigger its nuclear localization., Sci Signal, PMID 25872870

PXD001634 Dataset with its publication pending (from MassIVE)
Dataset title: KCMF1 links RAD6 to UBR4 and lysosome-mediated degradation
Possible reference: Hong, JH. et al. (2015) KCMF1 (potassium channel modulatory factor 1) Links RAD6 to UBR4 (ubiquitin N-recognin domain-containing E3 ligase 4) and lysosome-mediated degradation., Mol Cell Proteomics, PMID 25582440

PXD001618 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphatase POPX2 secretome SILAC
Possible reference: Zhang, S. et al. (2017) Phosphatase POPX2 Exhibits Dual Regulatory Functions in Cancer Metastasis., J Proteome Res, PMID 27976581

PXD001614 Dataset with its publication pending (from MassIVE)
Dataset title: Potato Aphid Salivary Proteome: Identification of Aphid Phosphoproteins and Tomato Host Proteins
Possible reference: Chaudhary, R. et al. (2015) Potato aphid salivary proteome: enhanced salivation using resorcinol and identification of aphid phosphoproteins., J Proteome Res, PMID 25722084

PXD001491 Dataset with its publication pending (from PRIDE)
Dataset title: The metabolic background is a global player in Saccharomyces gene expression epistasis
Possible reference: Alam, MT. et al. (2016) The metabolic background is a global player in Saccharomyces gene expression epistasis., Nat Microbiol, PMID 27572163

PXD001306 Dataset with its publication pending (from PRIDE)
Dataset title: Cell line adaptation Changes in the proteome level during a step-wise adaptation of an adherent Madin Darby canine kidney (MDCK) cell line
Possible reference: Kluge, S. et al. (2015) Monitoring changes in proteome during stepwise adaptation of a MDCK cell line from adherence to growth in suspension., Vaccine, PMID 25891398

PXD001092 Dataset with its publication pending (from MassIVE)
Dataset title: Extracellular Matrix Signatures of Human Primary Metastatic Colon Cancers and their Liver Metastases
Possible reference: Naba, A. et al. (2014) Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver., BMC Cancer, PMID 25037231

PXD000976 Dataset with its publication pending (from PRIDE)
Dataset title: Rat Neural Stem Cell Phosphoproteome
Possible reference: Wang, S. et al. (2016) Quantitative Phosphoproteomic Study Reveals that Protein Kinase A Regulates Neural Stem Cell Differentiation Through Phosphorylation of Catenin Beta-1 and Glycogen Synthase Kinase 3β., Stem Cells, PMID 27097102

PXD000812 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of WRN protein interactome
Possible reference: Abbasi, S. et al. (2019) Mapping the Ku Interactome Using Proximity-Dependent Biotin Identification in Human Cells., J Proteome Res, PMID 30585729

PXD000614 no publication (from PeptideAtlas)
Dataset title: Investigation of proximal phosphorylation and lysine acetylation crosstalk
Possible reference: Parker, BL. et al. (2014) Structural basis for phosphorylation and lysine acetylation cross-talk in a kinase motif associated with myocardial ischemia and cardioprotection., J Biol Chem, PMID 25008320

Summary of results:
33107 Datasets already with an assoctiated PubMed ID
1 Datasets of status ' Aaron R. Goldman, Benjamin G. Bitler, Zachary Schug, Jose R. Conejo-Garcia, Rugang Zhang, and David W. Speicher. The Primary Effect on the Proteome of ARID1A-Mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post' with no articles found
3 Datasets of status '' with a possible article found
35 Datasets of status '' with no articles found
1 Datasets of status ', Next Generation Sequencing identifies CDH11 and MRC1 as novel translational biomarkers of kidney fibrosis' with no articles found
1 Datasets of status '. . .' with a possible article found
1 Datasets of status '. Endophyte-Promoted Phosphorus Solubilization in Populus. Frontiers in Plant Science (accepted).' with no articles found
1 Datasets of status '. The discovery of a Legionella phage explains a key determinant of human disease. .' with no articles found
1 Datasets of status '. The molecular basis for nuclear pore destruction by a proximity-inducing molecular glue. https://doi.org/10.1016/j.chembiol.2026.04.016.' with a possible article found
1 Datasets of status '79) J.G. Meyer, A.K. D?Souza, D.J. Sorensen, M.J. Rardin, A.J. Wolfe, B.W. Gibson, B. Schilling. Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH). J. Amer. Soc.' with a possible article found
1 Datasets of status 'A. Katherine Hatstat Hannah D. Ahrendt Matthew W. Foster Leland Mayne M. Arthur Moseley S. Walter Englander Dewey G. McCafferty. Characterization of Small-Molecule-Induced Changes in Parkinson's-Related Trafficking via the Nedd4 Ubiquitin Signaling Cascad' with no articles found
1 Datasets of status 'Acar IE, Willems E, Kersten E, Keizer-Garritsen J, Kragt E, Bakker B, Galesloot TE, Hoyng CB, Fauser S, van Gool AJ, Lechanteur YTE, Koertvely E, Nogoceke E, Gloerich J, de Jonge MI, Lor�s-Motta L, den Hollander AI. Semi-Quantitative Multiplex Profiling o' with no articles found
1 Datasets of status 'Alessio Adamiano Stefania Scialla Francesca Carella Marialuisa Casella Serena Camerini Alessandra Quarta Alexandra Muntiu Francesca Ferrari Alberto Vitali Michele Iafisco Clara Piccirillo. Simultaneous extraction of calcium phosphates and proteins from fi' with no articles found
1 Datasets of status 'Alexander G�nter * , Mohamed Ali Jarboui , Regine Lotte Muehlfriedel and Mathias W Seeliger. Exploration of the visual streak of the Mongolian gerbil as a model for the human central retina. Front. Med. February 2025 (Submitted).' with no articles found
1 Datasets of status 'Alexander S. Dowdell, Maxwell D. Murphy, Christina Azodi, Selene K. Swanson , Laurence Florens, Shiyong Chenac & Wolfram R. Z�ckert. Comprehensive Spatial Analysis of the Borrelia burgdorferi Lipoproteome Reveals a Compartmentalization Bias Toward the B' with a possible article found
1 Datasets of status 'Andrew Frando, Vishant Boradia, Marina Gritsenko, Michael-Claude Beltejar, Le Day, David R. Sherman, Shuyi Ma, Jon M. Jacobs, Christoph Grundner. The Mycobacterium tuberculosis protein O-phosphorylation landscape. bioRxiv. Epub 2022 Feb 17. doi: https://d' with a possible article found
1 Datasets of status 'Angew. Chem. Int. Ed. 2024, e202409220' with no articles found
1 Datasets of status 'Anna Lisa Montemari, Valeria Marzano, Nour Essa, Stefano Levi Mortera, Martina Rossitto, Simone Gardini, Laura Selan, Gianluca Vrenna, Andrea Onetti Muda, Lorenza Putignani, Ersilia Vita Fiscarelli. A shaving proteomic approach to unveil surface proteins ' with no articles found
1 Datasets of status 'Banerjee D, Eng T, Lau AK, Sasaki Y, Wang B, Chen Y, Prahl J-P, Singan VR, Herbert RA, Liu Y, Tanjore D, Petzold CJ, Keasling JD, Mukhopadhyay A. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at sca' with no articles found
1 Datasets of status 'Bhosale SD, Moulder R, Suomi T, et al (2024) Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk. iScience 110048. https://doi.org/https://doi.org/10.1016/j.isci.2024.110048' with a possible article found
1 Datasets of status 'Bleem, Alissa; Kuatsjah, Eugene; Presley, Gerald N.; Hinchen, Daniel J.; Zahn, Michael; Garcia, David C.; Michener, William E.; K�nig, Gerhard; Tornesakis, Konstantinos; Allemann, Marco N.; Giannone, Richard J.; McGeehan, John E.; Beckham, Gregg T.; Miche' with no articles found
1 Datasets of status 'Bonarrigo M, Geisslitz S, Scherf KA, Messina B, Russo G, Sestili F, Masci S. ATI, fructans and predictive assessment of technological quality of Sicilian tetraploid conservation and modern wheat varieties. J Cereal Sci [Internet]. 2025;123:104190. Availab' with no articles found
1 Datasets of status 'Borte�en T, M�ller T, Krijgsveld J. An integrated workflow for quantitative analysis of the newly synthesized proteome. bioRxiv [Internet]. 2023 Jan 1;2023.03.03.530942. Available from: http://biorxiv.org/content/early/2023/03/03/2023.03.03.530942.abstrac' with no articles found
1 Datasets of status 'Brianna Bibel, Elad Elkayam, Steven Silletti, Elizabeth A Komives, and Leemor Joshua-Tor. Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release. eLife (in press).' with no articles found
1 Datasets of status 'Budnik B., Levy E., Harmange G., Slavov N. Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation. https://doi.org/10.1101/102681.' with no articles found
2 Datasets of status 'Caesar LK, Kellogg JJ, Kvalheim OM, Cech RA, Cech NB. Integration of Biochemometrics and Molecular Networking to Identify Antimicrobials in Angelica keiskei. Planta Med. 2018 Jul;84(9-10):721-728. doi: 10.1055/a-0590-5223.' with no articles found
1 Datasets of status 'Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics. Bo Wen, J. Sebastian Paez, Chris Hsu, Daniele Canzani, Alexis Taylor Chang, Nicholas Shulman, Brendan X. MacLean, Matthew D. Berg, Judi' with a possible article found
1 Datasets of status 'Caroline Solazzo, William W. Fitzhugh. Proteomics identify bowhead whale muscle tissue and baleen in cinder residues at a 16th c. Basque whaling site. https://doi.org/10.1016/j.jasrep.2024.104691.' with no articles found
1 Datasets of status 'Chaitanya Dingare, Jenny Yang, Ben Steventon. Mannose is crucial for mesoderm specification and symmetry breaking in gastruloids. https://www.biorxiv.org/content/10.1101/2023.06.05.543730v2.full.' with no articles found
1 Datasets of status 'Chen A, Franks, A & Slavov, N. DART-ID increases single-cell proteome coverage. (submitted).; Chen A, Franks A & Slavov N. DART-ID increases single-cell proteome coverage. biorXiv, DOI: 10.1101/399121. PLOS Comp Bio (submitted).' with a possible article found
1 Datasets of status 'Chen, S., J. L. Baumert, and M. L. Downs. 2025. Quantification, Risk Assessment, and Mitigation of Cashew Allergen Cross-Contact in Shared Roasting Oil Systems. Journal of Food Protection:100678.' with a possible article found
1 Datasets of status 'Chevenier A, Fanuel M, Sokolova E, Latorre DM, Jouanneau D, Jeudy A, et al. Structure, function and catalytic mechanism of the carrageenan-sulfatases from the marine bacterium Zobellia galactanivorans DsijT. Carbohydr Polym. 2025;358:123487' with a possible article found
1 Datasets of status 'Christopher B. Lietz, Thomas Toneff, Charles Mosier, Sonia Podvin, Anthony J. O’Donoghue, Vivian Hook. Phosphopeptidomics Reveals Differential Phosphorylation States and Novel SxE Phosphosite Motifs of Neuropeptides in Dense Core Secretory Vesicles. J. ' with no articles found
1 Datasets of status 'Christopher R. Below ? Oliver M. Bernhardt ? Stephanie Kaspar-Sch�nefeld ? Sander Willems ? Edoardo Coronado ? Ino D. Karemaker ? Bettina Streckenbach ? Monika Pepelnjak ? Luca R�ss ? Sandra Sch�r ? Dennis Trede ? Jonathan R. Krieger ? Tejas Gandhi ? Rola' with a possible article found
1 Datasets of status 'Christopher, et al., submitted' with no articles found
1 Datasets of status 'Corey M. Nemec, Fan Yang, Joshua M. Gilmore, Corinna Hintermair, Yi-Hsuan Ho, Sandra C. Tseng, Martin Heidemann, Ying Zhang, Laurence Florens, Audrey P. Gasch, Dirk Eick, Michael P. Washburn, Gabriele Varani, and Aseem Z. Ansari. Different phosphoisoforms' with no articles found
1 Datasets of status 'Cruz-Mireles N, Os�s-Ruiz M, Derbyshire P, J�gousse C, Ryder LS, Bautista MJ, Eseola AB, Sklenar J, Tang B, Yan X, Ma W, Findlay KC, Were V, MacLean D, Talbot NJ, Menke FLH. The phosphorylation landscape of infection-related development by the rice blast ' with a possible article found
1 Datasets of status 'Cruz-Morales, Pablo, et al. "Biosynthesis of polycyclopropanated high energy biofuels." Joule 6.7 (2022): 1590-1605.' with a possible article found
1 Datasets of status 'Cucina, A., Schmidt, A.L., Di Gianvincenzo, F. et al. Paleoproteomic identification of the species used in fourteenth century gut-skin garments from the archaeological site of Nuulliit, Greenland. Scientific Reports 2024 14(13431). doi: 10.1038/s41598-024' with a possible article found
1 Datasets of status 'D. Salvach�a, A.Z. Werner, I. Pardo, M. Michalska, B.A. Black, B.S. Donohoe, S. Haugen, R. Katahira, S. Notonier, K.J. Ramirez, S.O. Purvine, E.M. Zink, Paul Abraham, R.J. Giannone, S. Poudel, P. Laible, R.L. Hettich, G.T. Beckham. Outer membrane vesicles' with a possible article found
1 Datasets of status 'Dan, Q., Chiu, Y., Lee, N. et al. A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxy acids. Nat Catal 8, 147–161 (2025). https://doi.org/10.1038/s41929-025-01299-5' with no articles found
1 Datasets of status 'Darwinian Evolution of Self-Replicating DNA in a Synthetic Protocell Zhanar Abil, Ana Mar�a Restrepo Sierra, Andreea R. Stan, Am�lie Ch�ne, Alicia del Prado, Miguel de Vega, Yannick Rondelez, Christophe Danelon https://www.nature.com/articles/s41467-024' with no articles found
4355 Datasets of status 'Dataset with its publication pending' with a possible article found
12249 Datasets of status 'Dataset with its publication pending' with no articles found
1 Datasets of status 'Dhamija B, Marathe S, Sawant V, Basu M, Attrish D, Mukherjee D, Kumar S, Pai MGJ, Wad S, Sawant A, Nayak C, Venkatesh KV, Srivastava S, Barthel SR, Purwar R. IL-17A Orchestrates Reactive Oxygen Species/HIF1α-Mediated Metabolic Reprogramming in Psoriasis.' with no articles found
1 Datasets of status 'Donghua Hu, Min Tan, Dongliang Lu, Brian Kleiboeker, Xuejing Liu, Hongsuk Park, Alexxai V. Kravitz, Kooresh I. Shoghi, Yu-Hua Tseng, Babak Razani, Akihiro Ikeda, and Irfan J. Lodhi. TMEM135 Links Peroxisomes to the Regulation of Brown Fat Mitochondrial Fi' with no articles found
1 Datasets of status 'Duriez, et al. (submitted)' with no articles found
1 Datasets of status 'Elias Roihuvuo, Lee Sturgis, Ahmed B. Montaser, Marcin Tabaka, Elliot H. Choi, Deepa Mathew, Anthi-Styliani Makiou, Kristiina M. Huttunen, Krzysztof Palczewski, Frans Vinberg, Henri Leinonen; Presynaptic Changes in Mouse Rod Photoreceptors During Early Re' with no articles found
1 Datasets of status 'Eliza A. Zalis, Austin S. Nuxoll, Sylvie Manuse,G eremy Clair, Lauren C. Radlinski, Brian P. Conlon, Joshua Adkins, Kim Lewis. Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells. mBio 10:e01930-19. doi: 10.1128/mBi' with no articles found
1 Datasets of status 'Evan E. Hubbard, Kevin Reagle, Matthew K. Lui, Maxence Derbez-Morin, Gennifer E. Merrihew, Michael J. MacCoss, Ryan R. Julian, Spontaneous isomerization of tau is most prevalent in Alzheimer’s disease, NeuroMarkers, Volume 3, Issue 2, 2026, 100152, IS' with no articles found
1 Datasets of status 'Gollan PJ, Trotta A, Bajwa AA, Mancini I, Aro E-M. Characterization of the Free and Membrane-Associated Fractions of the Thylakoid Lumen Proteome in Arabidopsis thaliana. Vol. 22, International Journal of Molecular Sciences . 2021.' with no articles found
1 Datasets of status 'Gonz�lez-G�mez, P., Echeverria, V., Estades, C.F., Perez, J.H., Krause, J.S., Sabat, P., Li, J., K�ltz, D., Wingfield, J.C. Proteome and endocrine traits in relattion to timing of stages of the annual cycle and body condition in seasonal and aseasonal env' with no articles found
1 Datasets of status 'Graaf, et al.' with a possible article found
1 Datasets of status 'Hana Antonicka, Zhen-Yuan Lin, Alexandre Janer, Mari J. Aaltonen, Woranontee Weraarpachai, Anne-Claude Gingras, Eric A. Shoubridge. A high-density human mitochondrial proximity interaction network. Cell Metabolism (pre-acceptance).' with no articles found
1 Datasets of status 'Hartman, K.; Steiner, G.; Siegel, M.; Looney, C.M.; Hickling, T.P.; Bray-French, K.; Springer, S.; Marban-Doran, C.; Ducret, A. Expanding the MAPPs Assay to Accommodate MHC-II Pan Receptors for Improved Predictability of Potential T Cell Epitopes. accep' with no articles found
1 Datasets of status 'Hempel, B.-F.; Damm, M.; G��men, B.; Karis, M.; Oguz, M.A.; Nalbantsoy, A.; S�ssmuth, R.D. Comparative Venomics of the Vipera ammodytes transcaucasiana and Vipera ammodytes montandoni from Turkey Provides Insights into Kinship. Toxins 2018, 10 (1), 23. do' with a possible article found
1 Datasets of status 'Hillestad Nel T, Peters C, Korzow Richter K, Henshilwood C, van Niekerk K, Douka K. Peptide mass fingerprinting as a tool to assess micromammal biodiversity in Pleistocene South Africa: The case of Klipdrift Shelter. Quat. Sci. Rev. 2023 Dec; 322; 108380.' with no articles found
1 Datasets of status 'Ho, T.C., Blackburn, K., Goshe, M.B., and Williamson, J.D. Identification of multiple proteins whose interaction with mannitol dehydrogenase is induced by salicylic acid: Implications for unconventional secretion. Proteomics, [O1] DOI: 10.1002/pmic.202100' with no articles found
1 Datasets of status 'Huwa, N., Sch�nenberger, R., & Groh, K. J. (2025). Development and application of a targeted phosphoproteomics method for analysing the mTOR pathway dynamics in zebrafish PAC2 cell line. Journal of Proteomics, 319, 105469.' with a possible article found
1 Datasets of status 'Ivan Avilov, Yehor Horokhovskyi, Pooja Mehta, Luisa Welp, Jasmin Jakobi, Mingfang Cai, Aleksander Orzechowski, Henning Urlaub, Juliane Liepe and Peter Lenart. Phosphoproteomic identification of Mos-MAPK targets in meiotic cell cycle and asymmetric divisio' with no articles found
1 Datasets of status 'J. Li, B.B. Levitan, S. Gomez-Jimenez and D. Kültz. Development of a gill assay library for ecological proteomics of threespine sticklebacks (Gasterosteus aculeatus). Mol. Cell. Proteomics (2018) in press.' with no articles found
4 Datasets of status 'Jean-Philippe Lambert, Sarah Picaud, Takao Fujisawa, Huayun Hou, Pavel Savitsky, Liis Uusk�la-Reimand, Gagan D. Gupta, Hala Abdouni, Zhen-Yuan Lin, Monika Tucholska, James D.R. Knight, Beatriz Gonzalez-Badillo, Nicole St-Denis, Joseph A. Newman, Manuel St' with no articles found
1 Datasets of status 'Jihye, et al. (submitted)' with no articles found
1 Datasets of status 'Jinglin L. Xie, Iryna Bohovych, Erin O.Y. Wong, Jean-Philippe Lambert, Anne-Claude Gingras, Oleh Khalimonchuk, Leah E. Cowen and Michelle D. Leach. Ydj1 governs fungal morphogenesis and stress response, and facilitates mitochondrial protein import via Mas' with no articles found
1 Datasets of status 'John D. Lapek, Jr., Mary K Lewinski, Jacob M Wozniak, John Guatelli, and David J Gonzalez. Quantitative temporal viromics of an inducible HIV-1 model yields insight to global host targets and phospho-dynamics associated with Vpr. Mol Cell Proteomics mcp.M' with no articles found
1 Datasets of status 'Josiah Hardesty, Le Day, Jeffrey Warner, Dennis Warner, Marina Gritsenko, Aliya Asghar, Andrew Stolz, Timothy Morgan, Craig McClain, Jon Jacobs, Irina Kirpich. Hepatic Protein and Phosphoprotein Signatures of Alcohol-Associated Cirrhosis and Hepatitis. Am' with a possible article found
1 Datasets of status 'Journal of the World Aquaculture Society: Volume 56, Issue 6' with no articles found
1 Datasets of status 'Justin Sanders, Bo Wen, Paul Rudnick, Rich Johnson, Christine C. Wu, Sewoong Oh, Michael J. MacCoss, William Stafford Noble A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data bioRxiv 2024.06.03.597251; doi: h' with no articles found
1 Datasets of status 'Kai-Ting Fan, Aaron K. Rendahl, Wen-Ping Chen, Dana M. Freund, William M. Gray, Jerry D. Cohen, and Adrian D. Hegeman. Proteome scale-protein turnover analysis using high resolution mass spectrometric data from stable-isotope labeled plants. J. Proteome R' with a possible article found
2 Datasets of status 'Kai-Ting Fan, Aaron K. Rendahl, Wen-Ping Chen, Dana M. Freund, William M. Gray, Jerry D. Cohen, and Adrian D. Hegeman. Proteome scale-protein turnover analysis using high resolution mass spectrometric data from stable-isotope labeled plants. J. Proteome R' with no articles found
1 Datasets of status 'Kala M Dodson, Erica M Periandri, A Yadav, M Lopes, AJ Barfield, A Ola, FN de Luna Vitorino, C Cearlock, BA Garcia, CA Hill, SE Maloney, G Egervari. ACSS2 mediates prenatal alcohol exposure-related morphological and behavioral phenotypes. Neurobiology of ' with no articles found
1 Datasets of status 'Kankuri E, Finckenberg P, Leinonen J, Tarkia M, Bj�rk S, Purhonen J, Kallij�rvi J, Kankainen M, Soliymani R, Lalowski M, Mervaala E. Altered acylcarnitine metabolism and inflexible mitochondrial fuel utilization characterize the loss of neonatal myocardia' with no articles found
1 Datasets of status 'Kaouthar Louati, Fatma Kolsi, Manel Mellouli, Hanen Louati, Rania Zribi, Rim Kallel, Mahdi Borni, Yassine Gdoura, Leila Sellami Hakim, Amina Maalej, Sirine Choura, Mohamed Chamkha, Sami Sayadi, Basma Mnif, Zouheir Khemakhem, Tahya Sellami Boudawara, Moham' with no articles found
1 Datasets of status 'Kaouthar Louati,* Amina Maalej, Fatma Kolsi, Rim Kallel, Yassine Gdoura, Mahdi Borni, Leila Sellami Hakim, Rania Zribi, Sirine Choura, Sami Sayadi, Mohamed Chamkha, Basma Mnif, Zouheir Khemakhem, Tahya Sellami Boudawara, Mohamed Zaher Boudawara, Abderrahm' with no articles found
1 Datasets of status 'Kathryn Wolhuter, Lijiang Ma, Nicole S Bryce, Osvaldo Contreras, Natalie Mellett, Ling Zhong, Chris Thekkedam, Corey Giles, Richard P Harvey, Thomas Hennessy, Chris Fouracre, David Bradley, Peter J Meikle, Johan L M Bj�rkegren, Jason C Kovacic. Multi-omic' with no articles found
1 Datasets of status 'Kegley, N. R., Ito, A., Williamson, D. B., McArdle, C. C., and Haltiwanger, R. S. Marfan syndrome variation of the POGLUT2 and POGLUT3 consensus sequence can produce aberrant fibrillin-1 O-glucosylation. Journal of Biological Chemistry' with a possible article found
1 Datasets of status 'Kevin W. Cormier, Brett Larsen, Anne-Claude Gingras, James R. Woodgett. Interactomes of Glycogen Synthase Kinase-3 Isoforms. J. Proteome Res. 2023 (in preparation).' with no articles found
1 Datasets of status 'Kopylov, et al., submitted' with no articles found
1 Datasets of status 'Kuchaříková H, Dobrovolná P, Lochmanová G, Zdráhal Z. Trimethylacetic anhydride-based derivatization facilitates quantification of histone marks at the MS1 level. Mol Cell Proteomics [Internet]. 2021;100114. Available from: https://www.sciencedirect' with no articles found
1 Datasets of status 'Lacroix, et al. (submitted)' with no articles found
1 Datasets of status 'Lauer, S.M., Gasse, J., Krizsan, A. et al. The proline-rich antimicrobial peptide Api137 disrupts large ribosomal subunit assembly and induces misfolding. Nat Commun 16, 567 (2025). https://doi.org/10.1038/s41467-025-55836-8' with no articles found
1 Datasets of status 'Lexhaller B, Colgrave ML, Scherf KA. Characterization and relative quantitation of wheat, rye and barley gluten protein types by LC-MS/MS. Frontiers in Plant Science. 2019;10:1530' with no articles found
1 Datasets of status 'Li et al., submitted' with no articles found
1 Datasets of status 'Liang K, Volk AG, Haug JS, Marshal SA, Woodfin AR, Bartom ET, Gilmore JM, Florens L, Washburn MP, Sullivan KD, Espinosa JM, Cannova J, Zhang J, Smith ER, Crispino JD, Shilatifard A. Therapeutic Targeting of MLL Degradation Pathways in MLL-Rearranged Leuke' with no articles found
1 Datasets of status 'Liblova, Z., Maurencova, D., Salovska, B., Kratky, M., Mracek, T., Korandova, Z., Pecinova, A., Vasicova, P., Rysanek, D., Andera, L., Fabrik, I., Kupcik, R., Kashmel, P., Sultana, P., Tambor, V., Bartek, J., Novak, J., Vajrychova, M. and Hodny, Z. (2025)' with no articles found
1 Datasets of status 'Locard-Paulet, et al. (submitted)' with no articles found
1 Datasets of status 'Logan G. Johnson, Chaoyu Zhai, Kitty Brown, Jessica E. Prenni, Mahesh N. Nair., Elisabeth Huff-Lonergan, and Steven M. Lonergan. Secondary Lipid Oxidation Products as Modulators of Calpain-2 Functionality In Vitro. J. Agric. Food Chem. 2024. doi: 10.1021/' with no articles found
1 Datasets of status 'M. Brackhan, G. Calza, K.Lundgren, P. Bascu�ana. T. Br�ning, R. Soliymani, R. Kumar, A. Abelein, M. Baumann, M. Lalowski. J. Pahnke. Isotope-labeled amyloid-? does not transmit to the brain in a prion-like manner after peripheral administration. EMBO Repo' with no articles found
1 Datasets of status 'Makaía M. Papasergi-Scott, Hannah M. Stoveken, Lauren MacConnachie, Pui-Yee Chan, Meital Gabay, Dorothy Wong, Robert S. Freeman, Asim A. Beg, and Gregory G. Tall. Dual phosphorylation of Ric-8A enhances its ability to mediate G protein ? subunit folding ' with no articles found
1 Datasets of status 'Marie-Therese Bammert, Ines Kollak, Jan Hoffmann, Eva Peter, Meshal Ansari, Holger Schl�ter, Jun Li, Alexandre R. Campos, Coralie Viollet, Florian Gantner, Muriel Liz�, Matthew J. Thomas, Huy Q. Le. Dual roles of fibroblast-epithelial crosstalk in acute a' with no articles found
1 Datasets of status 'Maven et al., The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5, Stem Cell Reports (2023), https://doi.org/10.1016/j.stemcr.2023.09.014' with a possible article found
1 Datasets of status 'Mayfield AB. Proteomic Signatures of Corals from Thermodynamic Reefs. Mayfield AB (2020) Proteomic Signatures of Corals from Thermodynamic Reefs. Microorganisms (in press).' with a possible article found
1 Datasets of status 'Megan L. Ludwig, David Moline, Alec Horrmann, Ella Boytim, Gabrianne Larson, Ali T. Arafa, Masooma Sayeda, John R. Lozada, Hannah E. Bergom, Abderrahman Day, Sandhyarani Dasaraju, Scott M. Dehm, Paari Murugan, Justin Hwang, Justin M. Drake & Emmanuel S. A' with no articles found
1 Datasets of status 'Mona Gr�nwald, Nabil Adrar, George Francis, Nils Rugen, Matthias D�ring, Hans-Peter Braun, Tuba Esatbeyoglu. A comparative study of the nutritional and physiological potential of Xuta (edible Jatropha curcas L.) protein: Insights into its digestibility an' with a possible article found
1 Datasets of status 'Monsalve R.I., Gutierrez R., Hoof I., Lombardero M. Purification and molecular characterization of phospholipase, antigen 5 and hyaluronidases from the venom of the Asian hornet (Vespa velutina). PLOS ONE (submitted).; . . .; Monsalve R.I., Gutierrez R., ' with no articles found
2 Datasets of status 'Montaser AB, Gao F, Peters D, Vainionp�� K, Zhibin N, Skowronska-Krawczyk D, Figeys D, Palczewski K, Leinonen H. Retinal proteome profiling of inherited retinal degeneration across three different mouse models suggests common drug targets in retinitis pig' with a possible article found
1 Datasets of status 'Moskaleva, et al., submitted (submitted)' with no articles found
1 Datasets of status 'Mu A, Tak Shun Fung, Arminja N. Kettenbach, Rajarshi Chakrabarti, Henry Higgs. A complex containing lysine-acetylated actin inhibits the formin INF2. .' with a possible article found
1 Datasets of status 'N. Pierre, V.A. Huynh-Thu, D. Baiwir, et al., Serum proteome signatures associated with ileal and colonic ulcers in Crohn's disease, Journal of Proteomics (2023), https://doi.org/10.1016/j.jprot.2024.105199' with a possible article found
3 Datasets of status 'Nicole St-Denis, Gagan D. Gupta, Zhen Yuan Lin, Beatriz Gonzalez-Badillo, Amanda O. Veri, James D.R. Knight, Dushyandi Rajendran, Amber L. Couzens, Ko W. Currie, Johnny M. Tkach, Sally W.T. Cheung, Laurence Pelletier, Anne-Claude Gingras. Phenotypic and I' with no articles found
1 Datasets of status 'Nora Jahn, Ulla Konradl, Klaus Fleissner, Sabrina Geisslitz, Katharina A. Scherf, Protein composition in ancient wheats is determined by ploidy level, Journal of Cereal Science, Volume 123, 2025, 104185' with no articles found
1 Datasets of status 'Pinto N, Nissa MU, Yashwanth BS, Sathiyanarayanan A, Pai MGJ, Srivastava S, Goswami M. Proteomics analysis of differentially abundant proteins in the rohu kidney infected with Edwardsiella tarda. Comp Biochem Physiol Part D Genomics Proteomics. 2024 Jun;5' with no articles found
2 Datasets of status 'Poverennaya, et al., submitted' with no articles found
1 Datasets of status 'Ramachandran, B. and M.L. Downs, Development and validation of a targeted mass spectrometry method for the quantification of milk protein allergens in multiple complex food matrices using matrix-independent calibration. Food Control, 2024. 162: p. 110444.' with no articles found
1 Datasets of status 'Rams�e A, van Heekeren V, Ponce P, Fischer R, Barnes I, Speller C, Collins MJ. DeamiDATE 1.0: Site-specific deamidation as a tool to assess authenticity of members of ancient proteomes. J. Archaeol. Sci. 2020 March;115:105080 doi: 10.1016/j.jas.2020.10508' with no articles found
1 Datasets of status 'Remes PM, Jacob CC, Heil LR, Shulman N, MacLean BX, MacCoss MJ. Hybrid Quadrupole Mass Filter – Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics. bioRxiv [Internet]. 2024 Jan 1;2024.05.31.59684' with no articles found
1 Datasets of status 'Robert T. Lawrence, Brian C. Searle, Ariadna Llovet, Judit Villén. Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry. Nature Methods. 2016 Mar. doi: 10.1038/nmeth.3811.' with a possible article found
1 Datasets of status 'Rocio Prisby, Alessandra Luchini, Lance A. Liotta, Caroline Solazzo. Wheat-based glues in conservation and cultural heritage: (dis)solving the proteome of flour and starch pastes and their adhering properties. https://doi.org/10.1021/acs.jproteome.3c00804' with a possible article found
1 Datasets of status 'Ryan J. Lumpkin, Alla S. Ahmad, Rachel Blake, Christopher J. Condon and Elizabeth A. Komives. The Mechanism of NEDD8 Activation of CUL5 Ubiquitin E3 Ligases. Mol. Cel. Proteomics. 2020. doi: 10.1074/mcp.RA120.002414.' with no articles found
1 Datasets of status 'Samuel W. Entwisle, Joan Sanchez-Gurmaches, Robert T. Lawrence, David J. Pedersen, Su Myung Jung, Miguel Martin-Perez, Adilson Guilherme, Michael P. Czech, David A. Guertin, Judit Villen. Cold-Induced Thermogenesis Increases Acetylation on the Brown Fat P' with no articles found
1 Datasets of status 'Saxton MW, Perry BW, Evans Hutzenbiler BD, Trojahn S, Gee A, Brown AP, Merrihew GE, Park J, Cornejo OE, MacCoss MJ, Robbins CT, Jansen HT, Kelley JL. Serum plays an important role in reprogramming the seasonal transcriptional profile of brown bear adipocy' with no articles found
1 Datasets of status 'Schertzer, M.D., Stirn, A., Isaev, K. et al. Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox. Nat Commun 16, 6948 (2025).' with a possible article found
1 Datasets of status 'Schultzhaus JN, Hervey WJ IV, Fears KP, Spillmann CM. Proteomic comparison of the organic matrices from parietal and base plate of the acorn barnacle Amphibalanus amphitrite. Open Biology. (submitted, under final review).' with no articles found
1 Datasets of status 'Shashi Jain, Cheng Hu, Jerome Kluza, Wei Ke, Madalina Giurgiu, Andreas Bleilevens, Alexandre Rosa Campos, Adriana Charbono, Elmar Stickeler, Jochen Maurer, Elke Holinski-Feder, Angela Abicht, Arkadii Vaisburg, Guangcheng Luo, Philippe Marchetti, Yabin Che' with no articles found
1 Datasets of status 'Shelly Rozen, et al., CSNAP Is a Stoichiometric Subunit of the COP9Signalosome 2015 13(3):585-598' with a possible article found
1 Datasets of status 'Shetty A, Bhosale SD, Tripathi SK, Buchacher T, Biradar R, Rasool O, Moulder R, Galande S, Lahesmaa R. Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells. ACS Omega [Internet]. 2021 Sep 16; Available from: https://doi.org/10.1021/acsomega.1c03681' with no articles found
1 Datasets of status 'Shu Q, Rajagopal M, Fan J, Zhan L, Kong X, He Y, Rotcheewaphan S, Lyon CJ, Sha W, Zelazny AM, Hu T. Peptidomic analysis of mycobacterial secreted proteins enables species identification. VIEW [Internet]. 2022 Apr 18;n/a(n/a):20210019. Available from: http' with no articles found
1 Datasets of status 'Sortase A-cleavable CD1d identifies sphingomyelins as major class of CD1d-associated lipids' with no articles found
1 Datasets of status 'Stefano Doccini*, Maria Marchese, Federica Morani, Nicola Gammaldi, Serena Mero, Francesco Pezzini, Rabah Soliymani, Melissa Santi, Giovanni Signore, Asahi Ogi, Silvia Rocchiccioli, Katja M. Kanninen, Alessandro Simonati, Maciej M. Lalowski*, Filippo M. S' with a possible article found
1 Datasets of status 'Stephan Kamrad, Clara Correia-Melo, Lukasz Szyrwiel, Simran Kaur Aulakh, J�rg B�hler, Vadim Demichev, Michael M�lleder and Markus Ralser (2023). "Metabolic heterogeneity and cross-feeding within isogenic yeast populations captured by DILAC". Nature Microb' with no articles found
1 Datasets of status 'Takashi Nakasuji, Narumi Ogonuki, Tomoki Chiba, Tomomi Kato, Kumiko Shiozawa, Kenji Yamatoya, Hiromitsu Tanaka, Tadashi Kondo, Kenji Miyado, Naoyuki Miyasaka, Toshiro Kubota, Atsuo Ogura, and Hiroshi Asahara. Complementary critical functions of Zfy1 and Z' with a possible article found
1 Datasets of status 'Tamiko Nishimura, Hana Fakima, Tobias Brandmann, Ji-Young Youn, Anne-Claude Gingras, Martin Jinek and Marc R. Fabian. MARF1 is an endoribonuclease that interacts with the DCP1:2 decapping complex and degrades target mRNAs. Nucleic Acid Research (in press)' with no articles found
1 Datasets of status 'Tim MG MacKenzie, Lucia Ramirez, Ruiqi Jian, Lihua Jiang, Michael P Snyder. Comprehensive Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2. https://www.biorxiv.org/content/10.1101/2025.07.10.663086v1.' with a possible article found
1 Datasets of status 'Timmins-Schiffman E, Maas AE, Khanna R, Blanco-Bercial L, Huang E, Nunn BL. Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod. Journal of Proteome Research, doi: 10.1021/acs.jproteome.4c00086' with no articles found
1 Datasets of status 'Timmins-Schiffman et al. 2025.Proteomic Plasticity in the Coral Montipora capitata Gamete Bundles after Parent Thermal Bleaching. Journal of Proteome Research, doi: 10.1021/acs.jproteome.4c00946' with no articles found
1 Datasets of status 'Tong Zhang, Matthew J. Gaffrey, Dennis G. Thomas, Thomas J. Weber, Becky M. Hess, Karl K.Weitz, Paul D. Piehowski, Vladislav A. Petyuk, Ronald J. Moore, Wei-Jun Qian, and Brian D. Thrall. A proteome-wide assessment of the oxidative stress paradigm for met' with a possible article found
2 Datasets of status 'Unpublished' with no articles found
1 Datasets of status 'Venkataraman YR, Timmins-Schiffman E, Horwith MJ, Lowe AT, Nunn B, Vadopalas B, Spencer LH, Roberts SB. Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences. Marine Ecology Progress Series. 2019 Feb ' with a possible article found
1 Datasets of status 'Virpi Talman, Jaakko Teppo, Päivi Pöhö, Parisa Movahedi, Anu Vaikkinen, S. Tuuli Karhu, Kajetan Trošt, Tommi Suvitaival, Jukka Heikkonen, Tapio Pahikkala, Tapio Kotiaho, Risto Kostiainen, Markku Varjosalo, Heikki Ruskoaho. Molecular Atlas of Postnatal' with no articles found
1 Datasets of status 'Waldemarson, et al. (submitted)' with no articles found
1 Datasets of status 'Waugh S, Ranasinghe A, Gomez A, Houston S, Lithgow KV, Eshghi A, Fleetwood J, Conway K, Reynolds LA and Cameron CE. Syphilis and the host; multi-omic analysis of host cellular responses to Treponema pallidum provides novel insight into syphilis pathogenes' with a possible article found
1 Datasets of status 'Wei, et al. (submitted)' with no articles found
1 Datasets of status 'Willems E, Lor�s-Motta L, Zanichelli A, Suffritti C, van der Flier M, van der Molen RG, Langereis JD, van Drongelen J, van den Heuvel LP, Volokhina E, van de Kar NCAJ, Keizer-Garritsen J, Levin M, Herberg JA, Martinon-Torres F, Wessels HJTC, de Breuk A, F' with no articles found
1 Datasets of status 'Witzel, K., Matros, A. Fructans are differentially distributed in root tissues of asparagus. Cells, 2020, 9(9). doi: 10.3390/cells9091943.' with a possible article found
1 Datasets of status 'Xavier Mayali, Ty Samo, Jeff Kimbrel, Rhona K. Stuart, Megan Morris, Kristina Rolison, Christina Ramon, Young-Mo Kim, Nathalie Munoz-Munoz, Carrie Nicora, Sam Purvine, Mary Lipton, Peter K. Weber. Single cell carbon and nitrogen incorporation and reminera' with no articles found
1 Datasets of status 'Xiaowei Gao ,Bhagyashree N. Swarge, Henk L. Dekker, Winfried Roseboom, Stanley Brul, and Gertjan Kramer. The Membrane Proteome of Spores and Vegetative Cells of the Food-Borne Pathogen Bacillus cereus. Int. J. Mol. Sci. 2021, 22(22), 12475.' with a possible article found
1 Datasets of status 'Xiaowei Gao, Bhagyashree N. Swarge, Winfried Roseboom, Yan Wang, Henk L. Dekker, Peter Setlow, Stanley Brul and Gertjan Kramer. settings Open AccessArticle Changes in the Spore Proteome of Bacillus cereus in Response to Introduction of Plasmids. Microorga' with a possible article found
1 Datasets of status 'Yannone SM, Tuteja V, Goleva O, Leung DYM, Stotland A, Keoseyan AJ, Hendricks NG, Van Eyk JE, Kreimer S. Blood to Biomarker Quantitation in Under One Hour with Rapid Proteomics using a Hyperthermoacidic Protease. bioRxiv [Preprint]. 2024 Jun 2:2024.06.01.' with no articles found
1 Datasets of status 'Yixuan Huang, Bhagyashree N. Swarge, Winfried Roseboom, Jurre D. Bleeker, Stanley Brul, Peter Setlow, Gertjan Kramer. Integrative metabolomics and proteomics allow the global intracellular characterization of Bacillus subtilis cells and spores. bioRxiv 20' with a possible article found
1 Datasets of status 'Yoneyama, et al. (submitted)' with no articles found
1 Datasets of status 'Zelter A, Riffle M, Merrihew GE, Mutawe B, Shulman N, Sanders JA, Noble WS, Johnson Erickson DP, Morimoto A, Shaver BA, Steins TN, Cao N, Ford EC, Rudnick PA, Chelsky D, Wan KH, Inman JL, Chang H, Snijders AM, Mao JH, Celniker SE, De Chant J, Obst-Huebl L' with a possible article found
1 Datasets of status 'doi: https://doi.org/10.1101/2024.11.05.622109' with a possible article found
936 Datasets of status 'no publication' with a possible article found
2571 Datasets of status 'no publication' with no articles found
1 Datasets of status 'Červenka J, Tylečková J, Kupcová Skalníková H, Vodičková Kepková K, Poliakh I, Valekova I, Pfeiferová L, Kolář M, Vaškovičová M, Pánková T, Vodička P. Proteomic characterization of human neural stem cells and their secretome during in vi' with no articles found

Announced datasets with no listed publication but with a title that brings up a hit in PubMed

RPXD034726 no publication (from jPOST)
Dataset title: JPST000096-4 Beige adipocyte phosphoproteomics [Reanalysis: JPST000096]
Possible reference: Shinoda, K. et al. (2015) Phosphoproteomics Identifies CK2 as a Negative Regulator of Beige Adipocyte Thermogenesis and Energy Expenditure., Cell Metab, PMID 26525534

RPXD034725 no publication (from jPOST)
Dataset title: JPST000096-3 Beige adipocyte phosphoproteomics [Reanalysis: JPST000096]
Possible reference: Shinoda, K. et al. (2015) Phosphoproteomics Identifies CK2 as a Negative Regulator of Beige Adipocyte Thermogenesis and Energy Expenditure., Cell Metab, PMID 26525534

RPXD034723 no publication (from jPOST)
Dataset title: JPST000096-1 Beige adipocyte phosphoproteomics [Reanalysis: JPST000096]
Possible reference: Shinoda, K. et al. (2015) Phosphoproteomics Identifies CK2 as a Negative Regulator of Beige Adipocyte Thermogenesis and Energy Expenditure., Cell Metab, PMID 26525534

RPXD034671 no publication (from jPOST)
Dataset title: JPST000589-10 Mass Spectrometry-compatible Subcellular Fractionation [Reanalysis: JPST000589]
Possible reference: Grote, E. et al. (2013) Using pure protein to build a multiple reaction monitoring mass spectrometry assay for targeted detection and quantitation., Methods Mol Biol, PMID 23606259

PXD079373 Dataset with its publication pending (from iProX)
Dataset title: Analysis of Brassica napus L. TMT proteome
Possible reference: Cao, JY. et al. (2016) TMT-based quantitative proteomics analyses reveal novel defense mechanisms of Brassica napus against the devastating necrotrophic pathogen Sclerotinia sclerotiorum., J Proteomics, PMID 26947552

PXD079162 Dataset with its publication pending (from iProX)
Dataset title: FKBP8 affinity mass spectrometry
Possible reference: Willmann, KL. et al. (2016) Expanding the Interactome of the Noncanonical NF-κB Signaling Pathway., J Proteome Res, PMID 27416764

PXD079047 Dataset with its publication pending (from iProX)
Dataset title: Complexome profiling of mitochondrial complex and respirasome assembly during cell cycle phase with or without NDUFA3 knockdown
Possible reference: Rak, M. et al. (2014) Supernumerary subunits NDUFA3, NDUFA5 and NDUFA12 are required for the formation of the extramembrane arm of human mitochondrial complex I., FEBS Lett, PMID 24717771

PXD078996 no publication (from MassIVE)
Dataset title: Ribosomal stress responses in bacteria under starvation and hypoxia
Possible reference: Vargas-Blanco, DA. et al. (2020) Regulation of mRNA Stability During Bacterial Stress Responses., Front Microbiol, PMID 33013770

PXD078759 Dataset with its publication pending (from PRIDE)
Dataset title: Potential biomarker discovery in rheumatoid arthritis serum samples using LC–MS/MS
Possible reference: McArdle, A. et al. (2016) Developing clinically relevant biomarkers in inflammatory arthritis: A multiplatform approach for serum candidate protein discovery., Proteomics Clin Appl, PMID 26332844

PXD078604 Dataset with its publication pending (from iProX)
Dataset title: Androgen Rapidly Activates Phosphorylation Signaling Pathways in Sertoli Cells
Possible reference: Chojnacka, K. et al. (2016) Hydroxyflutamide affects connexin 43 via the activation of PI3K/Akt-dependent pathway but has no effect on the crosstalk between PI3K/Akt and ERK1/2 pathways at the Raf-1 kinase level in primary rat Sertoli cells., Toxicol In Vitro, PMID 26437446

PXD078533 Dataset with its publication pending (from iProX)
Dataset title: Proteomics reveals alterations in the protein profile of Staphylococcus aureus
Possible reference: Faralli, JA. et al. (2019) Genomic/proteomic analyses of dexamethasone-treated human trabecular meshwork cells reveal a role for GULP1 and ABR in phagocytosis., Mol Vis, PMID 31516309

PXD077643 Dataset with its publication pending (from iProX)
Dataset title: Chlamydomonas reinhardtii ciliary membrane proteome
Possible reference: Shiba, D. et al. (2012) The ciliary transitional zone and nephrocystins., Differentiation, PMID 22169048

PXD077491 Dataset with its publication pending (from PRIDE)
Dataset title: Atg7–Atg12 conjugation and autophagy are negatively regulated by the disordered region of Atg12
Possible reference: Popelka, H. et al. (2026) Atg7-Atg12 conjugation and autophagy are negatively regulated by the disordered region of Atg12., Commun Biol, PMID 42141163

PXD076846 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of Lactobacillus plantarum extracellular vesicles
Possible reference: Bajic, SS. et al. (2020) Proteomic profile of extracellular vesicles released by Lactiplantibacillus plantarum BGAN8 and their internalization by non-polarized HT29 cell line., Sci Rep, PMID 33311536

PXD076715 Dataset with its publication pending (from PRIDE)
Dataset title: RpS12-mediated induction of the Xrp1short isoform links ribosomal protein mutations to cell competition
Possible reference: Tsakiri, E. et al. (2026) RpS12-mediated induction of the Xrp1short isoform links ribosomal protein mutations to cell competition., Cell Rep, PMID 42176268

PXD076071 Dataset with its publication pending (from PRIDE)
Dataset title: Cell size-dependent mRNA transcription drives proteome remodeling
Possible reference: You, DS. et al. (2026) Cell size-dependent mRNA transcription drives proteome remodeling., Cell Rep, PMID 42275220

PXD076048 Dataset with its publication pending (from iProX)
Dataset title: The cleavage sites of GmPSK4a were identified in vitro via LC-MS/MS
Possible reference: Vandenbroucke, RE. et al. (2013) Matrix metalloproteinase 13 modulates intestinal epithelial barrier integrity in inflammatory diseases by activating TNF., EMBO Mol Med, PMID 23723167

PXD075933 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of extracellular vesicles from inflammatory fibroblasts in colorectal cancer lung metastasis
Possible reference: Ye, T. et al. (2026) Vesicular QSOX1-MMP2 from inflammatory cancer-associated fibroblasts degrades the extracellular matrix to drive colorectal cancer pulmonary dissemination., Cancer Lett, PMID 42217558

PXD075872 no publication (from MassIVE)
Dataset title: IP HeLa PINK1-YFP cells with CTRL or TIMM23 sgRNA
Possible reference: Arhzaouy, K. et al. (2019) VCP maintains lysosomal homeostasis and TFEB activity in differentiated skeletal muscle., Autophagy, PMID 30654731

PXD075838 Dataset with its publication pending (from iProX)
Dataset title: Proteomic of pulp from two different banana cultivars at different ripening stages
Possible reference: Campos, NA. et al. (2022) From fruit growth to ripening in plantain: a careful balance between carbohydrate synthesis and breakdown., J Exp Bot, PMID 35512676

PXD075505 Dataset with its publication pending (from PRIDE)
Dataset title: Unveiling Alternate Pathways for SARS-CoV-2 Infection via Extracellular Vesicle-Mediated Transfer of ACE2 and TMPRSS2
Possible reference: Rea-Moreno, M. et al. (2026) Unveiling alternate pathways for SARS-CoV-2 infection via extracellular vesicle-mediated transfer of ACE2 and TMPRSS2., Nat Commun, PMID 41963354

PXD074724 no publication (from MassIVE)
Dataset title: Tyloxapol and ESX-1 secretion in Mycobacterium marinum
Possible reference: Collars, OA. et al. (2026) Tyloxapol inhibits ESX-1 secretion in Mycobacterium marinum., bioRxiv, PMID 41676709

PXD074364 Dataset with its publication pending (from jPOST)
Dataset title: HeLa TurboID-MITOL and Organelle Fractionated Proteomics Dataset
Possible reference: Hung, V. et al. (2017) Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation., Elife, PMID 28441135

PXD074350 no publication (from MassIVE)
Dataset title: Protection of teleomere1b safeguards the Arabidopsis genome by regulating ROS homeostasis
Possible reference: Min, JH. et al. (2026) Protection of telomeres 1b safeguards the Arabidopsis genome by regulating ROS homeostasis., Nat Commun, PMID 41807397

PXD074236 Dataset with its publication pending (from PRIDE)
Dataset title: SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis
Possible reference: Liu, S. et al. (2026) SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis., bioRxiv, PMID 41676593

PXD074227 Dataset with its publication pending (from iProX)
Dataset title: The Potential Core Role of the FN1-Hippo Signaling Axis in the Pathological Mechanism of Autism spectrum disorder
Possible reference: Gargus, JJ. et al. (2025) Genetic Dissection of Energy Deficiency in Autism Spectrum Disorder., Genes (Basel), PMID 40869971

PXD074134 Dataset with its publication pending (from iProX)
Dataset title: Multi-omics integrative analysis reveals that burdock seed aglycone alleviates renal fibrosis by restoring mitochondrial oxidative phosphorylation function.
Possible reference: Luo, Y. et al. (2026) Multi-omics reveals that burdock seed aglycone alleviates renal fibrosis by restoring mitochondrial oxidative phosphorylation function., J Proteomics, PMID 42276167

PXD074113 no publication (from MassIVE)
Dataset title: Assessing extracellular vesicle proteins as predictive biomarkers for developing type 1 diabetes
Possible reference: Dakup, PP. et al. (2026) Assessing extracellular vesicle proteins as predictive biomarkers for developing type 1 diabetes., bioRxiv, PMID 41727080

PXD073941 Dataset with its publication pending (from PRIDE)
Dataset title: Mycobacterium tuberculosis VadK required for regulation of the methylcitrate cycle and virulence
Possible reference: Pascoe, J. et al. (2025) VadK, a Non-Canonical Kinase that Regulates the Methylcitrate Cycle and is Essential for Mycobacterium tuberculosis Virulence., bioRxiv, PMID 41279192

PXD073739 Dataset with its publication pending (from iProX)
Dataset title: Targeting RANKL-Independent Osteoclastogenesis Overcomes Denosumab Resistance in ER+ Breast Cancer Bone Metastasis
Possible reference: Lin, Q. et al. (2026) Targeting RANKL-independent osteoclastogenesis overcomes denosumab resistance in models of ER+ breast cancer bone metastasis., J Clin Invest, PMID 42138086

PXD073053 no publication (from MassIVE)
Dataset title: Tissue-layer resolved proteome landscape of Crohns disease strictures highlights potential drivers of fibrosis progression
Possible reference: Alfredsson, J. et al. (2026) Tissue-layer-resolved proteome landscape of Crohn's disease strictures highlights potential drivers of fibrosis progression., JCI Insight, PMID 41665933

PXD072912 Dataset with its publication pending (from iProX)
Dataset title: Mitochondria-related gene and protein changes in craniosynostosis: integrated transcriptomics and Fgfr2C361Y/+ cranial suture proteomics
Possible reference: Zeng, H. et al. (2026) Mitochondria-related gene and protein changes in craniosynostosis: integrated transcriptomics and Fgfr2C361Y/+ cranial suture proteomics., Funct Integr Genomics, PMID 42258016

PXD072412 Dataset with its publication pending (from iProX)
Dataset title: GSNOR drives age-related obesity by promoting adipose tissue whitening through de-nitrosation of Beclin-1
Possible reference: Qiao, X. et al. (2026) S-nitrosoglutathione reductase GSNOR drives age-related obesity by promoting adipose tissue whitening through de-nitrosation of Beclin-1., Nat Commun, PMID 41730881

PXD072373 Dataset with its publication pending (from jPOST)
Dataset title: Improved surfactant-assisted one-pot sample preparation for robust convenient single cell proteomics
Possible reference: Xu, Z. et al. (2024) Robust Surfactant-Assisted One-Pot Sample Preparation for Label-Free Single-Cell and Nanoscale Proteomics., Methods Mol Biol, PMID 38907149

PXD071171 Dataset with its publication pending (from PRIDE)
Dataset title: Mitochondrial IntegrityMitochondrial Integrity Modulates mTOR Signaling and Podocyte Function Modulates mTOR Signaling and Podocyte Function
Possible reference: Zhang, C. et al. (2025) The compound XueShuanTong promotes podocyte mitochondrial autophagy via the AMPK/mTOR pathway to alleviate diabetic nephropathy injury., Mitochondrion, PMID 40043830

PXD070981 Dataset with its publication pending (from iProX)
Dataset title: Donkey milk Extracellular Vesicles label-free quantitative proteomics
Possible reference: Liu, Y. et al. (2025) Proteomic Profiling of Donkey Milk Exosomes Highlights Bioactive Proteins with Immune-Related Functions., Int J Mol Sci, PMID 40243471

PXD070831 Dataset with its publication pending (from PRIDE)
Dataset title: MAP4K2 promotes Treg differentiation and suppresses antitumor immunity
Possible reference: Chuang, HC. et al. (2026) MAP4K2 suppresses antitumor immunity in a pancreatic cancer model by promoting Treg differentiation., J Clin Invest, PMID 41615953

PXD070752 Kala M Dodson, Erica M Periandri, A Yadav, M Lopes, AJ Barfield, A Ola, FN de Luna Vitorino, C Cearlock, BA Garcia, CA Hill, SE Maloney, G Egervari. ACSS2 mediates prenatal alcohol exposure-related morphological and behavioral phenotypes. Neurobiology of (from MassIVE)
Dataset title: ACSS2 mediates prenatal alcohol exposure-related morphological and behavioral phenotypes
Possible reference: Dodson, KM. et al. (2025) ACSS2 mediates prenatal alcohol exposure-related morphological and behavioral phenotypes., bioRxiv, PMID 41377519

PXD070706 Dataset with its publication pending (from iProX)
Dataset title: Neuroplastin-55 is a receptor of Manf and protects against diet-induced obesity by promoting adipose browning
Possible reference: Jia, Q. et al. (2025) Neuroplastin-55 is a receptor of Manf and protects against diet-induced obesity by promoting adipose browning., Proc Natl Acad Sci U S A, PMID 41284862

PXD070394 Dataset with its publication pending (from iProX)
Dataset title: Mass-spectrometry proteomics data of Legionella effector
Possible reference: Hoffmann, C. et al. (2014) Functional analysis of novel Rab GTPases identified in the proteome of purified Legionella-containing vacuoles from macrophages., Cell Microbiol, PMID 24373249

PXD070077 Dataset with its publication pending (from PRIDE)
Dataset title: Molecular mechanisms of recruitment, function and regulation of the RNA helicase UPF1 in replication-dependent histone mRNA decay
Possible reference: Choe, J. et al. (2014) The mRNP remodeling mediated by UPF1 promotes rapid degradation of replication-dependent histone mRNA., Nucleic Acids Res, PMID 25016523

PXD069921 Dataset with its publication pending (from iProX)
Dataset title: ARCN1 suppresses innate immune responses against respiratory syncytial virus by promoting STUB1-mediated IKKÎµ degradation
Possible reference: Cai, J. et al. (2025) ARCN1 suppresses innate immune responses against respiratory syncytial virus by promoting STUB1-mediated IKKε degradation., PLoS Pathog, PMID 41343552

PXD069630 Dataset with its publication pending (from PRIDE)
Dataset title: Spatial proteomics of ovarian cancer precursors delineates early disease changes and drug targets
Possible reference: Makhmut, A. et al. (2026) Spatial proteomics of ovarian cancer precursors delineates early disease changes and drug targets., Mol Syst Biol, PMID 41233595

PXD069372 Dataset with its publication pending (from iProX)
Dataset title: Qifu Huazhuo formula for gout recurrence prevention: an interim analysis combining clinical outcomes with proteomic and metabolomic profiling
Possible reference: Shen, Z. et al. (2025) Qifu Huazhuo formula for gout recurrence prevention: an interim analysis combining clinical outcomes with proteomic and metabolomic profiling., Front Pharmacol, PMID 41190022

PXD069116 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
Possible reference: Magnitov, MD. et al. (2026) Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning., Nat Commun, PMID 42056104

PXD069021 no publication (from PanoramaPublic)
Dataset title: Age- and cell type- specific effects of histone variant H2BE in the brain
Possible reference: Louzon, S. et al. (2025) Age- and cell-type-specific effects of histone variant H2BE in the brain., Cell Rep, PMID 41379615

PXD068910 Dataset with its publication pending (from PRIDE)
Dataset title: Site- and Structure-Specific Characterization of Glycoproteins of H11: Potent Vaccine Candidates against Parasitic Worm Haemonchus
Possible reference: Liu, X. et al. (2025) Site- and structure-specific characterization of glycoproteins of H11: potent vaccine candidates against parasitic worm Haemonchus., Front Immunol, PMID 41562092

PXD068887 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic insights into the effects of cryopreservation on sperm of endangered Eld’s deer
Possible reference: Nijaran, M. et al. (2026) Proteomic insights into the effects of cryopreservation on sperm of endangered Eld's deer (Rucervus eldii)., Reprod Biol, PMID 41806660

PXD068818 Dataset with its publication pending (from iProX)
Dataset title: Revealed the key targets for molecular breeding of fine cashmere traits in cashmere goats
Possible reference: Zhao, B. et al. (2024) Stress adaptation in Tibetan cashmere goats is governed by inherent metabolic differences and manifested through variable cashmere phenotypes., Genomics, PMID 38286347

PXD068666 Dataset with its publication pending (from iProX)
Dataset title: Identification of membrane-bound proteins interacting with PLK2
Possible reference: Khalaf, O. et al. (2014) The H50Q mutation enhances α-synuclein aggregation, secretion, and toxicity., J Biol Chem, PMID 24936070

PXD068663 Dataset with its publication pending (from iProX)
Dataset title: Multiomics analysis of iPSC-derived cardiomyocytes differentiation
Possible reference: Fan, H. et al. (2026) WNT5a-Mediated Aberrant Actin Filament Dynamics Drive Cardiac Pathogenic Phenotypes in LMNA-Related Emery-Dreifuss Muscular Dystrophy., Circulation, PMID 41993022

PXD068610 no publication (from MassIVE)
Dataset title: Development and validation of a streamlined workflow for proteomic analysis of proteins and post-translational modifications from dried blood
Possible reference: Foster, MW. et al. (2025) Development and validation of a streamlined workflow for proteomic analysis of proteins and post-translational modifications from dried blood., bioRxiv, PMID 41040385

PXD068428 no publication (from MassIVE)
Dataset title: Characterisation of the Tilapia Lake Virus proteome
Possible reference: Acharya, V. et al. (2019) Structural Characterization of Open Reading Frame-Encoded Functional Genes from Tilapia Lake Virus (TiLV)., Mol Biotechnol, PMID 31664705

PXD068386 no publication (from MassIVE)
Dataset title: Capturing the RNA-binding proteome from plants using orthogonal organic phase separation
Possible reference: Liu, J. et al. (2020) Comparative analysis of RNA-binding proteomes under Arabidopsis thaliana-Pst DC3000-PAMP interaction by orthogonal organic phase separation., Int J Biol Macromol, PMID 32454107

PXD068373 no publication (from MassIVE)
Dataset title: Heat shock induces silent ribosomes and reorganizes mRNA turnover
Possible reference: Rahaman, S. et al. (2025) Heat shock induces silent ribosomes and reorganizes mRNA turnover., Cell Rep, PMID 41108687

PXD067981 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting SKAP2-modulated cytoskeleton remodeling restores sperm motility
Possible reference: Gan, S. et al. (2025) Therapeutic Repair of Sperm Quality Decline Caused by Polytetrafluoroethylene., Adv Sci (Weinh), PMID 40709753

PXD067978 no publication (from MassIVE)
Dataset title: Toward Minimally Invasive Metabolomics: GC-MS metabolic fingerprints of Dried Blood Microsamples in comparison to Plasma
Possible reference: Marques de S� E Silva, D. et al. (2025) Toward minimally invasive metabolomics: GC-MS metabolic fingerprints of dried blood microsamples in comparison to plasma., Analyst, PMID 41221588

PXD067915 Dataset with its publication pending (from iProX)
Dataset title: mTORC1 Regulates Autophagosomal Components Recycling through SNX16 Phosphorylation
Possible reference: Que, H. et al. (2025) mTORC1 regulates autophagosomal components recycling through SNX16 phosphorylation., Proc Natl Acad Sci U S A, PMID 41237209

PXD067684 Dataset with its publication pending (from iProX)
Dataset title: A Multi-omics Comparison Unveils Convergent and Divergent Antidepressant Mechanisms of Fluoxetine and St. John's Wort extract
Possible reference: Zhang, J. et al. (2026) A multi-omics comparison unveils convergent and divergent antidepressant mechanisms of fluoxetine and St. John's wort extract., J Proteomics, PMID 41796893

PXD066897 Dataset with its publication pending (from iProX)
Dataset title: Aqueous Humor Proteome in RVO-Associated Macular Edema: Analysis During Three Consecutive Conbercept Treatments
Possible reference: Liu, S. et al. (2025) Aqueous Humor Proteome in RVO-Associated Macular Edema: Analysis during Three Consecutive Conbercept Treatments., ACS Omega, PMID 41280838

PXD066636 Dataset with its publication pending (from iProX)
Dataset title: A Resource for Exploring Regional Diversity in the Rat BrainSynaptic Proteome
Possible reference: Wang, Y. et al. (2025) A Resource for Exploring Regional Diversity in the Male Rat Brain Synaptic Proteome., Sci Data, PMID 40866373

PXD066557 Dataset with its publication pending (from PRIDE)
Dataset title: vaccination protects against COVID-associated pulmonary fibrin deposition
Possible reference: Ireland, J. et al. (2025) Vaccination protects against COVID-associated pulmonary fibrin deposition., J Virol, PMID 41196038

PXD066359 no publication (from MassIVE)
Dataset title: ERBB2 signaling drives immune cell evasion and resistance against immunotherapy in small cell lung cancer
Possible reference: Meder, L. et al. (2025) ERBB2 signaling drives immune cell evasion and resistance against immunotherapy in small cell lung cancer., Nat Commun, PMID 41361170

PXD066180 Dataset with its publication pending (from PRIDE)
Dataset title: Distinct Colitis-Associated Macrophages Drive NOD2-Dependent Bacterial Sensing and Gut Homeostasis
Possible reference: Katkar, GD. et al. (2025) Distinct Colitis-Associated Macrophages Drive NOD2-Dependent Bacterial Sensing and Gut Homeostasis., bioRxiv, PMID 40766554

PXD065682 Dataset with its publication pending (from jPOST)
Dataset title: Phosphorylated filamin-A at Serine 1459 from plasma-derived small extracellular vesicles as a promising biomarker for high-risk adenoma and colorectal cancer
Possible reference: Verathamjamras, C. et al. (2026) Phosphorylated filamin-A at serine 1459 from plasma-derived small extracellular vesicles as a promising biomarker for high-risk adenoma and colorectal cancer., Sci Rep, PMID 41998177

PXD065646 Dataset with its publication pending (from iProX)
Dataset title: CD169+ Macrophages Identify and Eliminate Tumor Cells in Colorectal Cancer through CD169/CD43 Interaction and FasL-Driven Apoptosis
Possible reference: Hu, J. et al. (2025) CD169+ macrophages identify and eliminate tumor cells in colorectal cancer through CD169/CD43 interaction and FasL-driven apoptosis., Cell Rep, PMID 41016034

PXD065626 no publication (from MassIVE)
Dataset title: ASPPs multimerize protein phosphatase 1
Possible reference: Wei, DT. et al. (2025) ASPPs multimerize protein phosphatase 1., bioRxiv, PMID 40475493

PXD065562 Dataset with its publication pending (from PRIDE)
Dataset title: Hypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity
Possible reference: Sanchez-Garcia, MA. et al. (2025) Hypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity., Nat Immunol, PMID 41152617

PXD065519 Dataset with its publication pending (from PRIDE)
Dataset title: Hypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity
Possible reference: Sanchez-Garcia, MA. et al. (2025) Hypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity., Nat Immunol, PMID 41152617

PXD065481 Dataset with its publication pending (from iProX)
Dataset title: Aggresomes protect mRNA under stress in Escherichia coli
Possible reference: Pei, L. et al. (2025) Aggresomes protect mRNA under stress in Escherichia coli., Nat Microbiol, PMID 40830717

PXD065470 no publication (from MassIVE)
Dataset title: Catabolism of lignin-related methoxylated compounds in white-rot fungi utilizes a non-canonical extradiol dioxygenase
Possible reference: Schwartz, A. et al. (2026) Catabolism of lignin-related methoxylated compounds in white-rot fungi utilizes non-canonical oxidoreductases., Cell Rep, PMID 42217187

PXD065219 no publication (from MassIVE)
Dataset title: Cell-Type Resolved Protein Atlas of Brain Lysosomes Identifies SLC45A1-Associated Disease as a Lysosomal Disorder
Possible reference: Ghoochani, A. et al. (2024) Cell-Type Resolved Protein Atlas of Brain Lysosomes Identifies SLC45A1-Associated Disease as a Lysosomal Disorder., bioRxiv, PMID 39464040

PXD065166 Dataset with its publication pending (from PRIDE)
Dataset title: Bariatric surgery fecal metaproteomics
Possible reference: Haange, SB. et al. (2020) Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss., Microbiome, PMID 32033593

PXD064713 Dataset with its publication pending (from iProX)
Dataset title: Exercise releases extracellular vesicles to inhibit immune response
Possible reference: Tong, J. et al. (2026) Physical activity reshapes intrapancreatic immune and inflammatory programmes to restrain chronic pancreatitis., Gut, PMID 42209195

PXD064162 no publication (from MassIVE)
Dataset title: Integrated multi-omic analysis reveals novel subtype-specific regulatory interactions in pediatric B-cell acute lymphoblastic leukemia
Possible reference: Pushel, I. et al. (2025) Integrated multi-omic analysis reveals novel subtype-specific regulatory interactions in pediatric B-cell acute lymphoblastic leukemia., bioRxiv, PMID 40832224

PXD063986 no publication (from MassIVE)
Dataset title: Proteomics of Z.mobilis resistance to ferulic acid
Possible reference: Eckmann, JB. et al. (2025) Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance in Zymomonas mobilis., bioRxiv, PMID 40791428

PXD063945 Dataset with its publication pending (from iProX)
Dataset title: Lactylome Reprogramming Mediates Therapeutic Response and Resistance to Neoadjuvant Chemotherapy in Esophageal Squamous Cell Carcinoma
Possible reference: Peng, P. et al. (2026) Lactylome Reprogramming Mediates Therapeutic Response and Adaptation to Neoadjuvant Chemotherapy in Esophageal Squamous Cell Carcinoma., Mol Cell Proteomics, PMID 41933727

PXD063938 Dataset with its publication pending (from PRIDE)
Dataset title: Age-related proteomic profiling of livers from Caspase-2 deficient mice
Possible reference: Wilson, CH. et al. (2015) Age-related proteostasis and metabolic alterations in Caspase-2-deficient mice., Cell Death Dis, PMID 25611376

PXD063423 Dataset with its publication pending (from iProX)
Dataset title: Photocatalytic Proximity Labeling Coupled with Cross-linking for Deciphering of the Lysosome Proteome in Living Cells
Possible reference: Wang, H. et al. (2025) Photocatalytic proximity labeling coupled with cross-linking for deciphering of the lysosome proteome in living cells., Anal Chim Acta, PMID 41167898

PXD063385 Dataset with its publication pending (from PRIDE)
Dataset title: Clinical investigation on nebulized human umbilical cord MSC-derived extracellular vesicles for pulmonary fibrosis treatment
Possible reference: Li, M. et al. (2025) Clinical investigation on nebulized human umbilical cord MSC-derived extracellular vesicles for pulmonary fibrosis treatment., Signal Transduct Target Ther, PMID 40461474

PXD063374 Dataset with its publication pending (from iProX)
Dataset title: Tandem mass tag-based proteomics analysis to reveal growth stage-dependent pathways in Dendrobium nobile Lindl
Possible reference: Chen, W. et al. (2025) Tandem mass tag-based proteomics analysis to reveal growth stage-dependent pathways in Dendrobium nobile Lindl., J Chromatogr B Analyt Technol Biomed Life Sci, PMID 40393349

PXD063172 Dataset with its publication pending (from iProX)
Dataset title: integrating transcriptomic, proteomic, and interactome identify potential therapeutic targets for COVID-19 and long COVID
Possible reference: Yang, X. et al. (2025) Multi-Omics Blood Atlas Reveals Host Immune Response Features of Immunocompromised Populations Following SARS-CoV-2 Infection., Mol Cell Proteomics, PMID 40939689

PXD062904 Dataset with its publication pending (from iProX)
Dataset title: Biocompatible and Antifouling Poly(N-(2-hydroxypropyl) methacrylamide)-Coated Capillaries via Aqueous RAFT Polymerization Method for Clinical Proteomics Analysis of Non-Small Cell Lung Cancer Tissue by CZE-ESI-MS/MS
Possible reference: Yang, M. et al. (2025) Biocompatible and Antifouling Linear Poly(N-(2-hydroxypropyl)methacrylamide)-Coated Capillaries via Aqueous RAFT Polymerization Method for Clinical Proteomics Analysis of Non-Small Cell Lung Cancer Tissue by CZE-ESI-MS/MS., Anal Chem, PMID 40560905

PXD062889 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery of a bifunctional PKMYT1-targeting PROTAC empowered by AI-generation
Possible reference: Wang, Y. et al. (2025) Discovery of a bifunctional PKMYT1-targeting PROTAC empowered by AI-generation., Nat Commun, PMID 41315240

PXD062788 no publication (from MassIVE)
Dataset title: Proteomic profiling of primary cilia in the developing brain uncovers new regulators of cortical development
Possible reference: Liu, X. et al. (2025) Proteomic profiling of primary cilia in the developing brain uncovers new regulators of cortical development., bioRxiv, PMID 40654709

PXD062767 Dataset with its publication pending (from iProX)
Dataset title: Deciphering Multi-Organ Protein Regulatory Strategies in Pelophylax nigromaculatus During Hibernation to Elucidate Energy Homeostasis Maintenance Mechanisms
Possible reference: Han, J. et al. (2025) Deciphering multi-organ protein regulatory strategies in the Asian frog, Pelophylax nigromaculatus during hibernation to elucidate energy homeostasis maintenance mechanisms., Comp Biochem Physiol Part D Genomics Proteomics, PMID 40795786

PXD062758 Dataset with its publication pending (from iProX)
Dataset title: New mechanistic understanding of FXR agonist Vonafexor: inducing sublethal damage of HBV-positive liver cancer cells via promoting anti-tumor immunity
Possible reference: Pan, B. et al. (2025) New mechanistic understanding of FXR agonist Vonafexor: inducing sublethal damage of HBV-positive liver cancer cells via promoting anti-tumor immunity., Br J Cancer, PMID 40588513

PXD061668 Dataset with its publication pending (from PRIDE)
Dataset title: Nucleus-translocated glucokinase functions as a protein kinase to phosphorylate TAZ and promote tumour growth
Possible reference: Zhao, G. et al. (2025) Nucleus-translocated glucokinase functions as a protein kinase to phosphorylate TAZ and promote tumour growth., Nat Commun, PMID 40759645

PXD061551 no publication (from MassIVE)
Dataset title: MS-based amyloidosis typing in FFPE tissue samples
Possible reference: Shen, K. et al. (2015) [Classification of amyloidosis by laser micro-dissection and mass spectrometry based proteomic analysis]., Zhonghua Xue Ye Xue Za Zhi, PMID 25778882

PXD061514 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of posttranslational modifications in the Vesicular Glutamate Transporter 2 (Slc17a6)
Possible reference: Zhang, CR. et al. (2015) Prenatal ethanol exposure alters adult hippocampal VGLUT2 expression with concomitant changes in promoter DNA methylation, H3K4 trimethylation and miR-467b-5p levels., Epigenetics Chromatin, PMID 26421062

PXD061087 no publication (from MassIVE)
Dataset title: An Unbiased Proteomic Platform for ATE1-based Arginylation Profiling-Ascend
Possible reference: Lin, Z. et al. (2025) An Unbiased Proteomic Platform for ATE1-based Arginylation Profiling., bioRxiv, PMID 38854050

PXD061086 Dataset with its publication pending (from PRIDE)
Dataset title: Reprogramming SREBP1-dependent lipogenesis and inflammation in high-risk breast with licochalcone A: a novel path to cancer prevention
Possible reference: Hajirahimkhan, A. et al. (2024) Reprogramming SREBP1-dependent lipogenesis and inflammation in high-risk breast with licochalcone A: a novel path to cancer prevention., bioRxiv, PMID 39651211

PXD061065 Dataset with its publication pending (from PRIDE)
Dataset title: Single cell proteomics of human brain neutrophils from glioblastoma patients
Possible reference: Song, L. et al. (2023) Integrated transcriptome, proteome and single-cell sequencing uncover the prognostic and immunological features of colony-stimulating factor 3 receptor in pan-cancer., J Gene Med, PMID 36998239

PXD060905 Dataset with its publication pending (from iProX)
Dataset title: The E3 ligase HRD1 enhances plant antiviral immunity by targeting viral movement proteins
Possible reference: Guo, ZH. et al. (2025) The E3 ligase HRD1 enhances plant antiviral immunity by targeting viral movement proteins., Cell Rep, PMID 40106437

PXD060851 Dataset with its publication pending (from PRIDE)
Dataset title: A nowhere-to-hide mechanism ensures complete piRNA-directed LINE1 methylation
Possible reference: Chowdhury, T. et al. (2026) A nowhere-to-hide mechanism ensures complete piRNA-directed DNA methylation., Nature, PMID 41535457

PXD060690 Dataset with its publication pending (from PRIDE)
Dataset title: Î±KG-mediated carnitine synthesis promotes homologous recombination via histone acetylation
Possible reference: Uboveja, A. et al. (2024) αKG-mediated carnitine synthesis promotes homologous recombination via histone acetylation., bioRxiv, PMID 38370789

PXD060557 Dataset with its publication pending (from PRIDE)
Dataset title: Ancient genomic linkage of alpha-globin and Nprl3 couples metabolism with erythropoiesis
Possible reference: Preston, AE. et al. (2023) Ancient genomic linkage couples metabolism with erythroid development., bioRxiv, PMID 37808769

PXD060537 Dataset with its publication pending (from iProX)
Dataset title: Integrated Proteomics and Metabolomics Profiling unveils biomarkers and immune characteristics for Pelvic Lymph Node Metastasis in Cervical Cancer
Possible reference: Pang, G. et al. (2025) Integrated Proteomics and Metabolomics Profiling Unveils Biomarkers and Immune Characteristics for Pelvic Lymph Node Metastasis in Cervical Cancer., J Proteome Res, PMID 41165339

PXD060534 no publication (from MassIVE)
Dataset title: Activity-based protein profiling of beta-lactam targets in Mycobacterium tuberculosis
Possible reference: Lopez Quezada, L. et al. (2020) Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases., Front Microbiol, PMID 32655524

PXD060511 no publication (from MassIVE)
Dataset title: Novel antimicrobial peptides and peptide-microbiome crosstalk in Appalachian salamander skin
Possible reference: Muletz-Wolz, CR. et al. (2025) Novel antimicrobial peptides and peptide-microbiome crosstalk in Appalachian salamander skin., NPJ Biofilms Microbiomes, PMID 41266339

PXD060404 Dataset with its publication pending (from PRIDE)
Dataset title: LONP1 regulation of mitochondrial protein folding provides insight into beta cell failure in type 2 diabetes
Possible reference: Li, J. et al. (2024) LONP1 regulation of mitochondrial protein folding provides insight into beta cell failure in type 2 diabetes., bioRxiv, PMID 38895283

PXD060223 no publication (from MassIVE)
Dataset title: A role for the autophagy receptor NBR1 in the degradation of Tau aggregates
Possible reference: Xu, Y. et al. (2019) The cargo receptor SQSTM1 ameliorates neurofibrillary tangle pathology and spreading through selective targeting of pathological MAPT (microtubule associated protein tau)., Autophagy, PMID 30290707

PXD060196 Dataset with its publication pending (from iProX)
Dataset title: MORC and ALKBH1 act antagonistically on PRC2 to control bivalent gene expression for stress tolerance
Possible reference: Zhang, X. et al. (2025) Microrchidia ATPases and DNA 6mA demethylase ALKBH1 act antagonistically on PRC2 to control chromatin structure and stress tolerance., Nat Plants, PMID 40817150

PXD060184 Dataset with its publication pending (from iProX)
Dataset title: Supernatant of ductular reactive cells
Possible reference: Chen, L. et al. (2019) Pinealectomy or light exposure exacerbates biliary damage and liver fibrosis in cholestatic rats through decreased melatonin synthesis., Biochim Biophys Acta Mol Basis Dis, PMID 30890428

PXD060099 Dataset with its publication pending (from PRIDE)
Dataset title: The HAUS6 CH domain binds microtubules to orient augmin for microtubule branching
Possible reference: W�rtz, M. et al. (2025) Conserved function of the HAUS6 calponin homology domain in anchoring augmin for microtubule branching., Nat Commun, PMID 40846850

PXD059923 Dataset with its publication pending (from PRIDE)
Dataset title: Precise Mycobacterial Species and Subspecies Identification Using the PEP-TORCH Peptidome Algorithm
Possible reference: Bao, D. et al. (2025) Precise mycobacterial species and subspecies identification using the PEP-TORCH peptidome algorithm., EMBO Mol Med, PMID 40038396

PXD059922 Dataset with its publication pending (from jPOST)
Dataset title: Increased BNIP3-mediated mitophagy attenuates GDAP1 loss of function - implications for Charcot-Marie-Tooth disease
Possible reference: Zhang, L. et al. (2025) Increased BNIP3-mediated mitophagy attenuates GDAP1 loss of function - implications for Charcot-Marie-Tooth disease 4A., Neurobiol Dis, PMID 40618856

PXD059703 Dataset with its publication pending (from iProX)
Dataset title: Metaproteomics of Daqu Samples
Possible reference: Zhao, J. et al. (2022) Quantitative metaproteomics reveals composition and metabolism characteristics of microbial communities in Chinese liquor fermentation starters., Front Microbiol, PMID 36699582

PXD059636 Dataset with its publication pending (from PRIDE)
Dataset title: Entamoeba histolytica extracellular vesicles drive pro-inflammatory monocyte signaling
Possible reference: Honecker, B. et al. (2025) Entamoeba histolytica extracellular vesicles drive pro-inflammatory monocyte signaling., PLoS Negl Trop Dis, PMID 40208874

PXD059632 no publication (from MassIVE)
Dataset title: Comparative Analysis of Glycoproteomic Software Using a Tailored Glycan Database
Possible reference: Hogan, RA. et al. (2024) "Comparative Analysis of Glycoproteomic Software Using a Tailored Glycan Database"., bioRxiv, PMID 39091841

PXD059545 Dataset with its publication pending (from PRIDE)
Dataset title: One-carbon fixation via the reductive glycine pathway exceeds yield of the Calvin cycle in bacteria
Possible reference: Dronsella, B. et al. (2025) One-carbon fixation via the synthetic reductive glycine pathway exceeds yield of the Calvin cycle., Nat Microbiol, PMID 40016510

PXD059321 Dataset with its publication pending (from iProX)
Dataset title: In-depth Spatial Proteomics for Whole Tissue Profiling by Sparse Sampling Strategy
Possible reference: Qin, R. et al. (2025) In-depth and high-throughput spatial proteomics for whole-tissue slice profiling by deep learning-facilitated sparse sampling strategy., Cell Discov, PMID 40064869

PXD058620 no publication (from MassIVE)
Dataset title: High-throughput proteomic and phosphoproteomic analysis of formalin-fixed paraffin-embedded tissue
Possible reference: Haines, M. et al. (2024) High-throughput proteomic and phosphoproteomic analysis of formalin-fixed paraffin-embedded tissue., bioRxiv, PMID 39605438

PXD058573 Dataset with its publication pending (from PRIDE)
Dataset title: Impact of exercise on the proteome of human peripheral blood mononuclear cells
Possible reference: Chen, YY. et al. (2024) Impact of Senescent Cell-Derived Extracellular Vesicles on Innate Immune Cell Function., Adv Biol (Weinh), PMID 39441562

PXD058299 Dataset with its publication pending (from iProX)
Dataset title: Proteomic Analysis of Cold Shock Protein Function in Haemaphysalis longicornis Cold Response
Possible reference: Wang, H. et al. (2025) Aquaporins modulate the cold response of Haemaphysalis longicornis via changes in gene and protein expression of fatty acids., Parasit Vectors, PMID 39994701

PXD058284 Dataset with its publication pending (from PRIDE)
Dataset title: Clinical Evaluation of Advanced MALDI-TOF MS for Carbapenemase Subtyping in Gram-negative Isolates
Possible reference: Cheon, DH. et al. (2025) Clinical evaluation of advanced MALDI-TOF MS for carbapenemase subtyping in Gram-negative isolates., J Clin Microbiol, PMID 39611795

PXD058028 Dataset with its publication pending (from jPOST)
Dataset title: Therapy-induced senescence is a drug resistance mechanism in breast cancer
Possible reference: McDermott, MSJ. et al. (2019) HER2-Targeted Tyrosine Kinase Inhibitors Cause Therapy-Induced-Senescence in Breast Cancer Cells., Cancers (Basel), PMID 30743996

PXD057744 Dataset with its publication pending (from PRIDE)
Dataset title: GLP-1R/GCGR dual agonism dissipates hepatic steatosis to restore insulin sensitivity and rescue pancreatic Î²-cell function in obese mice
Possible reference: Laker, RC. et al. (2025) GLP-1R/GCGR dual agonism dissipates hepatic steatosis to restore insulin sensitivity and rescue pancreatic β-cell function in obese male mice., Nat Commun, PMID 40399267

PXD057738 no publication (from MassIVE)
Dataset title: Pathogenesis of Diffuse Large B cell Lymphoma Proteogenotypes
Possible reference: Enssle, JC. et al. (2026) Pathogenesis of diffuse large B cell lymphoma proteogenotypes., Cancer Cell, PMID 42242231

PXD057615 Dataset with its publication pending (from PRIDE)
Dataset title: Platelet-phenotypes in chronic inflammation
Possible reference: Aslan, JE. et al. (2021) Platelet Proteomes, Pathways, and Phenotypes as Informants of Vascular Wellness and Disease., Arterioscler Thromb Vasc Biol, PMID 33441027

PXD057541 no publication (from MassIVE)
Dataset title: Small molecule-induced alterations of protein polyubiquitination revealed by mass-spectrometric ubiquitome analysis
Possible reference: F�hrer, S. et al. (2025) Small Molecule-Induced Alterations of Protein Polyubiquitination Revealed by Mass-Spectrometric Ubiquitome Analysis., Angew Chem Int Ed Engl, PMID 40444580

PXD057483 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Profiling of Latex from Hevea Species
Possible reference: Wang, D. et al. (2018) Subcellular proteome profiles of different latex fractions revealed washed solutions from rubber particles contain crucial enzymes for natural rubber biosynthesis., J Proteomics, PMID 29729991

PXD057426 Dataset with its publication pending (from PRIDE)
Dataset title: Mettl1-mediated B cell responses
Possible reference: Wang, S. et al. (2024) Aberrant METTL1-mediated tRNA m7G modification alters B-cell responses in systemic autoimmunity in humans and mice., Nat Commun, PMID 39638793

PXD057070 no publication (from MassIVE)
Dataset title: Inhibition of Ribosome Biogenesis in vivo Causes p53-Dependent Death and p53-Independent Dysfunction
Possible reference: Cho, CJ. et al. (2024) Inhibition of Ribosome Biogenesis in vivo Causes p53-Dependent Death and p53-Independent Dysfunction., bioRxiv, PMID 39386693

PXD056782 Dataset with its publication pending (from PRIDE)
Dataset title: GLP-1R associates with VAPB and SPHKAP at ERMCSs to regulate Î²-cell mitochondrial remodelling and function
Possible reference: Austin, G. et al. (2025) GLP-1R associates with VAPB and SPHKAP at ERMCSs to regulate β-cell mitochondrial remodelling and function., bioRxiv, PMID 40791518

PXD056638 Dataset with its publication pending (from iProX)
Dataset title: Quantitative Chemoproteomics Reveals Dopamine’s Protective Modification of Tau
Possible reference: Wang, Q. et al. (2025) Quantitative chemoproteomics reveals dopamine's protective modification of Tau., Nat Chem Biol, PMID 39979588

PXD056487 no publication (from MassIVE)
Dataset title: Human skeletal muscle bioenergetic pathways are altered in Alzheimers disease
Possible reference: Vina, J. et al. (2014) Pharmacological properties of physical exercise in the elderly., Curr Pharm Des, PMID 24079769

PXD056214 Dataset with its publication pending (from iProX)
Dataset title: Proteomic of anlotinib in TP53-mutated non-small cell lung cancer
Possible reference: Jiang, JM. et al. (2025) Proteomic insights into the molecular mechanism of anlotinib inhibition in TP53-mutated non-small cell lung cancer., J Proteomics, PMID 40113013

PXD055867 Dataset with its publication pending (from PRIDE)
Dataset title: Dipeptidyl peptidase DPF-3 is a gatekeeper of microRNA Argonaute compensation in animals
Possible reference: Harvey, LM. et al. (2025) Dipeptidyl peptidase DPF-3 is a gatekeeper of microRNA Argonaute compensation in animals., Nat Commun, PMID 40108168

PXD055431 Dataset with its publication pending (from iProX)
Dataset title: m5C methylome, transcriptome and proteome of sysnechocystis
Possible reference: Zuo, S. et al. (2023) NSUN2-mediated m5 C RNA methylation dictates retinoblastoma progression through promoting PFAS mRNA stability and expression., Clin Transl Med, PMID 37228185

PXD055179 Dataset with its publication pending (from PRIDE)
Dataset title: Heparin-binding human plasma proteins
Possible reference: Bjarnad�ttir, SG. et al. (2014) Affinity chromatography, two-dimensional electrophoresis, adapted immunodepletion and mass spectrometry used for detection of porcine and piscine heparin-binding human plasma proteins., J Chromatogr B Analyt Technol Biomed Life Sci, PMID 24316520

PXD055025 Dataset with its publication pending (from iProX)
Dataset title: Proteomic Analysis Reveals Differential Protein Expression in Early-Onset Preeclampsia Patients
Possible reference: Li, H. et al. (2015) Differential Proteomic Analysis of Syncytiotrophoblast Extracellular Vesicles from Early-Onset Severe Preeclampsia, using 8-Plex iTRAQ Labeling Coupled with 2D Nano LC-MS/MS., Cell Physiol Biochem, PMID 26113202

PXD054861 Dataset with its publication pending (from PRIDE)
Dataset title: Immunological landscape of human lymphoid explants during measles virus infection
Possible reference: Acklin, JA. et al. (2024) Immunological landscape of human lymphoid explants during measles virus infection., JCI Insight, PMID 39253971

PXD054650 Dataset with its publication pending (from jPOST)
Dataset title: dia-PASEF Proteomics of Tumor and Stroma LMD Enriched from Archived HNSCC Samples
Possible reference: Panigrahi, A. et al. (2024) dia-PASEF Proteomics of Tumor and Stroma LMD Enriched from Archived HNSCC Samples., bioRxiv, PMID 39149249

PXD054588 Dataset with its publication pending (from PRIDE)
Dataset title: Tumour sampling conditions perturb the metabolic landscape of clear cell renal cell carcinoma
Possible reference: Yong, C. et al. (2025) Tumour sampling conditions perturb the metabolic landscape of clear cell renal cell carcinoma., Nat Commun, PMID 41213938

PXD054059 no publication (from MassIVE)
Dataset title: Enhancing anti-EGFRvIII CAR T cell therapy against glioblastoma with a paracrine SIRPgamma-derived CD47 blocker
Possible reference: Martins, TA. et al. (2024) Enhancing anti-EGFRvIII CAR T cell therapy against glioblastoma with a paracrine SIRPγ-derived CD47 blocker., Nat Commun, PMID 39521782

PXD053959 no publication (from MassIVE)
Dataset title: Acid cleavable biotin-alkyne improves sensitivity for direct detection of biotin labeled peptides in BONCAT analysis.
Possible reference: McClatchy, DB. et al. (2024) Acid cleavable biotin-alkyne improves sensitivity for direct detection of biotin labeled peptides in BONCAT analysis., bioRxiv, PMID 39071280

PXD053512 Dataset with its publication pending (from PRIDE)
Dataset title: Longitudinal omics data and preclinical treatment identify proteasome inhibition as therapy for ibrutinib-resistant CLL
Possible reference: Arseni, L. et al. (2025) Longitudinal omics data and preclinical treatment suggest the proteasome inhibitor carfilzomib as therapy for ibrutinib-resistant CLL., Nat Commun, PMID 39863584

PXD053263 no publication (from MassIVE)
Dataset title: Characterization of PROTAC specificity and endogenous protein interactomes using ProtacID
Possible reference: Shrestha, S. et al. (2025) Characterization of PROTAC specificity and endogenous protein interactomes using ProtacID., Nat Commun, PMID 40883309

PXD052966 no publication (from MassIVE)
Dataset title: GSK3 inhibition reduces ECM production and prevents age-related macular degeneration-like pathology
Possible reference: DiCesare, SM. et al. (2023) GSK3 inhibition reduces ECM production and prevents age-related macular degeneration-like pathology., bioRxiv, PMID 38168310

PXD052838 no publication (from MassIVE)
Dataset title: Localized K63 ubiquitin signaling is regulated by VCP/p97 during oxidative stress
Possible reference: Maduka, AO. et al. (2024) Localized K63 ubiquitin signaling is regulated by VCP/p97 during oxidative stress., bioRxiv, PMID 38948861

PXD052801 Dataset with its publication pending (from PRIDE)
Dataset title: Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines
Possible reference: Bakhtina, AA. et al. (2024) Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines., bioRxiv, PMID 38915502

PXD052641 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic profiles of adult, aged, and hypertrophic mouse hearts
Possible reference: Barallobre-Barreiro, J. et al. (2021) Extracellular Matrix in Heart Failure: Role of ADAMTS5 in Proteoglycan Remodeling., Circulation, PMID 34806902

PXD052588 Dataset with its publication pending (from PRIDE)
Dataset title: Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells
Possible reference: McCreery, KP. et al. (2024) Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells., bioRxiv, PMID 39372762

PXD052440 Dataset with its publication pending (from PRIDE)
Dataset title: Restriction of Arginine Induces Antibiotic Tolerance in Staphylococcus aureus
Possible reference: Freiberg, JA. et al. (2023) Restriction of Arginine Induces Antibiotic Tolerance in Staphylococcus aureus., bioRxiv, PMID 37873095

PXD051631 Dataset with its publication pending (from iProX)
Dataset title: Burkholderia pseudomallei BipD hijacks host KLHL9/KLHL13/CUL3 E3 ligase to ubiquitinate IMMT that initiates mitophagy to evade killing
Possible reference: Nan, D. et al. (2024) Burkholderia pseudomallei BipD modulates host mitophagy to evade killing., Nat Commun, PMID 38834545

PXD051245 Dataset with its publication pending (from iProX)
Dataset title: Clinical study on the plasma of COVID-19 vaccination and breakthrough infection
Possible reference: Zhu, X. et al. (2023) Dynamics of inflammatory responses after SARS-CoV-2 infection by vaccination status in the USA: a prospective cohort study., Lancet Microbe, PMID 37659419

PXD051216 Dataset with its publication pending (from PRIDE)
Dataset title: Deciphering hepatitis B virus phospho-signature in primary human hepatocytes
Possible reference: Pastor, F. et al. (2024) Deciphering the phospho-signature induced by hepatitis B virus in primary human hepatocytes., Front Microbiol, PMID 38841065

PXD050850 Dataset with its publication pending (from iProX)
Dataset title: The Role of DNA Origami in Treating Diabetic Sepsis
Possible reference: Luo, X. et al. (2024) Role of Deoxyribonucleic Acid Origami for Alleviating Kidney and Liver Injury in Diabetic Sepsis., J Proteome Res, PMID 39264033

PXD050279 Dataset with its publication pending (from PRIDE)
Dataset title: BAG3 regulates cilia homeostasis of glioblastoma via its WW domain
Possible reference: Roth, C. et al. (2024) BAG3 regulates cilia homeostasis of glioblastoma via its WW domain., Biofactors, PMID 38655699

PXD050263 no publication (from MassIVE)
Dataset title: Deficiency in the SNARE protein SYNTAXIN-11 causes a secondary B cell defect
Possible reference: K�gl, T. et al. (2024) Patients and mice with deficiency in the SNARE protein SYNTAXIN-11 have a secondary B cell defect., J Exp Med, PMID 38722309

PXD049704 Dataset with its publication pending (from iProX)
Dataset title: Proteostatic reactivation of the developmental transcription factor TBX3 drives BRAF/MAPK-mediated tumorigenesis
Possible reference: Zhang, Z. et al. (2024) Proteostatic reactivation of the developmental transcription factor TBX3 drives BRAF/MAPK-mediated tumorigenesis., Nat Commun, PMID 38750011

PXD049255 no publication (from MassIVE)
Dataset title: Deep Proteome Turnover of Human iPSC-derived Neurons
Possible reference: Cavarischia-Rega, C. et al. (2024) Proteome Dynamics in iPSC-Derived Human Dopaminergic Neurons., Mol Cell Proteomics, PMID 39251023

PXD049121 no publication (from MassIVE)
Dataset title: Delineating Bovine Milk Derived Microvesicles from Exosomes Using Proteomics
Possible reference: Couse, AD. et al. (2024) Delineating Bovine Milk Derived Microvesicles from Exosomes Using Proteomics., J Proteome Res, PMID 38805445

PXD048829 Dataset with its publication pending (from PRIDE)
Dataset title: Fibroblasts’ secretome from calcified and non-calcified dermis in Pseudoxanthoma elasticum differently contributes to elastin calcification.
Possible reference: Lofaro, FD. et al. (2024) Fibroblasts' secretome from calcified and non-calcified dermis in Pseudoxanthoma elasticum differently contributes to elastin calcification., Commun Biol, PMID 38755434

PXD048755 Dataset with its publication pending (from PRIDE)
Dataset title: PFKFB3 activates CAD to enhance de novo pyrimidine synthesis for cell growth
Possible reference: Da, Q. et al. (2025) PFKFB3 activates CAD to enhance de novo pyrimidine synthesis for cell growth., Cell Rep, PMID 40742808

PXD048700 no publication (from MassIVE)
Dataset title: Mitochondrial respiration is a targetable vulnerability of endocrine persistence in ER+ breast cancer
Possible reference: Tau, S. et al. (2024) Endocrine persistence in ER+ breast cancer is accompanied by metabolic vulnerability in oxidative phosphorylation., bioRxiv, PMID 39386444

PXD048134 Dataset with its publication pending (from iProX)
Dataset title: Comparative analysis of phosphorylated proteomes between plerocercoid and adult Spirometra mansoni reveal phosphoproteomic proflings of the medical tapeworm
Possible reference: Liu, YY. et al. (2024) Comparative analysis of phosphorylated proteomes between plerocercoid and adult Spirometra mansoni reveals phosphoproteomic profiles of the medical tapeworm., Parasit Vectors, PMID 39217359

PXD048004 Dataset with its publication pending (from PRIDE)
Dataset title: A pathogenic role for mitochondrial dysfunction and oxidative stress in myositis
Possible reference: Abad, C. et al. (2024) IFNγ causes mitochondrial dysfunction and oxidative stress in myositis., Nat Commun, PMID 38926363

PXD047999 Dataset with its publication pending (from PRIDE)
Dataset title: Magnesium Transporter MgtA revealed as a Dimeric P-type ATPase
Possible reference: Zeinert, R. et al. (2024) Magnesium Transporter MgtA revealed as a Dimeric P-type ATPase., bioRxiv, PMID 38464158

PXD047583 Dataset with its publication pending (from PRIDE)
Dataset title: Ubiquitin-specific proximity labeling for the identification of E3 ubiquitin ligase substrates
Possible reference: Huang, HT. et al. (2024) Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates., Nat Chem Biol, PMID 38514884

PXD047500 Dataset with its publication pending (from PRIDE)
Dataset title: Explorative study of stimulated saliva proteome in head and neck cancer patients pre-and post-treatment
Possible reference: Almh�jd, U. et al. (2024) Explorative study of stimulated saliva proteome in head and neck cancer patients pre- and post-treatment., Heliyon, PMID 39640734

PXD047492 Dataset with its publication pending (from iProX)
Dataset title: The effect of semaglutide on high-fat diet-induced liver cancer in obese mice
Possible reference: Hansen, HH. et al. (2023) Semaglutide reduces tumor burden in the GAN diet-induced obese and biopsy-confirmed mouse model of NASH-HCC with advanced fibrosis., Sci Rep, PMID 38155202

PXD047439 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes
Possible reference: Almeida, MV. et al. (2024) Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes., bioRxiv, PMID 38617250

PXD047019 Dataset with its publication pending (from PRIDE)
Dataset title: RNF212B E3 ligase is essential for crossing over maturation and mouse fertility
Possible reference: Condezo, YB. et al. (2024) RNF212B E3 ligase is essential for crossover designation and maturation during male and female meiosis in the mouse., Proc Natl Acad Sci U S A, PMID 38865271

PXD046902 Dataset with its publication pending (from PRIDE)
Dataset title: Two distinct ferredoxins are essential for nitrogen fixation by the iron nitrogenase in Rhodobacter capsulatus
Possible reference: Addison, H. et al. (2024) Two distinct ferredoxins are essential for nitrogen fixation by the iron nitrogenase in Rhodobacter capsulatus., mBio, PMID 38377621

PXD046736 Dataset with its publication pending (from PRIDE)
Dataset title: TRIM24 as therapeutic target in endocrine treatment resistant breast cancer
Possible reference: Padr�o, N. et al. (2025) TRIM24 as a therapeutic target in endocrine treatment-resistant breast cancer., Proc Natl Acad Sci U S A, PMID 40815626

PXD046294 Dataset with its publication pending (from iProX)
Dataset title: Protein expression signature in cell competition in HCC
Possible reference: Zhang, HY. et al. (2024) A prognostic four-gene signature and a therapeutic strategy for hepatocellular carcinoma: Construction and analysis of a circRNA-mediated competing endogenous RNA network., Hepatobiliary Pancreat Dis Int, PMID 37407412

PXD045938 Dataset with its publication pending (from iProX)
Dataset title: Exogenous pyruvate promotes gentamicin uptake to kill antibiotic-resistant Vibrio alginolyticus
Possible reference: Zhang, S. et al. (2019) Reduced redox-dependent mechanism and glucose-mediated reversal in gentamicin-resistant Vibrio alginolyticus., Environ Microbiol, PMID 31595636

PXD045915 no publication (from MassIVE)
Dataset title: Systematic perturbations of SETD2, NSD1, NSD2, NSD3 and ASH1L reveals their distinct contributions to H3K36 methylation
Possible reference: Shipman, GA. et al. (2023) Systematic perturbations of SETD2, NSD1, NSD2, NSD3 and ASH1L reveals their distinct contributions to H3K36 methylation., bioRxiv, PMID 37905045

PXD045834 no publication (from MassIVE)
Dataset title: NCLX proximity biotinylation screen
Possible reference: Garbincius, JF. et al. (2023) TMEM65 regulates NCLX-dependent mitochondrial calcium efflux., bioRxiv, PMID 37873405

PXD045690 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of cassava storage roots before and after shoot pruning
Possible reference: David, LC. et al. (2026) Understanding and modifying starch metabolism to limit yield losses in field-grown cassava., Plant Physiol, PMID 42243644

PXD045671 Dataset with its publication pending (from PRIDE)
Dataset title: Parkinson’s VPS35[D620N] mutation induces LRRK2 mediated lysosomal association of RILPL1 and TMEM55B
Possible reference: Pal, P. et al. (2023) Parkinson's VPS35[D620N] mutation induces LRRK2-mediated lysosomal association of RILPL1 and TMEM55B., Sci Adv, PMID 38091401

PXD045180 no publication (from MassIVE)
Dataset title: Assessing the precision of a detergent-assisted cartridge precipitation workflow for quantitative proteomics
Possible reference: Nickerson, JL. et al. (2024) Assessing the precision of a detergent-assisted cartridge precipitation workflow for non-targeted quantitative proteomics., Proteomics, PMID 38299459

PXD045012 Dataset with its publication pending (from PRIDE)
Dataset title: Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology
Possible reference: Burns, KM. et al. (2015) HX-MS2 for high performance conformational analysis of complex protein states., Protein Sci, PMID 26009873

PXD044818 Dataset with its publication pending (from PRIDE)
Dataset title: DUSP8 induces TGF-Î²-stimulated IL-9 transcription and Th9-mediated allergic inflammation by promoting nuclear export of Pur-Î±
Possible reference: Chuang, HC. et al. (2023) DUSP8 induces TGF-β-stimulated IL-9 transcription and Th9-mediated allergic inflammation by promoting nuclear export of Pur-α., J Clin Invest, PMID 37909329

PXD044773 Dataset with its publication pending (from PRIDE)
Dataset title: Cell-specific crosstalk proteomics reveals cathepsin B signaling as a driver of glioblastoma malignancy near the subventricular zone
Possible reference: Norton, ES. et al. (2023) Cell-specific crosstalk proteomics reveals cathepsin B signaling as a driver of glioblastoma malignancy near the subventricular zone., bioRxiv, PMID 37662251

PXD043879 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omic stratification of the missense variant cysteinome
Possible reference: Desai, H. et al. (2023) Multi-omic stratification of the missense variant cysteinome., bioRxiv, PMID 37645963

PXD043671 Dataset with its publication pending (from PRIDE)
Dataset title: Native Prohibitin Complex Enrichment
Possible reference: Van Strien, J. et al. (2019) COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome., Bioinformatics, PMID 30649188

PXD043666 Dataset with its publication pending (from jPOST)
Dataset title: Identify BZR1 interactome by IP-MS in Arabidopsis
Possible reference: Zhang, Z. et al. (2026) Protocol for identifying the BZR1 interactome under starvation in Arabidopsis by metabolic stable isotope labeling quantitative IP-MS., STAR Protoc, PMID 41563890

PXD043663 Dataset with its publication pending (from iProX)
Dataset title: Mechanisms research on Solasonine inhibiting Non-Small Cell Lung Cancer (NSCLC) progression
Possible reference: Wang, Y. et al. (2026) Solasonine inhibits NSCLC malignant progression by regulating SLC7A11 ubiquitination degradation and inducing ferroptosis., Respir Res, PMID 41606605

PXD043554 Dataset with its publication pending (from jPOST)
Dataset title: Deciphering cellular processes responding to lethality of 17Î²-estradiol by quantitative phosphoproteomics
Possible reference: Li, Y. et al. (2024) [Deciphering cellular processes responding to lethality of 17β-estradiol by quantitative phosphoproteomics]., Se Pu, PMID 38566422

PXD043149 Dataset with its publication pending (from iProX)
Dataset title: Autolysosomal SNX16 regulates autophagosomal components recycling
Possible reference: Que, H. et al. (2025) mTORC1 regulates autophagosomal components recycling through SNX16 phosphorylation., Proc Natl Acad Sci U S A, PMID 41237209

PXD043055 no publication (from MassIVE)
Dataset title: WNT2B is required for development and function of human intestine
Possible reference: Singh, A. et al. (2025) Mesenchymal WNT2B is required for the development and function of the human intestine., bioRxiv, PMID 40654667

PXD042986 no publication (from MassIVE)
Dataset title: Functional proteomics analyses of human PHRF1
Possible reference: Schlosser, P. et al. (2021) Meta-analyses identify DNA methylation associated with kidney function and damage., Nat Commun, PMID 34887417

PXD042749 Dataset with its publication pending (from PRIDE)
Dataset title: Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies
Possible reference: Schmidt, M. et al. (2023) Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies., ACS Synth Biol, PMID 37851920

PXD042725 no publication (from MassIVE)
Dataset title: Impaired age-associated mitochondrial translation is mitigated by exercise and PGC-1alpha
Possible reference: de Smalen, LM. et al. (2023) Impaired age-associated mitochondrial translation is mitigated by exercise and PGC-1α., Proc Natl Acad Sci U S A, PMID 37639610

PXD042700 Dataset with its publication pending (from PRIDE)
Dataset title: Ubiquitin-specific proximity labeling for the identification of E3 ubiquitin ligase substrates
Possible reference: Huang, HT. et al. (2024) Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates., Nat Chem Biol, PMID 38514884

PXD042551 no publication (from MassIVE)
Dataset title: Extracellular matrix orchestration of tissue remodelling during chronic colitis
Possible reference: Moutin, EB. et al. (2024) Extracellular Matrix Orchestration of Tissue Remodeling in the Chronically Inflamed Mouse Colon., Cell Mol Gastroenterol Hepatol, PMID 38199279

PXD042543 Dataset with its publication pending (from PRIDE)
Dataset title: Screening of exosome-derived proteins and their potential as biomarkers to diagnostic and prognostic for pancreatic cancer
Possible reference: Marin, AM. et al. (2023) Screening of Exosome-Derived Proteins and Their Potential as Biomarkers in Diagnostic and Prognostic for Pancreatic Cancer., Int J Mol Sci, PMID 37628784

PXD042477 no publication (from MassIVE)
Dataset title: A Shift Between Mineral and Nonmineral Sources of Iron and Sulfur Causes Proteome-wide Changes in Methanosarcina barkeri
Possible reference: Fausset, H. et al. (2024) A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri., Microbiol Spectr, PMID 38179920

PXD042154 Dataset with its publication pending (from PRIDE)
Dataset title: Blood RNAs predictive of molecular changes in the brain and clinical outcome in Parkinson’s disease
Possible reference: Irmady, K. et al. (2023) Blood transcriptomic signatures associated with molecular changes in the brain and clinical outcomes in Parkinson's disease., Nat Commun, PMID 37407548

PXD041630 Dataset with its publication pending (from PRIDE)
Dataset title: Cellular stiffness sensing through talin 1 in tissue mechanical homeostasis
Possible reference: Chanduri, MVL. et al. (2024) Mechanosensing through talin 1 contributes to tissue mechanical homeostasis., bioRxiv, PMID 38328095

PXD041546 (from jPOST)
Dataset title: Use of data-independent acquisition mass spectrometry to identify an objective serum indicator of the need for osteoporotic therapeutic intervention
Possible reference: Nakai, Y. et al. (2024) Use of data-independent acquisition mass spectrometry to identify an objective serum indicator of the need for osteoporotic therapeutic intervention., J Proteomics, PMID 38574990

PXD041503 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of bone marrow cells of benzene exposed mice
Possible reference: Zhang, W. et al. (2022) Iron-dependent ferroptosis participated in benzene-induced anemia of inflammation through IRP1-DHODH-ALOX12 axis., Free Radic Biol Med, PMID 36244588

PXD041437 Dataset with its publication pending (from iProX)
Dataset title: Quantitative proteomic detection of TMT labeling in cell samples based on LC-MS/MS
Possible reference: Sandberg, A. et al. (2014) Quantitative accuracy in mass spectrometry based proteomics of complex samples: the impact of labeling and precursor interference., J Proteomics, PMID 24211767

PXD041399 Dataset with its publication pending (from PRIDE)
Dataset title: Ultrasensitive proteomics depicted an in-depth landscape for the very early stage of mouse maternal-to-zygotic transition
Possible reference: Gu, L. et al. (2023) Ultrasensitive proteomics depicted an in-depth landscape for the very early stage of mouse maternal-to-zygotic transition., J Pharm Anal, PMID 37719194

PXD041240 Dataset with its publication pending (from PRIDE)
Dataset title: A translational regulator MHZ9 modulates ethylene signaling in rice
Possible reference: Huang, YH. et al. (2023) A translational regulator MHZ9 modulates ethylene signaling in rice., Nat Commun, PMID 37542048

PXD041039 no publication (from MassIVE)
Dataset title: The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 Gamma variant
Possible reference: Aloor, A. et al. (2022) Glycosylation in SARS-CoV-2 variants: A path to infection and recovery., Biochem Pharmacol, PMID 36328134

PXD040959 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling of serum N-glycome in ovarian cancer by MALDI-MS
Possible reference: Park, CW. et al. (2013) Enhancement of ovarian tumor classification by improved reproducibility in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of serum glycans., Anal Biochem, PMID 23969014

PXD040882 Dataset with its publication pending (from jPOST)
Dataset title: Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2 complexes
Possible reference: Homma, MK. et al. (2024) Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexes., Life Sci Alliance, PMID 37907238

PXD040683 Dataset with its publication pending (from PRIDE)
Dataset title: Immunometabolic interference between cancer and COVID-19
Possible reference: Sica, A. et al. (2020) Immunometabolic Status of COVID-19 Cancer Patients., Physiol Rev, PMID 32721181

PXD040563 Dataset with its publication pending (from jPOST)
Dataset title: Mass spectrometric analysis of purified megalin
Possible reference: Lee, A. et al. (2015) Chloride channel ClC-5 binds to aspartyl aminopeptidase to regulate renal albumin endocytosis., Am J Physiol Renal Physiol, PMID 25587118

PXD040467 Dataset with its publication pending (from PRIDE)
Dataset title: Metabolic influence of core ciliates within the rumen microbiome
Possible reference: Andersen, TO. et al. (2023) Metabolic influence of core ciliates within the rumen microbiome., ISME J, PMID 37169869

PXD040458 Dataset with its publication pending (from PRIDE)
Dataset title: Photophthora sojae extracellular vesicles proteins
Possible reference: Li, D. et al. (2013) PsVPS1, a dynamin-related protein, is involved in cyst germination and soybean infection of Phytophthora sojae., PLoS One, PMID 23516518

PXD040430 Dataset with its publication pending (from PRIDE)
Dataset title: A HUWE1 defect causes PARP inhibitor resistance by modulating the BRCA1-â11q splice variant
Possible reference: Pettitt, SJ. et al. (2023) A HUWE1 defect causes PARP inhibitor resistance by modulating the BRCA1-∆11q splice variant., Oncogene, PMID 37491606

PXD039840 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic characterization of Foreign Body Response towards silicone breast implants identifies chronological disease-relevant biomarker dynamics
Possible reference: Schoberleitner, I. et al. (2023) Quantitative Proteomic Characterization of Foreign Body Response towards Silicone Breast Implants Identifies Chronological Disease-Relevant Biomarker Dynamics., Biomolecules, PMID 36830674

PXD039642 Dataset with its publication pending (from jPOST)
Dataset title: Human Hair Shaft Proteome profiling using label free proteomics
Possible reference: Milan, JA. et al. (2019) Comparison of protein expression levels and proteomically-inferred genotypes using human hair from different body sites., Forensic Sci Int Genet, PMID 30939338

PXD039600 no publication (from MassIVE)
Dataset title: MRTX1133 mechanism of action in KRASG12D mutant cancer cell lines by proteomics and single cell proteomics
Possible reference: Orsburn, BC. et al. (2023) Metabolomic, proteomic and single cell proteomic analysis of cancer cells treated with the KRASG12D inhibitor MRTX1133., bioRxiv, PMID 36993160

PXD039519 Dataset with its publication pending (from PRIDE)
Dataset title: RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly
Possible reference: Khanduja, JS. et al. (2024) RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly., Cell, PMID 38815580

PXD039061 Dataset with its publication pending (from PRIDE)
Dataset title: The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition
Possible reference: Ganji, R. et al. (2023) The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition., Nat Commun, PMID 36746962

PXD038951 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting N-linked Glycosylation for the Therapy 1 of Aggressive Lymphomas
Possible reference: Rosato, F. et al. (2022) A bispecific, crosslinking lectibody activates cytotoxic T cells and induces cancer cell death., J Transl Med, PMID 36494671

PXD038865 no publication (from MassIVE)
Dataset title: Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity
Possible reference: Yu, Y. et al. (2024) Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity., Elife, PMID 38240316

PXD038751 no publication (from MassIVE)
Dataset title: Trans-Golgi protein TVP23B regulates host-microbe interactions via Paneth cell homeostasis and Goblet cell glycosylation
Possible reference: Song, R. et al. (2023) Trans-Golgi protein TVP23B regulates host-microbe interactions via Paneth cell homeostasis and Goblet cell glycosylation., Nat Commun, PMID 37339972

PXD038560 Dataset with its publication pending (from PRIDE)
Dataset title: The phosphoproteome of choroid plexus epithelial cells following infection with Neisseria meningitidis
Possible reference: Herold, R. et al. (2023) The phosphoproteome of choroid plexus epithelial cells following infection with Neisseria meningitidis., Front Cell Infect Microbiol, PMID 37065199

PXD038474 Dataset with its publication pending (from PRIDE)
Dataset title: Pol II preferentially regulates ribosomal protein expression by trapping disassociated subunits
Possible reference: Li, Y. et al. (2023) RNA Pol II preferentially regulates ribosomal protein expression by trapping disassociated subunits., Mol Cell, PMID 36924766

PXD038314 Dataset with its publication pending (from PRIDE)
Dataset title: IQGAP1 mediates the communication between the nucleus and the mitochondria via NDUFS4 alternative splicing
Possible reference: Papadaki, V. et al. (2023) IQGAP1 mediates the communication between the nucleus and the mitochondria via NDUFS4 alternative splicing., NAR Cancer, PMID 37636315

PXD038208 Dataset with its publication pending (from iProX)
Dataset title: Screening of SPOP interacting proteins in hepatocellular carcinoma
Possible reference: Deng, Y. et al. (2024) SPOP point mutations regulate substrate preference and affect its function., Cell Death Dis, PMID 38409107

PXD038190 Dataset with its publication pending (from jPOST)
Dataset title: HDL proteome in the sleep apnea syndrome
Possible reference: Feliciano, A. et al. (2017) Effects of positive airway pressure therapy on cardiovascular and metabolic markers in males with obstructive sleep apnea., Rev Port Pneumol (2006), PMID 28596012

PXD038132 Dataset with its publication pending (from PRIDE)
Dataset title: Chemoproteomic discovery of a human RNA ligase
Possible reference: Armenta, DA. et al. (2020) Investigating Nonapoptotic Cell Death Using Chemical Biology Approaches., Cell Chem Biol, PMID 32220334

PXD038092 Dataset with its publication pending (from iProX)
Dataset title: Proteomics analysis of saliva in mice with Sjogren's syndrome
Possible reference: Misuno, K. et al. (2014) Quantitative analysis of protein and gene expression in salivary glands of Sjogren's-like disease NOD mice treated by bone marrow soup., PLoS One, PMID 24489858

PXD038045 Dataset with its publication pending (from PRIDE)
Dataset title: Systematic analysis of lysine malonylation in Streptococcus mutans
Possible reference: Li, Z. et al. (2022) Systematic analysis of lysine malonylation in Streptococcus mutans., Front Cell Infect Microbiol, PMID 36519128

PXD037889 Dataset with its publication pending (from iProX)
Dataset title: Proteomic analysis of extracellular proteins of Clostridium cellulovorans
Possible reference: Matsui, K. et al. (2013) Exoproteome profiles of Clostridium cellulovorans grown on various carbon sources., Appl Environ Microbiol, PMID 23956399

PXD037874 Dataset with its publication pending (from PRIDE)
Dataset title: Coordinate control of endoplasmic reticulum chaperone biosynthesis and peptide hormone secretion revealed by a Î²-cell model of Prader-Willi syndrome
Possible reference: Koppes, EA. et al. (2023) Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones., PLoS Genet, PMID 37068109

PXD037227 Dataset with its publication pending (from PRIDE)
Dataset title: Phospho heavy-labeled-spiketide FAIMS stepped-CV DDA (pHASED) provides real-time phosphoproteomics data to aid in cancer drug selection
Possible reference: Staudt, DE. et al. (2022) Phospho-heavy-labeled-spiketide FAIMS stepped-CV DDA (pHASED) provides real-time phosphoproteomics data to aid in cancer drug selection., Clin Proteomics, PMID 36536316

PXD037201 no publication (from MassIVE)
Dataset title: IKACH IS CONSTITUTIVELY ACTIVE VIA PKC EPSILON IN AGING MEDIATED ATRIAL FIBRILLATION
Possible reference: Chang, M. et al. (2022) IKACh is constitutively active via PKC epsilon in aging mediated atrial fibrillation., iScience, PMID 36388956

PXD037051 Dataset with its publication pending (from jPOST)
Dataset title: Utilizing MALDI-TOF mass spectrometry and liquid chromatography-tandem mass spectrometry to access serum peptidome-based biomarkers in canine oral tumors
Possible reference: Ploypetch, S. et al. (2022) Utilizing MALDI-TOF MS and LC-MS/MS to access serum peptidome-based biomarkers in canine oral tumors., Sci Rep, PMID 36517562

PXD036846 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic analysis of the mouse cerebral cortex in ketamine-induced schizophrenia
Possible reference: Xiao, L. et al. (2024) Proteomic Characteristics of the Prefrontal Cortex and Hippocampus in Mice with Chronic Ketamine-Induced Anxiety and Cognitive Impairment., Neuroscience, PMID 38266908

PXD036520 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of tissue-engineered, small-diameter vascular grafts implanted into the ovine carotid artery
Possible reference: Antonova, L. et al. (2022) Controlled and Synchronised Vascular Regeneration upon the Implantation of Iloprost- and Cationic Amphiphilic Drugs-Conjugated Tissue-Engineered Vascular Grafts into the Ovine Carotid Artery: A Proteomics-Empowered Study., Polymers (Basel), PMID 36501545

PXD036318 Dataset with its publication pending (from jPOST)
Dataset title: Quantification of mature lamin A and progerin in HGPS patient cells
Possible reference: Camafeita, E. et al. (2022) Quantification of Farnesylated Progerin in Hutchinson-Gilford Progeria Patient Cells by Mass Spectrometry., Int J Mol Sci, PMID 36233036

PXD036209 Dataset with its publication pending (from iProX)
Dataset title: RI-FIGS for DI-SPA data-independent acquisition mass spectrometry
Possible reference: Meyer, JG. et al. (2020) Quantitative shotgun proteome analysis by direct infusion., Nat Methods, PMID 33230323

PXD036148 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative Proteomic Analysis of the Mitochondria of Menstrual Stem Cells and Ovarian Cancer Cells
Possible reference: Chen, X. et al. (2023) Comparative proteomic analysis of the mitochondria of menstrual stem cells and ovarian cancer cells., Exp Ther Med, PMID 36761005

PXD035924 Dataset with its publication pending (from PRIDE)
Dataset title: Selective Macrocyclic Peptide Modulators of Lys63-linked Ubiquitin Chains Disrupt DNA Damage Repair
Possible reference: Vamisetti, GB. et al. (2022) Selective macrocyclic peptide modulators of Lys63-linked ubiquitin chains disrupt DNA damage repair., Nat Commun, PMID 36257952

PXD035632 Dataset with its publication pending (from PRIDE)
Dataset title: Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803
Possible reference: Jackson, PJ. et al. (2023) Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803., Photosynth Res, PMID 36542271

PXD035524 no publication (from MassIVE)
Dataset title: Temporal Proteomic and Phosphoproteomic Analysis of EV-A71-infected Human Cells
Possible reference: Zhao, Y. et al. (2022) Temporal Proteomic and Phosphoproteomic Analysis of EV-A71-Infected Human Cells., J Proteome Res, PMID 36106392

PXD035523 no publication (from MassIVE)
Dataset title: Temporal Proteomic and Phosphoproteomic Analysis of EV-A71-infected Human Cells
Possible reference: Zhao, Y. et al. (2022) Temporal Proteomic and Phosphoproteomic Analysis of EV-A71-Infected Human Cells., J Proteome Res, PMID 36106392

PXD035518 no publication (from MassIVE)
Dataset title: Regulation of PaRBOH1-mediated ROS production
Possible reference: Nickolov, K. et al. (2022) Regulation of PaRBOH1-mediated ROS production in Norway spruce by Ca2+ binding and phosphorylation., Front Plant Sci, PMID 36311083

PXD035494 Dataset with its publication pending (from PRIDE)
Dataset title: PROTEOMIC ANALYSIS OF URINARY EXTRACELLULAR VESICLES OF KIDNEY TRANSPLANT RECIPIENTS WITH BKV VIRURIA AND VIREMIA.
Possible reference: Bruschi, M. et al. (2022) Proteomic analysis of urinary extracellular vesicles of kidney transplant recipients with BKV viruria and viremia: A pilot study., Front Med (Lausanne), PMID 36465937

PXD035309 Dataset with its publication pending (from PRIDE)
Dataset title: Lysine Acetylome Profiling Reveals Diverse Functions of Acetylation in Deinococcus Radiodurans
Possible reference: Zhang, Y. et al. (2022) Lysine Acetylome Profiling Reveals Diverse Functions of Acetylation in Deinococcus radiodurans., Microbiol Spectr, PMID 35972276

PXD035300 no publication (from MassIVE)
Dataset title: An apical protein, Pcr2, is required for persistent movement by the human parasite Toxoplasma gondii
Possible reference: Munera Lopez, J. et al. (2022) An apical protein, Pcr2, is required for persistent movement by the human parasite Toxoplasma gondii., PLoS Pathog, PMID 35994509

PXD034986 Dataset with its publication pending (from PRIDE)
Dataset title: RNA-DNA hybrids prevent resection at dysfunctional telomeres
Possible reference: Pires, VB. et al. (2023) RNA-DNA hybrids prevent resection at dysfunctional telomeres., Cell Rep, PMID 36729832

PXD034808 Dataset with its publication pending (from PRIDE)
Dataset title: Succinlylome profiling of bermudagrass stolons
Possible reference: Zhang, B. et al. (2017) Comparative transcriptome analysis provides new insights into erect and prostrate growth in bermudagrass (Cynodon dactylon L.)., Plant Physiol Biochem, PMID 29080425

PXD034806 Dataset with its publication pending (from PRIDE)
Dataset title: The human milk proteome: exploring associations with allergy of mother and child
Possible reference: Dekker, PM. et al. (2022) The human milk proteome and allergy of mother and child: Exploring associations with protein abundances and protein network connectivity., Front Immunol, PMID 36311719

PXD034770 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of canine (dog) serum and urine
Possible reference: Rouillon, J. et al. (2014) Proteomics profiling of urine reveals specific titin fragments as biomarkers of Duchenne muscular dystrophy., Neuromuscul Disord, PMID 24813925

PXD034571 Dataset with its publication pending (from PRIDE)
Dataset title: Proteogenomic characterization of pancreatic neuroendocrine tumor
Possible reference: Tanaka, A. et al. (2024) Proteogenomic characterization of pancreatic neuroendocrine tumors uncovers hypoxia and immune signatures in clinically aggressive subtypes., iScience, PMID 39206147

PXD034486 Dataset with its publication pending (from iProX)
Dataset title: Proteomics of human placenta-derived exosome
Possible reference: Familari, M. et al. (2017) Placenta-derived extracellular vesicles: their cargo and possible functions., Reprod Fertil Dev, PMID 26411402

PXD034479 Dataset with its publication pending (from PRIDE)
Dataset title: Perturbation of protein homeostasis brings plastids at the crossroad between repairment and dismantling
Possible reference: Tadini, L. et al. (2023) Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling., PLoS Genet, PMID 37418499

PXD034172 no publication (from MassIVE)
Dataset title: Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics
Possible reference: White, MEH. et al. (2024) Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics., Nat Biomed Eng, PMID 37474612

PXD034170 no publication (from MassIVE)
Dataset title: Bioprospecting the American Alligator Peptidome for Antiviral Peptides Against Venezuelan Equine Encephalitis Virus
Possible reference: Carfagno, A. et al. (2023) Bioprospecting the American Alligator Peptidome for antiviral peptides against Venezuelan equine encephalitis virus., Proteomics, PMID 36480152

PXD034056 Dataset with its publication pending (from PRIDE)
Dataset title: inSPIRE Spectral Rescoring Tool
Possible reference: Cormican, JA. et al. (2022) inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction., Mol Cell Proteomics, PMID 36280141

PXD033640 Dataset with its publication pending (from PRIDE)
Dataset title: Plasmid manipulation of bacterial behaviour through translational regulatory crosstalk
Possible reference: Thompson, CMA. et al. (2023) Plasmids manipulate bacterial behaviour through translational regulatory crosstalk., PLoS Biol, PMID 36787297

PXD033480 Dataset with its publication pending (from iProX)
Dataset title: fish-Cynoglossus semilaevis skin mucus and exosome proteome
Possible reference: Zhao, N. et al. (2021) Proteomics of mucosal exosomes of Cynoglossus semilaevis altered when infected by Vibrio harveyi., Dev Comp Immunol, PMID 33582105

PXD033360 Dataset with its publication pending (from PRIDE)
Dataset title: Korean Lung Adenocarcinoma proteogenomics
Possible reference: Kim, H. et al. (2024) Proteogenomic characterization identifies clinical subgroups in EGFR and ALK wild-type never-smoker lung adenocarcinoma., Exp Mol Med, PMID 39300154

PXD033148 Dataset with its publication pending (from PRIDE)
Dataset title: human lung adenocarcinoma cell lines TMT based proteomics
Possible reference: V�gv�ri, �. et al. (2022) Single Cell Proteomics Using Multiplexed Isobaric Labeling for Mass Spectrometric Analysis., Methods Mol Biol, PMID 34766268

PXD033060 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics of the dentate gyrus reveals semantic dementia specific molecular pathology
Possible reference: Mol, MO. et al. (2022) Proteomics of the dentate gyrus reveals semantic dementia specific molecular pathology., Acta Neuropathol Commun, PMID 36578035

PXD031568 no publication (from MassIVE)
Dataset title: Cysteine residues are responsible for the sulfurous off-flavor formed in heated whey protein solutions
Possible reference: Li, C. et al. (2022) Cysteine residues are responsible for the sulfurous off-flavor formed in heated whey protein solutions., Food Chem (Oxf), PMID 35865714

PXD031461 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics of airway epithelial cells from COPD and control pre- and post-influenza virus infection
Possible reference: Nakayama, M. et al. (2022) Quantitative proteomics of differentiated primary bronchial epithelial cells from chronic obstructive pulmonary disease and control identifies potential novel host factors post-influenza A virus infection., Front Microbiol, PMID 36713229

PXD031434 no publication (from MassIVE)
Dataset title: Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality
Possible reference: Wattrus, SJ. et al. (2022) Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality., Science, PMID 36137040

PXD031421 Dataset with its publication pending (from PRIDE)
Dataset title: Structure and molecular assembly of a MuvB transcription factor complex with the nucleosome
Possible reference: Asthana, A. et al. (2022) The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes., Nat Commun, PMID 35082292

PXD031369 no publication (from MassIVE)
Dataset title: High-light-inducible proteins HliA and HliB: pigment binding and protein-protein interactions
Possible reference: Konert, MM. et al. (2022) High-light-inducible proteins HliA and HliB: pigment binding and protein-protein interactions., Photosynth Res, PMID 35218444

PXD031072 Dataset with its publication pending (from PRIDE)
Dataset title: A plant tethering system for the functional study of protein-RNA interactions in vivo
Possible reference: Cuerda-Gil, D. et al. (2022) A plant tethering system for the functional study of protein-RNA interactions in vivo., Plant Methods, PMID 35658900

PXD030839 Dataset with its publication pending (from PRIDE)
Dataset title: Data of chemical composition of the particles from OH-initiated oxidation of 1,3,5-trimethylbenzene
Possible reference: Lin, X. et al. (2022) Data of chemical composition of the particles from OH-initiated oxidation of 1,3,5-trimethylbenzene., Data Brief, PMID 35496493

PXD030837 Dataset with its publication pending (from PRIDE)
Dataset title: A G-protein-coupled receptor modulates gametogenesis via PKG-mediated signaling cascade in Plasmodium berghei
Possible reference: Wang, PP. et al. (2022) A G-Protein-Coupled Receptor Modulates Gametogenesis via PKG-Mediated Signaling Cascade in Plasmodium berghei., Microbiol Spectr, PMID 35404079

PXD030776 Dataset with its publication pending (from PRIDE)
Dataset title: The proto-oncogene TCL1A deregulates mitotic checkpoint transition and genomic stability in CLL
Possible reference: Stachelscheid, J. et al. (2023) The proto-oncogene TCL1A deregulates cell cycle and�genomic stability in CLL., Blood, PMID 36179280

PXD030580 Dataset with its publication pending (from PRIDE)
Dataset title: UBIQUITIN LIGASE STUB1 DESTABILIZES IFNÎ³-RECEPTOR COMPLEX TO SUPPRESS TUMOR IFNÎ³ SIGNALING
Possible reference: Apriamashvili, G. et al. (2022) Ubiquitin ligase STUB1 destabilizes IFNγ-receptor complex to suppress tumor IFNγ signaling., Nat Commun, PMID 35395848

PXD030537 Dataset with its publication pending (from PRIDE)
Dataset title: Metal removal capability of two cyanobacterial species in autotrophic and mixotrophic mode of nutrition
Possible reference: Ghorbani, E. et al. (2022) Metal removal capability of two cyanobacterial species in autotrophic and mixotrophic mode of nutrition., BMC Microbiol, PMID 35176992

PXD030494 Dataset with its publication pending (from PRIDE)
Dataset title: Baseline Proteomics Characterisation of Biomanufacturing Organism Halomonas Bluephagenesis
Possible reference: Russell, M. et al. (2022) Baseline proteomics characterisation of the emerging host biomanufacturing organism Halomonas bluephagenesis., Sci Data, PMID 35963929

PXD030492 Dataset with its publication pending (from PRIDE)
Dataset title: Dynamics of allosteric regulation of the phospholipase C-gamma isoform
Possible reference: Hajicek, N. et al. (2019) Structural basis for the activation of PLC-γ isozymes by phosphorylation and cancer-associated mutations., Elife, PMID 31889510

PXD030490 no publication (from MassIVE)
Dataset title: Proximity proteomics of C9orf72 dipeptide repeat proteins
Possible reference: Božič, J. et al. (2022) Interactome screening of C9orf72 dipeptide repeats reveals VCP sequestration and functional impairment by polyGA., Brain, PMID 34534264

PXD030427 Dataset with its publication pending (from PRIDE)
Dataset title: TEFM variants impair mitochondrial transcription elongation causing childhood-onset neurological disease
Possible reference: Van Haute, L. et al. (2023) TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease., Nat Commun, PMID 36823193

PXD030283 Dataset with its publication pending (from PRIDE)
Dataset title: Potential Role of Lysine Acetylation in Antibiotic Resistance of Escherichia coli
Possible reference: Dash, A. et al. (2021) Protein Acetyltransferases Mediate Bacterial Adaptation to a Diverse Environment., J Bacteriol, PMID 34251868

PXD030265 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis
Possible reference: Demond, H. et al. (2023) Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis., Genome Res, PMID 36690445

PXD029955 Dataset with its publication pending (from PRIDE)
Dataset title: Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases
Possible reference: Arguello, AE. et al. (2022) Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases., Nat Commun, PMID 35853884

PXD029954 Dataset with its publication pending (from PRIDE)
Dataset title: Altered Subgenomic RNA Abundance in SARS-CoV-2 B.1.1.7 Infections
Possible reference: Parker, MD. et al. (2022) Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections., Commun Biol, PMID 35790808

PXD029876 no publication (from MassIVE)
Dataset title: Amyloid fibrils in disease FTLD-TDP are composed of TMEM106B, rather than TDP-43
Possible reference: Chang, A. et al. (2022) Homotypic fibrillization of TMEM106B across diverse neurodegenerative diseases., Cell, PMID 35247328

PXD029828 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic signatures of antimicrobial resistance in Yersinia pestis and Francisella tularensis
Possible reference: Deatherage Kaiser, BL. et al. (2022) Proteomic Signatures of Antimicrobial Resistance in Yersinia pestis and Francisella tularensis., Front Med (Lausanne), PMID 35223919

PXD029825 Dataset with its publication pending (from PRIDE)
Dataset title: Sex differences in the role of protein sumoylation in the amygdala during fear memory formation
Possible reference: Gustin, A. et al. (2022) Protein SUMOylation is a sex-specific regulator of fear memory formation in the amygdala., Behav Brain Res, PMID 35597476

PXD029800 no publication (from MassIVE)
Dataset title: Identification of Endogenous Peptides in MALDI-TOF-MS based COVID-19 diagnostics
Possible reference: Tsai, H. et al. (2022) Identification of Endogenous Peptides in Nasal Swab Transport Media used in MALDI-TOF-MS Based COVID-19 Screening., ACS Omega, PMID 35600141

PXD029793 Dataset with its publication pending (from PRIDE)
Dataset title: Serum proteomic profile of asthmatic patients after 6 months of Benralizumab and Mepolizumab treatment
Possible reference: Landi, C. et al. (2021) Differential redox proteomic profiles of serum from severe asthma patients after one month of benralizumab and mepolizumab treatment., Pulm Pharmacol Ther, PMID 34303823

PXD029792 Dataset with its publication pending (from PRIDE)
Dataset title: Improved identification of proteoforms using FAIMS with internal CV stepping in top-down proteomics
Possible reference: Kaulich, PT. et al. (2022) Improved Identification of Proteoforms in Top-Down Proteomics Using FAIMS with Internal CV Stepping., Anal Chem, PMID 35172570

PXD029756 no publication (from MassIVE)
Dataset title: Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma
Possible reference: Vedula, P. et al. (2022) Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma., Front Cell Dev Biol, PMID 35223838

PXD029746 Dataset with its publication pending (from PRIDE)
Dataset title: The human disease gene TMEM251 is essential for lysosomal transport and viral infection
Possible reference: Richards, CM. et al. (2022) The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection., Science, PMID 36074821

PXD029739 Dataset with its publication pending (from iProX)
Dataset title: Phytophthora capsici mycelia proteome
Possible reference: He, L. et al. (2022) iTRAQ proteomic analysis of the inhibitory effect of 1,6-O,O-diacetylbritannilactone on the plant pathogenic oomycete Phytophthora capsici., Pestic Biochem Physiol, PMID 35715063

PXD029737 Dataset with its publication pending (from PRIDE)
Dataset title: Paracrine Interleukin 6 induces cerebral remodeling at early stages after unilateral common carotid artery occlusion in mice
Possible reference: Kuffner, MTC. et al. (2021) Paracrine Interleukin 6 Induces Cerebral Remodeling at Early Stages After Unilateral Common Carotid Artery Occlusion in Mice., Front Cardiovasc Med, PMID 35155612

PXD029700 Dataset with its publication pending (from PRIDE)
Dataset title: Improving statistical certainty of glycosylation similarity between influenza A virus variants using data-independent acquisition mass spectrometry
Possible reference: Chang, D. et al. (2022) Improving Statistical Certainty of Glycosylation Similarity between Influenza A Virus Variants Using Data-Independent Acquisition Mass Spectrometry., Mol Cell Proteomics, PMID 36103992

PXD029582 no publication (from MassIVE)
Dataset title: Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids
Possible reference: Chirania, P. et al. (2022) Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids., Nat Commun, PMID 35790765

PXD029537 Dataset with its publication pending (from PRIDE)
Dataset title: Effects of SHetA2 on SiHa and C-33 A human cervical cancer cell lines
Possible reference: Rai, R. et al. (2024) Manipulation of metabolic responses enhances SHetA2 efficacy without toxicity in cervical cancer cell lines and xenografts., Gynecol Oncol, PMID 38052108

PXD029535 Dataset with its publication pending (from PRIDE)
Dataset title: tRNA Biogenesis and Specific Aminoacyl-tRNA Synthetases Regulate Senescence Stability Under the Control of mTOR
Possible reference: Guillon, J. et al. (2021) tRNA biogenesis and specific aminoacyl-tRNA synthetases regulate senescence stability under the control of mTOR., PLoS Genet, PMID 34928935

PXD029523 Liblova, Z., Maurencova, D., Salovska, B., Kratky, M., Mracek, T., Korandova, Z., Pecinova, A., Vasicova, P., Rysanek, D., Andera, L., Fabrik, I., Kupcik, R., Kashmel, P., Sultana, P., Tambor, V., Bartek, J., Novak, J., Vajrychova, M. and Hodny, Z. (2025) (from PanoramaPublic)
Dataset title: Determination of ADP/ATP translocase isoform ratios in malignancy and cellular senescence
Possible reference: Liblova, Z. et al. (2025) Determination of ADP/ATP translocase isoform ratios in malignancy and cellular senescence., Mol Oncol, PMID 40288905

PXD029511 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic analysis reveals the different hepatotoxic mechanisms of human hepatocytes exposed to silver nanoparticles
Possible reference: Wong, TY. et al. (2023) Comparative proteomic analysis reveals the different hepatotoxic mechanisms of human hepatocytes exposed to silver nanoparticles., J Hazard Mater, PMID 37055998

PXD029500 Dataset with its publication pending (from PRIDE)
Dataset title: SP3-enabled rapid and high coverage chemoproteomic identification of redox-sensitive cysteines
Possible reference: Desai, HS. et al. (2022) SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State-Dependent Redox-Sensitive Cysteines., Mol Cell Proteomics, PMID 35219905

PXD029496 Dataset with its publication pending (from PRIDE)
Dataset title: A novel C-terminal DxRSDxE motif in ceramide synthases involved in dimer formation
Possible reference: Kim, JL. et al. (2022) A novel C-terminal DxRSDxE motif in ceramide synthases involved in dimer formation., J Biol Chem, PMID 34942147

PXD029463 Dataset with its publication pending (from PRIDE)
Dataset title: PIM1 controls GBP1 activity to limit self-damage and guard against pathogen infection
Possible reference: Fisch, D. et al. (2023) PIM1 controls GBP1 activity to limit self-damage and to guard against pathogen infection., Science, PMID 37797010

PXD029447 no publication (from MassIVE)
Dataset title: TIMSFolding allows the use of ion mobility enhanced spectral libraries
Possible reference: Shen, T. et al. (2023) The unknown lipids project: harmonized methods improve compound identification and data reproducibility in an inter-laboratory untargeted lipidomics study., bioRxiv, PMID 36778509

PXD029431 Dataset with its publication pending (from PRIDE)
Dataset title: Enrichment and Proteomic Identification of Cryptosporidium parvum Oocyst Wall
Possible reference: Wang, L. et al. (2022) Enrichment and proteomic identification of Cryptosporidium parvum oocyst wall., Parasit Vectors, PMID 36151578

PXD029411 no publication (from MassIVE)
Dataset title: Label free proteomic and complementary metabolomic analysis of leaves of the resurrection plant Xerophyta schlechteri during dehydration
Possible reference: Gabier, H. et al. (2021) A Label-Free Proteomic and Complementary Metabolomic Analysis of Leaves of the Resurrection Plant Xerophytaschlechteri during Dehydration., Life (Basel), PMID 34833116

PXD029320 Dataset with its publication pending (from PRIDE)
Dataset title: Real-Time Search Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics
Possible reference: Furtw�ngler, B. et al. (2022) Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics., Mol Cell Proteomics, PMID 35219906

PXD029285 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic profiling identifies reciprocal expression of mitochondrial proteins between white and grey matter lesions from multiple sclerosis brains
Possible reference: Rai, NK. et al. (2021) Comparative Proteomic Profiling Identifies Reciprocal Expression of Mitochondrial Proteins Between White and Gray Matter Lesions From Multiple Sclerosis Brains., Front Neurol, PMID 35002930

PXD029227 Dataset with its publication pending (from PRIDE)
Dataset title: Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington’s disease
Possible reference: Mullari, M. et al. (2023) Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington's disease., Nat Commun, PMID 37468457

PXD029105 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of new amniotic fluid prognostic biomarkers of congenital cytomegalovirus infection severity
Possible reference: Desveaux, C. et al. (2016) Identification of Symptomatic Fetuses Infected with Cytomegalovirus Using Amniotic Fluid Peptide Biomarkers., PLoS Pathog, PMID 26808779

PXD029076 Dataset with its publication pending (from PRIDE)
Dataset title: Antioxidant, Immunomodulatory and Potential Anticancer Capacity of Polysaccharides (Glucans) from Euglena gracilis G.A. Klebs
Possible reference: Casas-Arrojo, V. et al. (2022) Antioxidant, Immunomodulatory and Potential Anticancer Capacity of Polysaccharides (Glucans) from Euglena gracilis G.A. Klebs., Pharmaceuticals (Basel), PMID 36355551

PXD028963 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain
Possible reference: Krishna, S. et al. (2021) Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain., Dev Cell, PMID 34715012

PXD028898 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omics analysis of microglial extracellular vesicles from human Alzheimer’s Disease brain reveals disease-associated signatures
Possible reference: Cohn, W. et al. (2021) Multi-Omics Analysis of Microglial Extracellular Vesicles From Human Alzheimer's Disease Brain Tissue Reveals Disease-Associated Signatures., Front Pharmacol, PMID 34925024

PXD028825 Dataset with its publication pending (from PRIDE)
Dataset title: Citrullination of glucokinase is linked to autoimmune diabetes
Possible reference: Yang, ML. et al. (2022) Citrullination of glucokinase is linked to autoimmune diabetes., Nat Commun, PMID 35388005

PXD028824 Dataset with its publication pending (from PRIDE)
Dataset title: DOT1L regulates pericentromeric heterochromatin
Possible reference: Ooga, M. et al. (2013) Involvement of DOT1L in the remodeling of heterochromatin configuration during early preimplantation development in mice., Biol Reprod, PMID 24132959

PXD028747 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic response of Pediococcus pentosaceus M41 under different environmental stresses
Possible reference: Baig, MA. et al. (2021) Potential Probiotic Pediococcus pentosaceus M41 Modulates Its Proteome Differentially for Tolerances Against Heat, Cold, Acid, and Bile Stresses., Front Microbiol, PMID 34721329

PXD028745 no publication (from MassIVE)
Dataset title: Atg8ylation coordinates stress granule formation and mTOR inactivation in response to lysosomal damage
Possible reference: Jia, J. et al. (2022) Stress granules and mTOR are regulated by membrane atg8ylation during lysosomal damage., J Cell Biol, PMID 36179369

PXD028709 Dataset with its publication pending (from PRIDE)
Dataset title: Mapping the Melanoma Plasma Proteome (MPP) using Single-Shot Proteomics and Custom Protein Databases
Possible reference: Almeida, N. et al. (2021) Mapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database., Cancers (Basel), PMID 34944842

PXD028698 Dataset with its publication pending (from PRIDE)
Dataset title: Regulation of Plant Phototropic Growth by NPH3/RPT2-like Substrate Phosphorylation and 14-3-3 Binding
Possible reference: Sullivan, S. et al. (2021) Regulation of plant phototropic growth by NPH3/RPT2-like substrate phosphorylation and 14-3-3 binding., Nat Commun, PMID 34675214

PXD028694 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors
Possible reference: Shi, G. et al. (2023) Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors., Sci Signal, PMID 36626580

PXD028660 Dataset with its publication pending (from PRIDE)
Dataset title: A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening 293T cells]
Possible reference: Ren, Y. et al. (2021) A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation., Genome Biol, PMID 34649616

PXD028613 Dataset with its publication pending (from PRIDE)
Dataset title: Muc2-dependent microbial colonization of the jejunal mucus layer is diet sensitive and confers resistance to enteric pathogen infection
Possible reference: Birchenough, GMH. et al. (2023) Muc2-dependent microbial colonization of the jejunal mucus layer is diet sensitive and confers local resistance to enteric pathogen infection., Cell Rep, PMID 36753416

PXD028594 Dataset with its publication pending (from PRIDE)
Dataset title: Radiotherapy changes the salivary proteome in head and neck cancer patients: evaluation before, during and after treatment
Possible reference: Ventura, TMO. et al. (2021) Is there difference in the comparative and quantitative salivary proteome between stimulated and unstimulated saliva in head and neck cancer patients treated by radiotherapy?, Oral Oncol, PMID 33985911

PXD028544 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomics demonstrates altered Metabolism pathways in cotrimoxazole-resistant and amikacin-resistant Klebsiella pneumoniae isolates
Possible reference: Shen, C. et al. (2021) Comparative Proteomics Demonstrates Altered Metabolism Pathways in Cotrimoxazole- Resistant and Amikacin-Resistant Klebsiella pneumoniae Isolates., Front Microbiol, PMID 34867912

PXD028521 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-omics reveals molecular responses to aneuploidy in Leishmania
Possible reference: Cuypers, B. et al. (2022) Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania., PLoS Pathog, PMID 36149920

PXD028494 Dataset with its publication pending (from PRIDE)
Dataset title: RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage
Possible reference: Lin, C. et al. (2024) RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage., Sci Data, PMID 38177134

PXD028481 Dataset with its publication pending (from PRIDE)
Dataset title: ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia
Possible reference: Dickerson, KM. et al. (2022) ZNF384 Fusion Oncoproteins Drive Lineage Aberrancy in Acute Leukemia., Blood Cancer Discov, PMID 35247902

PXD028432 Dataset with its publication pending (from PRIDE)
Dataset title: Salvi_PNAS_Phosphoproteome_ATRwt-cko
Possible reference: Salvi, JS. et al. (2022) ATR activity controls stem cell quiescence via the cyclin F-SCF complex., Proc Natl Acad Sci U S A, PMID 35476521

PXD028426 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Aspergillus niger in Peanuts
Possible reference: Xu, M. et al. (2021) Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in Aspergillus niger in Peanuts., Front Microbiol, PMID 34489910

PXD028405 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling 4-thiouridine across E. coli tRNAs
Possible reference: Bommisetti, P. et al. (2022) Site-Specific Profiling of 4-Thiouridine Across Transfer RNA Genes in Escherichia coli., ACS Omega, PMID 35155896

PXD028398 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive chemical proteomics analyses reveal that the new TRi-1 and TRi-2 compounds are more specific thioredoxin reductase 1 inhibitors than Auranofin
Possible reference: Sabatier, P. et al. (2021) Comprehensive chemical proteomics analyses reveal that the new TRi-1 and TRi-2 compounds are more specific thioredoxin reductase 1 inhibitors than auranofin., Redox Biol, PMID 34788728

PXD028328 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of Arabidopsis fsd1 mutants in response to methyl viologen
Possible reference: Melicher, P. et al. (2022) Arabidopsis Iron Superoxide Dismutase FSD1 Protects Against Methyl Viologen-Induced Oxidative Stress in a Copper-Dependent Manner., Front Plant Sci, PMID 35360337

PXD028074 Dataset with its publication pending (from PRIDE)
Dataset title: Karyopherin enrichment and compensation fortifies the nuclear pore complex against nucleocytoplasmic leakage
Possible reference: Kalita, J. et al. (2022) Karyopherin enrichment and compensation fortifies the nuclear pore complex against nucleocytoplasmic leakage., J Cell Biol, PMID 35089308

PXD027971 Dataset with its publication pending (from PRIDE)
Dataset title: Simple, single-shot phosphoproteomic analysis of heat-stable tau
Possible reference: Leslie, SN. et al. (2021) Simple, Single-Shot Phosphoproteomic Analysis of Heat-Stable Tau Identifies Age-Related Changes in pS235- and pS396-Tau Levels in Non-human Primates., Front Aging Neurosci, PMID 34867294

PXD027856 Dataset with its publication pending (from PRIDE)
Dataset title: Calcineurin increases expression of aldosterone synthase via dephosphorylation of NFATc4
Possible reference: Berber, M. et al. (2023) Calcineurin regulates aldosterone production via dephosphorylation of NFATC4., JCI Insight, PMID 37310791

PXD027728 Dataset with its publication pending (from PRIDE)
Dataset title: Emergence and intensification of dairying in the Caucasus and Eurasian steppes
Possible reference: Scott, A. et al. (2022) Emergence and intensification of dairying in the Caucasus and Eurasian steppes., Nat Ecol Evol, PMID 35393601

PXD027680 no publication (from MassIVE)
Dataset title: The immunopeptidome of HCT116 cell line
Possible reference: Xiang, H. et al. (2022) A Novel Proteogenomic Integration Strategy Expands the Breadth of Neo-Epitope Sources., Cancers (Basel), PMID 35740681

PXD027679 Dataset with its publication pending (from jPOST)
Dataset title: Sample Size-comparable Spectral Library Enhances Data-Independent Acquisition-based Proteome Coverage of Low-input Cells
Possible reference: Siyal, AA. et al. (2021) Sample Size-Comparable Spectral Library Enhances Data-Independent Acquisition-Based Proteome Coverage of Low-Input Cells., Anal Chem, PMID 34904835

PXD027677 Dataset with its publication pending (from jPOST)
Dataset title: ALK substrate identification and validation
Possible reference: Adachi, J. et al. (2022) Systematic identification of ALK substrates by integrated phosphoproteome and interactome analysis., Life Sci Alliance, PMID 35508387

PXD027667 Dataset with its publication pending (from PRIDE)
Dataset title: Beta-synuclein potentiates synaptic vesicle dopamine uptake and rescues dopaminergic neurons from MPTP-induced death in the absence of other synucleins
Possible reference: Ninkina, N. et al. (2021) β-synuclein potentiates synaptic vesicle dopamine uptake and rescues dopaminergic neurons from MPTP-induced death in the absence of other synucleins., J Biol Chem, PMID 34736896

PXD027612 Dataset with its publication pending (from PRIDE)
Dataset title: The SR protein kinase Sky2 is involved in regulation of dipeptide transport in Candida albicans
Possible reference: Brandt, P. et al. (2022) Candida albicans SR-Like Protein Kinases Regulate Different Cellular Processes: Sky1 Is Involved in Control of Ion Homeostasis, While Sky2 Is Important for Dipeptide Utilization., Front Cell Infect Microbiol, PMID 35601106

PXD027609 Dataset with its publication pending (from PRIDE)
Dataset title: Low temperature exposure has immediate and lasting effects on the stress tolerance, chemotaxis and proteome of entomopathogenic nematodes
Possible reference: Lillis, PE. et al. (2023) Low-temperature exposure has immediate and lasting effects on the stress tolerance, chemotaxis and proteome of entomopathogenic nematodes., Parasitology, PMID 36328953

PXD027605 no publication (from MassIVE)
Dataset title: Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Top-Down Mass Spectrometry
Possible reference: Roberts, DS. et al. (2021) Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Native Top-Down Mass Spectrometry., bioRxiv, PMID 33688648

PXD027603 Dataset with its publication pending (from PRIDE)
Dataset title: “Identifying the SLC25A46 interactome in transgenic mice: Thymus"
Possible reference: Perivolidi, VI. et al. (2022) Proteomic Identification of the SLC25A46 Interactome in Transgenic Mice Expressing SLC25A46-FLAG., J Proteome Res, PMID 34983179

PXD027544 Dataset with its publication pending (from PRIDE)
Dataset title: Sex differences in the role of protein degradation in the amygdala during fear memory formation
Possible reference: Farrell, K. et al. (2023) Sex-differences in proteasome-dependent K48-polyubiquitin signaling in the amygdala are developmentally regulated in rats., Biol Sex Differ, PMID 37950270

PXD027479 Dataset with its publication pending (from PRIDE)
Dataset title: Translational repression of NMD targets by GIGYF2 and EIF4E2
Possible reference: Zinshteyn, B. et al. (2021) Translational repression of NMD targets by GIGYF2 and EIF4E2., PLoS Genet, PMID 34665823

PXD027476 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy
Possible reference: Eapen, VV. et al. (2021) Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy., Elife, PMID 34585663

PXD027442 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis reveals the protective effects of Yiqi Fumai lyophilized injection on chronic heart failure by improving myocardial energy metabolism
Possible reference: Han, X. et al. (2021) Proteomic Analysis Reveals the Protective Effects of Yiqi Fumai Lyophilized Injection on Chronic Heart Failure by Improving Myocardial Energy Metabolism., Front Pharmacol, PMID 34630097

PXD027440 Dataset with its publication pending (from PRIDE)
Dataset title: Emiliania huxleyi coccosphere associated proteins identification
Possible reference: Walker, CE. et al. (2018) The requirement for calcification differs between ecologically important coccolithophore species., New Phytol, PMID 29916209

PXD027422 no publication (from MassIVE)
Dataset title: Effect of GP130 Antagonism on Microtubule Associated Proteins
Possible reference: Prisco, SZ. et al. (2022) Inflammatory Glycoprotein 130 Signaling Links Changes in Microtubules and Junctophilin-2 to Altered Mitochondrial Metabolism and Right Ventricular Contractility., Circ Heart Fail, PMID 34923829

PXD027413 Dataset with its publication pending (from PRIDE)
Dataset title: A direct interplay between the co-chaperones Hop and p23 regulates cycle progression and client folding in the Hsp70/Hsp90 chaperone machineries
Possible reference: Dahiya, V. et al. (2022) The switch from client holding to folding in the Hsp70/Hsp90 chaperone machineries is regulated by a direct interplay between co-chaperones., Mol Cell, PMID 35176233

PXD027410 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomics reveals an increase in the abundance of glycolytic and ethanolic fermentation enzymes in developing sugarcane culms during sucrose accumulation
Possible reference: Boaretto, LF. et al. (2021) Proteomics Reveals an Increase in the Abundance of Glycolytic and Ethanolic Fermentation Enzymes in Developing Sugarcane Culms During Sucrose Accumulation., Front Plant Sci, PMID 34659289

PXD027387 Dataset with its publication pending (from PRIDE)
Dataset title: Conserved exchange of paralog proteins during neuronal differentiation
Possible reference: Schmidt, S. et al. (2014) Function and regulation of the Rho guanine nucleotide exchange factor Trio., Small GTPases, PMID 24987837

PXD027383 Dataset with its publication pending (from PRIDE)
Dataset title: A Multiplexed Parallel Reaction Monitoring Assay to monitor bovine Pregnancy-Associated Glycoproteins throughout pregnancy and after gestation
Possible reference: Krebs, T. et al. (2022) A multiplexed parallel reaction monitoring assay to monitor bovine pregnancy-associated glycoproteins throughout pregnancy and after gestation., PLoS One, PMID 36149860

PXD027375 Dataset with its publication pending (from jPOST)
Dataset title: Quantitative protein profiling of phenobarbital-induced drug metabolizing enzymes in rat liver by liquid chromatography mass spectrometry using FFPE sample
Possible reference: Yamauchi, H. et al. (2021) Quantitative protein profiling of phenobarbital-induced drug metabolizing enzymes in rat liver by liquid chromatography mass spectrometry using formalin-fixed paraffin-embedded samples., J Pharmacol Toxicol Methods, PMID 34363961

PXD027365 Dataset with its publication pending (from PRIDE)
Dataset title: MPK3/6-induced degradation of ARR1/10/12 promotes salt tolerance in Arabidopsis
Possible reference: Yan, Z. et al. (2021) MPK3/6-induced degradation of ARR1/10/12 promotes salt tolerance in Arabidopsis., EMBO Rep, PMID 34402578

PXD027350 Dataset with its publication pending (from PRIDE)
Dataset title: PLCG2 regulates endocannabinoid and eicosanoid networks in innate immune cells
Possible reference: Jing, H. et al. (2021) Phospholipase Cγ2 regulates endocannabinoid and eicosanoid networks in innate immune cells., Proc Natl Acad Sci U S A, PMID 34607960

PXD027311 no publication (from MassIVE)
Dataset title: Drone honey bees are disproportionately sensitive to abiotic stressors relative to workers, despite expressing high levels of stress response proteins
Possible reference: McAfee, A. et al. (2022) Drone honey bees are disproportionately sensitive to abiotic stressors despite expressing high levels of stress response proteins., Commun Biol, PMID 35177754

PXD027297 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome-Level Functional Redundancy in the Human Gut Microbiome
Possible reference: Li, L. et al. (2023) Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics., Nat Commun, PMID 37301875

PXD027294 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of novel salivary candidate protein biomarkers for tuberculosis diagnosis: a preliminary biomarker discovery study.
Possible reference: Mutavhatsindi, H. et al. (2021) Identification of novel salivary candidate protein biomarkers for tuberculosis diagnosis: A preliminary biomarker discovery study., Tuberculosis (Edinb), PMID 34371310

PXD027291 Dataset with its publication pending (from jPOST)
Dataset title: CXCL5 secreted from macrophages during cold exposure mediates white adipose tissue browning
Possible reference: Lee, D. et al. (2021) CXCL5 secreted from macrophages during cold exposure mediates white adipose tissue browning., J Lipid Res, PMID 34537202

PXD027248 Dataset with its publication pending (from PRIDE)
Dataset title: Prior Signal Acquisition Software Versions For Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments
Possible reference: Smith, TS. et al. (2022) Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments., ACS Meas Sci Au, PMID 35726249

PXD027241 Dataset with its publication pending (from PRIDE)
Dataset title: A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum-infected red blood cell proteome
Possible reference: Siddiqui, G. et al. (2022) A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum-infected red blood cell proteome., Gigascience, PMID 35254426

PXD027238 Dataset with its publication pending (from PRIDE)
Dataset title: Identifying Specific Protein Interactors of Nucleosomes Carrying Methylated Histones using Quantitative Mass Spectrometry
Possible reference: Tvardovskiy, A. et al. (2022) Identifying Specific Protein Interactors of Nucleosomes Carrying Methylated Histones Using Quantitative Mass Spectrometry., Methods Mol Biol, PMID 35733023

PXD027187 Dataset with its publication pending (from PRIDE)
Dataset title: ATR inhibition enables complete tumour regression in ALK-driven NB mouse models
Possible reference: Szydzik, J. et al. (2021) ATR inhibition enables complete tumour regression in ALK-driven NB mouse models., Nat Commun, PMID 34819497

PXD027164 Dataset with its publication pending (from PRIDE)
Dataset title: Global protein responses of multi-drug resistant plasmid containing Escherichia coli to beta-lactams and ciprofloxacin.
Possible reference: Margalit, A. et al. (2022) Global protein responses of multidrug resistance plasmid-containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin., J Glob Antimicrob Resist, PMID 34922055

PXD027118 Dataset with its publication pending (from jPOST)
Dataset title: Antibiotic-like Activity of Atomic Layer Boron Nitride for Combating Resistant Bacteria
Possible reference: Pan, Y. et al. (2022) Antibiotic-Like Activity of Atomic Layer Boron Nitride for Combating Resistant Bacteria., ACS Nano, PMID 35511445

PXD027110 Dataset with its publication pending (from PRIDE)
Dataset title: Surfaceome proteomic of glioblastoma revealed potential targets for immunotherapy
Possible reference: Rose, M. et al. (2021) Surfaceome Proteomic of Glioblastoma Revealed Potential Targets for Immunotherapy., Front Immunol, PMID 34646273

PXD027081 Dataset with its publication pending (from jPOST)
Dataset title: Reference Proteome-Based Characterization of Liver Cancer
Possible reference: Sanyal, AJ. et al. (2023) Defining the serum proteomic signature of hepatic steatosis, inflammation, ballooning and fibrosis in non-alcoholic fatty liver disease., J Hepatol, PMID 36528237

PXD027048 no publication (from MassIVE)
Dataset title: Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples
Possible reference: Klaeger, S. et al. (2021) Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples., Mol Cell Proteomics, PMID 34391888

PXD027019 no publication (from MassIVE)
Dataset title: Vitamin C differentially impacts the serum proteome profile in female and male mice
Possible reference: Aumailley, L. et al. (2021) Vitamin C Differentially Impacts the Serum Proteome Profile in Female and Male Mice., J Proteome Res, PMID 34643398

PXD027017 Dataset with its publication pending (from PRIDE)
Dataset title: Indentification of CaMKK2-binding proteins in 293T cells
Possible reference: Gee, MH. et al. (2018) Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes., Cell, PMID 29275860

PXD027006 Dataset with its publication pending (from PRIDE)
Dataset title: Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV‐2 S1 Spike Glycoprotein
Possible reference: Stamatakis, G. et al. (2021) Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV-2 S1 spike glycoprotein., J Biol Chem, PMID 34688668

PXD026982 Dataset with its publication pending (from PRIDE)
Dataset title: Mildly pathogenic Rickettsia-macrophage interactions
Possible reference: Curto, P. et al. (2021) Spotted Fever Group Rickettsia Trigger Species-Specific Alterations in Macrophage Proteome Signatures with Different Impacts in Host Innate Inflammatory Responses., Microbiol Spectr, PMID 34935429

PXD026919 Dataset with its publication pending (from iProX)
Dataset title: Corosolic Acid inhibits bladder cancer
Possible reference: Cui, A. et al. (2023) Quantitative transcriptomic and proteomic analysis reveals corosolic acid inhibiting bladder cancer via suppressing cell cycle and inducing mitophagy in vitro and in vivo., Toxicol Appl Pharmacol, PMID 37939859

PXD026894 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphorylation regulates arginine-rich RNA-binding protein solubility and oligomerization
Possible reference: Kundinger, SR. et al. (2021) Phosphorylation regulates arginine-rich RNA-binding protein solubility and oligomerization., J Biol Chem, PMID 34673031

PXD026887 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic profiling of astrocytic O-GlcNAc transferase related proteins in the mPFC
Possible reference: Fan, J. et al. (2021) Proteomic Profiling of Astrocytic O-GlcNAc Transferase-Related Proteins in the Medial Prefrontal Cortex., Front Mol Neurosci, PMID 34803603

PXD026852 Dataset with its publication pending (from PRIDE)
Dataset title: Targeting conserved N-glycosylation eradicates SARS-CoV-2 variants infection
Possible reference: Huang, HC. et al. (2021) Targeting conserved N-glycosylation blocks SARS-CoV-2 variant infection in vitro., EBioMedicine, PMID 34839261

PXD026828 Dataset with its publication pending (from PRIDE)
Dataset title: Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density
Possible reference: Schott, J. et al. (2021) Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density., Nat Methods, PMID 34480152

PXD026809 no publication (from MassIVE)
Dataset title: Ulengin-Talkish_calcineurin_PI4KA_2021
Possible reference: Ulengin-Talkish, I. et al. (2021) Palmitoylation targets the calcineurin phosphatase to the phosphatidylinositol 4-kinase complex at the plasma membrane., Nat Commun, PMID 34663815

PXD026790 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation of mass spectrometry MS/MS spectra for the presence of isopeptide crosslinked peptides
Possible reference: Schopfer, LM. et al. (2021) Evaluation of mass spectrometry MS/MS spectra for the presence of isopeptide crosslinked peptides., PLoS One, PMID 34242352

PXD026789 Dataset with its publication pending (from PRIDE)
Dataset title: Calcitriol promotes differentiation of glioma stem-like cells and increases their susceptibility to temozolomide
Possible reference: Gerstmeier, J. et al. (2021) Calcitriol Promotes Differentiation of Glioma Stem-Like Cells and Increases Their Susceptibility to Temozolomide., Cancers (Basel), PMID 34298790

PXD026776 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling of glioma C6 and astrocytes rat cell lines before and after co-cultivation.
Possible reference: Gerhartl, A. et al. (2020) The pivotal role of micro-environmental cells in a human blood-brain barrier in vitro model of cerebral ischemia: functional and transcriptomic analysis., Fluids Barriers CNS, PMID 32138745

PXD026774 Dataset with its publication pending (from PRIDE)
Dataset title: Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation
Possible reference: Gockert, M. et al. (2022) Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation., Nucleic Acids Res, PMID 35048984

PXD026773 Dataset with its publication pending (from PRIDE)
Dataset title: Integrated analysis of proteomics on rat hearts with aging and hypertension
Possible reference: Shay, JW. et al. (2016) Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015., BMC Genomics, PMID 27454254

PXD026725 Dataset with its publication pending (from PRIDE)
Dataset title: RNA-bound PGC-1Î± controls gene expression in liquid-like nuclear condensates
Possible reference: Pérez-Schindler, J. et al. (2021) RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates., Proc Natl Acad Sci U S A, PMID 34465622

PXD026674 Dataset with its publication pending (from PRIDE)
Dataset title: Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation
Possible reference: Brabbs, TR. et al. (2013) The stochastic silencing phenotype of Arabidopsis morc6 mutants reveals a role in efficient RNA-directed DNA methylation., Plant J, PMID 23675613

PXD026622 Dataset with its publication pending (from PRIDE)
Dataset title: The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infective Trypanosoma brucei
Possible reference: Das, A. et al. (2023) The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infective Trypanosoma brucei., mSphere, PMID 37581443

PXD026572 no publication (from MassIVE)
Dataset title: Mouse Intestinal HMGCR complex
Possible reference: Zhang, L. et al. (2023) High-Carbohydrate Diet Consumption Poses a More Severe Liver Cholesterol Deposition than a High-Fat and High-Calorie Diet in Mice., Int J Mol Sci, PMID 37834148

PXD026504 Dataset with its publication pending (from iProX)
Dataset title: Proteome of pig uterine luminal fluid
Possible reference: He, Y. et al. (2022) iTRAQ-based quantitative proteomic analysis of porcine uterine fluid during pre-implantation period of pregnancy., J Proteomics, PMID 35354084

PXD026467 Dataset with its publication pending (from PRIDE)
Dataset title: Analysis of the effect of Bacillus velezensis culture filtrate on the growth and proteome of Cladobotryum mycophilum
Possible reference: Clarke, J. et al. (2022) Analysis of the effect of Bacillus velezensis culture filtrate on the growth and proteome of Cladobotryum mycophilum., Fungal Biol, PMID 34930555

PXD026450 Dataset with its publication pending (from PRIDE)
Dataset title: SARS-CoV-2 spike protein glycosylation enriched by HILIC and Ti-IMAC
Possible reference: Huang, J. et al. (2021) Simultaneous enrichment and separation of neutral and sialyl glycopeptides of SARS-CoV-2 spike protein enabled by dual-functionalized Ti-IMAC material., Anal Bioanal Chem, PMID 34155551

PXD026354 Dataset with its publication pending (from jPOST)
Dataset title: Heart and skeletal muscle of young adult and early aging mice
Possible reference: Wei, B. et al. (2015) Dysferlin deficiency blunts β-adrenergic-dependent lusitropic function of mouse heart., J Physiol, PMID 26415898

PXD026322 Dataset with its publication pending (from PRIDE)
Dataset title: Activated interleukin-7 receptor signaling drives B-cell acute lymphoblastic leukemia in mice
Possible reference: Thomas, KR. et al. (2022) Activated interleukin-7 receptor signaling drives B-cell acute lymphoblastic leukemia in mice., Leukemia, PMID 34193976

PXD026241 Dataset with its publication pending (from iProX)
Dataset title: Proteomic Profiles of Extracellular Vesicles from Miscarriage Placentae
Possible reference: Jena, SR. et al. (2023) Comparative proteome profiling of seminal components reveal impaired immune cell signalling as paternal contributors in recurrent pregnancy loss patients., Am J Reprod Immunol, PMID 35998016

PXD026120 Dataset with its publication pending (from PRIDE)
Dataset title: The EDS1-PAD4-ADR1 node mediates Arabidopsis pattern-triggered immunity
Possible reference: Pruitt, RN. et al. (2021) The EDS1-PAD4-ADR1 node mediates Arabidopsis pattern-triggered immunity., Nature, PMID 34497423

PXD026060 Dataset with its publication pending (from PRIDE)
Dataset title: Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule disassembly
Possible reference: Cereghetti, G. et al. (2021) Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule disassembly., Nat Cell Biol, PMID 34616026

PXD026031 Dataset with its publication pending (from iProX)
Dataset title: Proteome of mouse testis at postnatal days 30
Possible reference: Couto-Santos, F. et al. (2021) Prepubertal arsenic exposure alters phosphoproteins profile, quality, and fertility of epididymal spermatozoa in sexually mature rats., Toxicology, PMID 34352348

PXD025942 no publication (from MassIVE)
Dataset title: Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing
Possible reference: Bhattacharya, S. et al. (2021) Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing., Nat Commun, PMID 34750379

PXD025918 Dataset with its publication pending (from jPOST)
Dataset title: Facile one-pot nanoproteomics for label-free proteome profiling of 50-1000 mammalian cells
Possible reference: Martin, K. et al. (2021) Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50-1000 Mammalian Cells., J Proteome Res, PMID 34351778

PXD025870 Dataset with its publication pending (from PRIDE)
Dataset title: Characterisation of a nucleo-adhesome
Possible reference: Byron, A. et al. (2022) Characterisation of a nucleo-adhesome., Nat Commun, PMID 35650196

PXD025828 Dataset with its publication pending (from PRIDE)
Dataset title: Allergenicity Assessment and Allergen Profile Analysis of Different Chinese Wheat Cultivars
Possible reference: Wang, Y. et al. (2021) Allergenicity assessment and allergen profile analysis of different Chinese wheat cultivars., World Allergy Organ J, PMID 34257797

PXD025811 Dataset with its publication pending (from jPOST)
Dataset title: IMTACT - mitochondrial enrichment
Possible reference: Boussardon, C. et al. (2022) Cell Type-Specific Isolation of Mitochondria in Arabidopsis., Methods Mol Biol, PMID 34545482

PXD025793 Dataset with its publication pending (from jPOST)
Dataset title: Proteomic profiling uncovers potential proteins for biomonitoring equine melanocytic neoplasm
Possible reference: Tesena, P. et al. (2021) Preliminary Study: Proteomic Profiling Uncovers Potential Proteins for Biomonitoring Equine Melanocytic Neoplasm., Animals (Basel), PMID 34199079

PXD025782 Dataset with its publication pending (from PRIDE)
Dataset title: The RNA-binding proteins SRP14 and HMGB3 control HIV-1 Tat mRNA processing and translation during HIV-1 latency
Possible reference: Khoury, G. et al. (2021) The RNA-Binding Proteins SRP14 and HMGB3 Control HIV-1 Tat mRNA Processing and Translation During HIV-1 Latency., Front Genet, PMID 34194479

PXD025766 Dataset with its publication pending (from PRIDE)
Dataset title: The use of linear ion traps in data independent acquisition methods benefits low-input proteomics
Possible reference: Borr�s, E. et al. (2021) Use of Linear Ion Traps in Data-Independent Acquisition Methods Benefits Low-Input Proteomics., Anal Chem, PMID 34404205

PXD025677 no publication (from MassIVE)
Dataset title: EZH2-dependent transcriptional complex promotes aberrant epithelial remodelling after injury
Possible reference: Le, HQ. et al. (2021) An EZH2-dependent transcriptional complex promotes aberrant epithelial remodelling after�injury., EMBO Rep, PMID 34224201

PXD025676 Dataset with its publication pending (from PRIDE)
Dataset title: Suv4-20h2 protects from influenza virus infection through suppression of chromatin loop formation
Possible reference: Shiimori, M. et al. (2021) Suv4-20h2 protects against influenza virus infection by suppression of chromatin loop formation., iScience, PMID 34169237

PXD025675 Dataset with its publication pending (from PRIDE)
Dataset title: Genomic locus proteomic screening identifies the NF-kB signaling pathway components NFkB1 and IKBKG as transcriptional regulators of Ripk3 in endothelial cells
Possible reference: Gao, S. et al. (2021) Genomic locus proteomic screening identifies the NF-κB signaling pathway components NFκB1 and IKBKG as transcriptional regulators of Ripk3 in endothelial cells., PLoS One, PMID 34153072

PXD025674 Dataset with its publication pending (from PRIDE)
Dataset title: Rne-HupB interaction fosters mycobacterial single-cell homeostasis and fitness during drug treatment and infection
Possible reference: Griego, A. et al. (2022) RNase E and HupB dynamics foster mycobacterial cell homeostasis and fitness., iScience, PMID 35521527

PXD025652 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation of fully functionalized diazirine tags for chemical proteomic applications
Possible reference: Conway, LP. et al. (2021) Evaluation of fully-functionalized diazirine tags for chemical proteomic applications., Chem Sci, PMID 34168837

PXD025627 (from jPOST)
Dataset title: MALDI spectra of Cutibacterium and Staphylococcus species
Possible reference: Dekio, I. et al. (2021) What Do We See in Spectra?: Assignment of High-Intensity Peaks of Cutibacterium and Staphylococcus Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics., Microorganisms, PMID 34201063

PXD025603 no publication (from MassIVE)
Dataset title: The acyl-proteome of Syntrophus aciditrophicus reveals metabolic relationship with benzoate degradation
Possible reference: Muroski, JM. et al. (2022) The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation., Mol Cell Proteomics, PMID 35189333

PXD025598 no publication (from MassIVE)
Dataset title: A three-organelle complex made by wrappER contacts with peroxisomes and mitochondria responds to liver lipid flux changes
Possible reference: Ilacqua, N. et al. (2022) A three-organelle complex made by wrappER contacts with peroxisomes and mitochondria responds to liver lipid flux changes., J Cell Sci, PMID 34672330

PXD025574 Dataset with its publication pending (from PRIDE)
Dataset title: Click-enabled analogues reveal pregnenolone interactomes in cancer and immune cells
Possible reference: Roy, S. et al. (2021) CLICK-enabled analogues reveal pregnenolone interactomes in cancer and immune cells., iScience, PMID 34036248

PXD025562 Dataset with its publication pending (from PRIDE)
Dataset title: In-cell structures of a conserved supramolecular array at the mitochondria-cytoskeleton interface in mammalian sperm
Possible reference: Leung, MR. et al. (2021) In-cell structures of conserved supramolecular protein arrays at the mitochondria-cytoskeleton interface in mammalian sperm., Proc Natl Acad Sci U S A, PMID 34737233

PXD025547 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic Analysis of Urinary Extracellular Vesicles Reveals a Role for the Complement System in Medullary Sponge Kidney Disease
Possible reference: Bruschi, M. et al. (2019) Proteomic Analysis of Urinary Extracellular Vesicles Reveals a Role for the Complement System in Medullary Sponge Kidney Disease., Int J Mol Sci, PMID 31694344

PXD025537 Dataset with its publication pending (from PRIDE)
Dataset title: On-tissue spatially-resolved glycoproteomics guided by N-glycan imaging reveal global dysregulation of canine glioma glycoproteomic landscape
Possible reference: Malaker, SA. et al. (2022) On-tissue spatially resolved glycoproteomics guided by N-glycan imaging reveal global dysregulation of canine glioma glycoproteomic landscape., Cell Chem Biol, PMID 34102146

PXD025485 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic study of fig fruit latex
Possible reference: Cui, Y. et al. (2019) Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.)., BMC Plant Biol, PMID 30991947

PXD025459 Dataset with its publication pending (from PRIDE)
Dataset title: Automated Phosphopeptide Enrichment for Gram Positive Bacteria
Possible reference: Birk, MS. et al. (2021) Automated Phosphopeptide Enrichment for Gram-Positive Bacteria., J Proteome Res, PMID 34473931

PXD025449 no publication (from MassIVE)
Dataset title: Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs
Possible reference: Weingarten-Gabbay, S. et al. (2021) Profiling SARS-CoV-2 HLA-I peptidome reveals T�cell epitopes from out-of-frame ORFs., Cell, PMID 34171305

PXD025444 no publication (from MassIVE)
Dataset title: The Histone H1-Like Protein AlgP Facilitates Even Spacing of Polyphosphate Granules in Pseudomonas aeruginosa
Possible reference: Chawla, R. et al. (2022) The Histone H1-Like Protein AlgP Facilitates Even Spacing of Polyphosphate Granules in Pseudomonas aeruginosa., mBio, PMID 35435704

PXD025413 Dataset with its publication pending (from PRIDE)
Dataset title: The E3 ubiquitin ligase adaptor cereblon targets the C-terminal cyclic imide degron
Possible reference: Ichikawa, S. et al. (2024) The cyclimids: Degron-inspired cereblon binders for targeted protein degradation., Cell Chem Biol, PMID 38320555

PXD025359 Dataset with its publication pending (from PRIDE)
Dataset title: Advanced fiber type-specific protein profiles derived from adult murine skeletal muscle
Possible reference: Eggers, B. et al. (2021) Advanced Fiber Type-Specific Protein Profiles Derived from Adult Murine Skeletal Muscle., Proteomes, PMID 34201234

PXD025349 Dataset with its publication pending (from PRIDE)
Dataset title: Engineered yeast strains expressing human glycolytic enzymes
Possible reference: Kuijpers, NG. et al. (2016) Pathway swapping: Toward modular engineering of essential cellular processes., Proc Natl Acad Sci U S A, PMID 27956602

PXD025319 Dataset with its publication pending (from PRIDE)
Dataset title: Redox regulation of PTPN22 affects the severity of T cell dependent autoimmune inflammation
Possible reference: James, J. et al. (2022) Redox regulation of PTPN22 affects the severity of T-cell-dependent autoimmune inflammation., Elife, PMID 35587260

PXD025304 Dataset with its publication pending (from PRIDE)
Dataset title: Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability
Possible reference: Geijer, ME. et al. (2021) Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability., Nat Cell Biol, PMID 34108662

PXD025301 Dataset with its publication pending (from PRIDE)
Dataset title: TBK1 interacts with tau and enhances neurodegeneration in tauopathy
Possible reference: Abreha, MH. et al. (2021) TBK1 interacts with tau and enhances neurodegeneration in tauopathy., J Biol Chem, PMID 33965374

PXD025295 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of S-nitrosylation in HUVECs
Possible reference: Xu, X. et al. (2019) The protein S-nitrosylation of splicing and translational machinery in vascular endothelial cells is susceptible to oxidative stress induced by oxidized low-density lipoprotein., J Proteomics, PMID 30630120

PXD025271 Dataset with its publication pending (from PRIDE)
Dataset title: IKAROS and MENIN are Functionally Cooperative Therapeutic Targets in Acute Myeloid Leukemia
Possible reference: Aubrey, BJ. et al. (2022) IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia., Nat Cancer, PMID 35534777

PXD025230 Dataset with its publication pending (from PRIDE)
Dataset title: IKAROS and MENIN are Functionally Cooperative Therapeutic Targets in Acute Myeloid Leukemia
Possible reference: Aubrey, BJ. et al. (2022) IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia., Nat Cancer, PMID 35534777

PXD025180 Dataset with its publication pending (from PRIDE)
Dataset title: White matter integrity requires continuous myelin synthesis at the inner tongue
Possible reference: Meschkat, M. et al. (2022) White matter integrity in mice�requires continuous myelin synthesis at the inner tongue., Nat Commun, PMID 35246535

PXD025136 no publication (from MassIVE)
Dataset title: JAK2-CHK2 signaling safeguards the integrity of the mitotic spindle assembly checkpoint and genome stability
Possible reference: Chowdhury, MAN. et al. (2022) JAK2-CHK2 signaling safeguards the integrity of the mitotic spindle assembly checkpoint and genome stability., Cell Death Dis, PMID 35851582

PXD025095 Dataset with its publication pending (from PRIDE)
Dataset title: Epulorhiza-responsive proteins found in tubers of Dactylorhiza
Possible reference: Ghorbani, A. et al. (2017) DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep., Mol Ecol Resour, PMID 27768252

PXD025002 Dataset with its publication pending (from PRIDE)
Dataset title: The extracellular matrix landscape identifies different etiologies behind bicuspid and tricuspid aortic valve degeneration
Possible reference: Beusch, CM. et al. (2023) Analysis of local extracellular matrix identifies different aetiologies behind bicuspid and tricuspid aortic valve degeneration and suggests therapies., Cell Mol Life Sci, PMID 37632572

PXD024807 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteomic Profiling of T-Cell Acute Lymphoblastic Leukemia Identifies Targetable Kinases and Combination Treatments
Possible reference: Degryse, S. et al. (2018) Mutant JAK3 phosphoproteomic profiling predicts synergism between JAK3 inhibitors and MEK/BCL2 inhibitors for the treatment of T-cell acute lymphoblastic leukemia., Leukemia, PMID 28852199

PXD024764 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomics of Hsp90 inhibition in Leishmania mexicana
Possible reference: Kalesh, K. et al. (2021) Quantitative Proteomics Reveals that Hsp90 Inhibition Dynamically Regulates Global Protein Synthesis in Leishmania mexicana., mSystems, PMID 33975965

PXD024709 Dataset with its publication pending (from iProX)
Dataset title: Proteomes analysis of exosome from HCC PDX models
Possible reference: Zuo, T. et al. (2025) Exosomal Proteome from Hepatocellular Carcinoma Patient-Derived Xenograft Mice Serves as Identity of Liver Cancer., J Proteome Res, PMID 40923719

PXD024701 Dataset with its publication pending (from PRIDE)
Dataset title: TMT-based quantitative proteomics analysis reveals the function of ester cyclase in the rice false smut fungus Ustilaginoidea virens
Possible reference: Chen, X. et al. (2021) Quantitative Proteomics Analysis Reveals the Function of the Putative Ester Cyclase UvEC1 in the Pathogenicity of the Rice False Smut Fungus Ustilaginoidea virens., Int J Mol Sci, PMID 33920773

PXD024679 Dataset with its publication pending (from PRIDE)
Dataset title: An ERK5-KLF2 signalling module regulates early embryonic gene expression dynamics and stem cell rejuvenation
Possible reference: Brown, HA. et al. (2021) An ERK5-KLF2 signalling module regulates early embryonic gene expression and telomere rejuvenation in stem cells., Biochem J, PMID 34780645

PXD024625 Dataset with its publication pending (from PRIDE)
Dataset title: The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder
Possible reference: Berendse, K. et al. (2019) Liver disease predominates in a mouse model for mild human Zellweger spectrum disorder., Biochim Biophys Acta Mol Basis Dis, PMID 31207289

PXD024531 no publication (from MassIVE)
Dataset title: Alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability
Possible reference: Li, L. et al. (2021) An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability., Nat Genet, PMID 33986536

PXD024419 Dataset with its publication pending (from PRIDE)
Dataset title: Cargo and lipid profiling of isolated autophagosomes upon basal autophagy, starvation, and proteasome inhibition
Possible reference: Schmitt, D. et al. (2022) Lipid and protein content profiling of isolated native autophagic vesicles., EMBO Rep, PMID 36215690

PXD024398 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic landscape of SARS-CoV-2- and MERS-CoV-infected primary human renal epithelial cells
Possible reference: Kohli, A. et al. (2022) Proteomic landscape of SARS-CoV-2- and MERS-CoV-infected primary human renal epithelial cells., Life Sci Alliance, PMID 35110370

PXD024342 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative proteomic analysis of the defense response to Gibberella stalk rot in maize
Possible reference: Bai, H. et al. (2021) Comparative Proteomic Analysis of the Defense Response to Gibberella Stalk Rot in Maize and Reveals That ZmWRKY83 Is Involved in Plant Disease Resistance., Front Plant Sci, PMID 34489999

PXD024322 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of archival breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes
Possible reference: Asleh, K. et al. (2022) Proteomic analysis of archival breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes., Nat Commun, PMID 35173148

PXD024281 Dataset with its publication pending (from PRIDE)
Dataset title: Lactate Dehydrogenase B and Pyruvate Oxidation Pathway associated with Carfilzomib-Related Cardiotoxicity in Multiple Myeloma Patients: Result of a Multi-Omics Integrative Analysis
Possible reference: Tantawy, M. et al. (2021) Lactate Dehydrogenase B and Pyruvate Oxidation Pathway Associated With Carfilzomib-Related Cardiotoxicity in Multiple Myeloma Patients: Result of a Multi-Omics Integrative Analysis., Front Cardiovasc Med, PMID 33996940

PXD024245 no publication (from MassIVE)
Dataset title: Coupling of Cdc20 inhibition and activation by BubR1
Possible reference: Hein, JB. et al. (2021) Coupling of Cdc20 inhibition and activation by BubR1., J Cell Biol, PMID 33819340

PXD024177 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative profiling of axonal guidance proteins during the differentiation of human neurospheres
Possible reference: Goto-Silva, L. et al. (2021) Quantitative profiling of axonal guidance proteins during the differentiation of human neurospheres., Biochim Biophys Acta Proteins Proteom, PMID 33857633

PXD024158 Dataset with its publication pending (from PRIDE)
Dataset title: Hepatic cytochrome P450 abundance and activity in the developing and adult G�ttingen Minipig: pivotal data for PBPK modeling
Possible reference: Buyssens, L. et al. (2021) Hepatic Cytochrome P450 Abundance and Activity in the Developing and Adult G�ttingen Minipig: Pivotal Data for PBPK Modeling., Front Pharmacol, PMID 33935788

PXD024101 Dataset with its publication pending (from PRIDE)
Dataset title: Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies for Glycopeptide Analysis
Possible reference: Kawahara, R. et al. (2021) Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis., Nat Methods, PMID 34725484

PXD024075 Dataset with its publication pending (from PRIDE)
Dataset title: Synaptic accumulation of FUS triggers early misregulation of synaptic RNAs in ALS-FUS mice
Possible reference: Sahadevan, S. et al. (2021) Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS., Nat Commun, PMID 34021139

PXD024060 Dataset with its publication pending (from PRIDE)
Dataset title: Alteration of microbiota antibody-mediated immune selection contributes to dysbiosis in IBD
Possible reference: Michaud, E. et al. (2022) Alteration of microbiota antibody-mediated immune selection contributes to dysbiosis in inflammatory bowel diseases., EMBO Mol Med, PMID 35785473

PXD023983 Dataset with its publication pending (from PRIDE)
Dataset title: Discovery of RSV-induced BRD4 protein interactions using native immunoprecipitation and parallel accumulation – serial fragmentation (PASEF) mass spectrometry
Possible reference: Mann, M. et al. (2021) Discovery of RSV-Induced BRD4 Protein Interactions Using Native Immunoprecipitation and Parallel Accumulation-Serial Fragmentation (PASEF) Mass Spectrometry., Viruses, PMID 33799525

PXD023974 Dataset with its publication pending (from PRIDE)
Dataset title: E2F6 initiates stable epigenetic silencing of germline genes during embryonic development
Possible reference: Dahlet, T. et al. (2021) E2F6 initiates stable epigenetic silencing of germline genes during embryonic development., Nat Commun, PMID 34117224

PXD023965 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis of Laodelphax striatellus in response to rice stripe virus infection
Possible reference: Huang, HJ. et al. (2021) Proteomic analysis of Laodelphax striatellus in response to Rice stripe virus infection reveal a potential role of ZFP36L1 in restriction of viral proliferation., J Proteomics, PMID 33711487

PXD023936 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring the glycosylation state of the Cryptosporidium parvum CpTSP protein family-HILIC glycopeptide enrichment
Possible reference: John, A. et al. (2023) Conservation, abundance, glycosylation profile, and localization of the TSP protein family in Cryptosporidium parvum., J Biol Chem, PMID 36775128

PXD023935 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring the glycosylation state of the Cryptosporidium parvum CpTSP protein family-FAIMS proteome
Possible reference: John, A. et al. (2023) Conservation, abundance, glycosylation profile, and localization of the TSP protein family in Cryptosporidium parvum., J Biol Chem, PMID 36775128

PXD023858 Dataset with its publication pending (from PRIDE)
Dataset title: Response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius to solvent stress
Possible reference: Benninghoff, JC. et al. (2021) Exposure to 1-Butanol Exemplifies the Response of the Thermoacidophilic Archaeon Sulfolobus acidocaldarius to Solvent Stress., Appl Environ Microbiol, PMID 33741627

PXD023854 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic analysis of Toxoplasma gondii mutants of the mitochondrial and plastidic Iron sulfur cluster synthesis pathways.
Possible reference: Pamukcu, S. et al. (2021) Differential contribution of two organelles of endosymbiotic origin to iron-sulfur cluster synthesis and overall fitness in Toxoplasma., PLoS Pathog, PMID 34793583

PXD023822 Dataset with its publication pending (from PRIDE)
Dataset title: Impact of sulfamethoxazole on a riverine microbiome
Possible reference: Borsetto, C. et al. (2021) Impact of sulfamethoxazole on a riverine microbiome., Water Res, PMID 34225233

PXD023811 Dataset with its publication pending (from PRIDE)
Dataset title: Staphylococcus aureus Trigger factor is involved in biofilm formation and cooperates with the chaperone PpiB
Possible reference: Keogh, RA. et al. (2021) Staphylococcus aureus Trigger Factor Is Involved in Biofilm Formation and Cooperates with the Chaperone PpiB., J Bacteriol, PMID 33468596

PXD023802 Dataset with its publication pending (from PRIDE)
Dataset title: Heading towards a dead end: the role of DND1 in germ line differentiation of human iPSCs
Possible reference: Mall, EM. et al. (2021) Heading towards a dead end: The role of DND1 in germ line differentiation of human iPSCs., PLoS One, PMID 34653201

PXD023794 no publication (from MassIVE)
Dataset title: Triazine pyridine chemistry for selective tyrosine labelling of proteins
Possible reference: Wang, C. et al. (2025) Achieving cysteine-selective peptide/protein bioconjugation via tunable triazine-pyridine chemistry., Sci Adv, PMID 41337588

PXD023756 Dataset with its publication pending (from PRIDE)
Dataset title: Comparative Proteomic Analysis of Fucosylated Glycoproteins in Bacteroides thetaiotaomicron under Different Polysaccharide Nutrition Conditions
Possible reference: Tian, X. et al. (2022) Comparative Proteomic Analysis of Fucosylated Glycoproteins Produced by Bacteroides thetaiotaomicron Under Different Polysaccharide Nutrition Conditions., Front Microbiol, PMID 35308349

PXD023745 no publication (from MassIVE)
Dataset title: A BLOOD BANK STANDARDIZED PRODUCTION OF HUMAN PLATELET LYSATE FOR MESENCHYMAL STROMAL CELLS EXPANSION: PROTEOMIC CHARACTERIZATION AND BIOLOGICAL EFFECTS
Possible reference: Bianchetti, A. et al. (2021) A Blood Bank Standardized Production of Human Platelet Lysate for Mesenchymal Stromal Cell Expansion: Proteomic Characterization and Biological Effects., Front Cell Dev Biol, PMID 34055779

PXD023707 Dataset with its publication pending (from PRIDE)
Dataset title: Profiling of the human Fallopian tube matrisome
Possible reference: Renner, C. et al. (2022) Multi-modal Profiling of the Extracellular Matrix of Human Fallopian Tubes and Serous Tubal Intraepithelial Carcinomas., J Histochem Cytochem, PMID 34866441

PXD023676 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic analysis identifies novel BRCA1-associated protein 1 binding proteins
Possible reference: Baas, R. et al. (2021) Proteomic analysis identifies novel binding partners of BAP1., PLoS One, PMID 34591877

PXD023637 no publication (from MassIVE)
Dataset title: The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFNb pathway Phospho
Possible reference: Takahashi, M. et al. (2021) The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway., Nat Immunol, PMID 33767426

PXD023609 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome analysis of Culter alburnus egg and egg envelope
Possible reference: Chen, H. et al. (2026) Comparison of transcriptomics and proteomics revealed distinct molecular mechanisms underlying egg development of Culter alburnus between northern and southern China., Comp Biochem Physiol Part D Genomics Proteomics, PMID 41687135

PXD023608 Dataset with its publication pending (from PRIDE)
Dataset title: Time-resolved proteome analysis of Listeria monocytogenes during infection reveals the role of the AAA+ chaperone ClpC for host cell adaptation
Possible reference: Birk, MS. et al. (2021) Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation., mSystems, PMID 34342529

PXD023601 Dataset with its publication pending (from PRIDE)
Dataset title: Nitric Oxide Is Associated with Heterosis of Salinity Tolerance in Brassica napus L.
Possible reference: Zhang, Y. et al. (2021) Nitric Oxide Is Associated With Heterosis of Salinity Tolerance in Brassica napus L., Front Plant Sci, PMID 34122475

PXD023562 Dataset with its publication pending (from PRIDE)
Dataset title: Broad Kinase Inhibition Mitigates Early Neuronal Dysfunction in Tauopathy
Possible reference: Koren, SA. et al. (2021) Broad Kinase Inhibition Mitigates Early Neuronal Dysfunction in Tauopathy., Int J Mol Sci, PMID 33530349

PXD023550 Dataset with its publication pending (from PRIDE)
Dataset title: The Pentose Phosphate Pathway in pathogenic Francisella
Possible reference: Chen, F. et al. (2017) Differential Substrate Usage and Metabolic Fluxes in Francisella tularensis Subspecies holarctica and Francisella novicida., Front Cell Infect Microbiol, PMID 28680859

PXD023547 Dataset with its publication pending (from PRIDE)
Dataset title: Defining Essential Regulators of Na�ve Human Pluripotent Cell Reprogramming
Possible reference: Collier, AJ. et al. (2022) Genome-wide screening identifies Polycomb repressive complex 1.3 as an essential regulator of human na�ve pluripotent cell reprogramming., Sci Adv, PMID 35333572

PXD023534 no publication (from MassIVE)
Dataset title: Cardiac proteome of Western painted turtle
Possible reference: Alderman, SL. et al. (2021) Cold acclimation induces life stage-specific responses in the cardiac proteome of western painted turtles (Chrysemys picta bellii): implications for anoxia tolerance., J Exp Biol, PMID 34328184

PXD023491 Dataset with its publication pending (from PRIDE)
Dataset title: A long-term 3D organoid (tubuloid) model of the adult mouse kidney
Possible reference: Myszczyszyn, A. et al. (2024) Mice with renal-specific alterations of stem cell-associated signaling develop symptoms of chronic kidney disease but surprisingly no tumors., PLoS One, PMID 38512983

PXD023450 Dataset with its publication pending (from PRIDE)
Dataset title: Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells
Possible reference: Chen, X. et al. (2021) Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells., Cell Death Discov, PMID 34006825

PXD023446 no publication (from MassIVE)
Dataset title: Elucidation of Familial Relationships Using Hair Shaft Proteomics
Possible reference: Karim, N. et al. (2021) Elucidation of familial relationships using hair shaft proteomics., Forensic Sci Int Genet, PMID 34315035

PXD023433 Dataset with its publication pending (from PRIDE)
Dataset title: Stress-induced tyrosine phosphorylation of RtcB modulates IRE1 activity and signaling outputs.
Possible reference: Papaioannou, A. et al. (2022) Stress-induced tyrosine phosphorylation of RtcB modulates IRE1 activity and signaling outputs., Life Sci Alliance, PMID 35193953

PXD023431 Dataset with its publication pending (from PRIDE)
Dataset title: Secretomic analysis of a novel strain SM1988
Possible reference: Li, J. et al. (2021) Taxonomic and Enzymatic Characterization of Flocculibacter collagenilyticus gen. nov., sp. nov., a Novel Gammaproteobacterium With High Collagenase Production., Front Microbiol, PMID 33786038

PXD023331 no publication (from MassIVE)
Dataset title: Phosphoproteomic Response of Cardiac Endothelial Cells to Ischemic Injury and Ultrasound
Possible reference: Emechebe, U. et al. (2021) Phosphoproteomic response of cardiac endothelial cells to ischemia and ultrasound., Biochim Biophys Acta Proteins Proteom, PMID 34119693

PXD023255 no publication (from MassIVE)
Dataset title: Genetic inactivation of RIP1 kinase activity in rats protects against ischemic brain injury
Possible reference: Stark, K. et al. (2021) Genetic inactivation of RIP1 kinase activity in rats protects against ischemic brain injury., Cell Death Dis, PMID 33828080

PXD023124 Dataset with its publication pending (from PRIDE)
Dataset title: Nucleotide sugar biosynthesis occurs in the glycosomes of procyclic and bloodstream form Trypanosoma brucei
Possible reference: Sampaio Guther, ML. et al. (2021) Nucleotide sugar biosynthesis occurs in the glycosomes of procyclic and bloodstream form Trypanosoma brucei., PLoS Negl Trop Dis, PMID 33592041

PXD023121 Dataset with its publication pending (from PRIDE)
Dataset title: FAM83F regulates canonical Wnt signalling through an interaction with CK1Î±
Possible reference: Dunbar, K. et al. (2021) FAM83F regulates canonical Wnt signalling through an interaction with CK1α., Life Sci Alliance, PMID 33361109

PXD023116 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative Beer SWATH-MS Proteomics
Possible reference: Schulz, BL. et al. (2018) Process Proteomics of Beer Reveals a Dynamic Proteome with Extensive Modifications., J Proteome Res, PMID 29457908

PXD023096 Dataset with its publication pending (from PRIDE)
Dataset title: : The effects of chronic morphine on the endogenous cannabinoid system in the ventral tegmental area
Possible reference: Zhang, H. et al. (2021) The Effects of Repeated Morphine Treatment on the Endogenous Cannabinoid System in the Ventral Tegmental Area., Front Pharmacol, PMID 33953672

PXD022985 Dataset with its publication pending (from PRIDE)
Dataset title: PDGFR signaling in recessive dystrophic epidermolysis bullosa
Possible reference: Iinuma, S. et al. (2015) Transplanted bone marrow-derived circulating PDGFRα+ cells restore type VII collagen in recessive dystrophic epidermolysis bullosa mouse skin graft., J Immunol, PMID 25601922

PXD022969 Dataset with its publication pending (from PRIDE)
Dataset title: Mycobacterium tuberculosis H2S functions as a sink to modulate central metabolism, bioenergetics, and drug susceptibility
Possible reference: Kunota, TTR. et al. (2021) Mycobacterium tuberculosis H2S Functions as a Sink to Modulate Central Metabolism, Bioenergetics, and Drug Susceptibility., Antioxidants (Basel), PMID 34439535

PXD022934 no publication (from MassIVE)
Dataset title: PTEN DEFICIENCY LEADS TO PROTEASOME ADDICTION, A NOVEL VULNERABILITY IN GLIOBLASTOMA
Possible reference: Benitez, JA. et al. (2021) PTEN deficiency leads to proteasome addiction: a novel vulnerability in glioblastoma., Neuro Oncol, PMID 33428749

PXD022932 no publication (from MassIVE)
Dataset title: Impaired phosphatidylethanolamine metabolism activates a reversible stress response that detects and resolves mutant mitochondrial precursors
Possible reference: Sam, PN. et al. (2021) Impaired phosphatidylethanolamine metabolism activates a reversible stress response that detects and resolves mutant mitochondrial precursors., iScience, PMID 33718843

PXD022916 Dataset with its publication pending (from PRIDE)
Dataset title: Nuclear substrates of the CDKL5 kinase - Phosphoproteomics
Possible reference: Khanam, T. et al. (2021) CDKL5 kinase controls transcription-coupled responses to DNA damage., EMBO J, PMID 34605059

PXD022703 Dataset with its publication pending (from PRIDE)
Dataset title: The deubiquitinase TRABID stabilises the K29/K48-specific E3 ubiquitin ligase HECTD1
Possible reference: Harris, LD. et al. (2021) The deubiquitinase TRABID stabilizes the K29/K48-specific E3 ubiquitin ligase HECTD1., J Biol Chem, PMID 33853758

PXD022596 Dataset with its publication pending (from PRIDE)
Dataset title: SOX4 AND SMARCA4 COOPERATIVELY REGULATE PI3K SIGNALING THROUGH TRANSCRIPTIONAL ACTIVATION OF TGFBR2 IN TRIPLE NEGATIVE BREAST CANCER
Possible reference: Mehta, GA. et al. (2021) SOX4 and SMARCA4 cooperatively regulate PI3k signaling through transcriptional activation of TGFBR2., NPJ Breast Cancer, PMID 33837205

PXD022540 Dataset with its publication pending (from iProX)
Dataset title: RLR-MAVS signaling related proteins.
Possible reference: Zhang, LK. et al. (2016) Activation of the RLR/MAVS Signaling Pathway by the L Protein of Mopeia Virus., J Virol, PMID 27605671

PXD022473 Dataset with its publication pending (from PRIDE)
Dataset title: Exploring the molecular machinery of denitrification in Haloferax mediterranei through proteomics
Possible reference: Torregrosa-Crespo, J. et al. (2020) Exploring the Molecular Machinery of Denitrification in Haloferax mediterranei Through Proteomics., Front Microbiol, PMID 33363526

PXD022432 Dataset with its publication pending (from PRIDE)
Dataset title: Nucleolin rescues TDP-43 toxicity in yeast and human cell models
Possible reference: Peggion, C. et al. (2021) Nucleolin Rescues TDP-43 Toxicity in Yeast and Human Cell Models., Front Cell Neurosci, PMID 33912014

PXD022419 Dataset with its publication pending (from PRIDE)
Dataset title: Dissecting the molecular diversity and commonality of bovine and human treponemes identifies key survival and adhesion mechanisms
Possible reference: Staton, GJ. et al. (2021) Dissecting the molecular diversity and commonality of bovine and human treponemes identifies key survival and adhesion mechanisms., PLoS Pathog, PMID 33780514

PXD022414 no publication (from MassIVE)
Dataset title: Cardiomyocyte Contractile Impairment in Heart Failure Results from Reduced BAG3-mediated Sarcomeric Protein Turnover
Possible reference: Martin, TG. et al. (2021) Cardiomyocyte contractile impairment in heart failure results from reduced BAG3-mediated sarcomeric protein turnover., Nat Commun, PMID 34011988

PXD022412 Dataset with its publication pending (from PRIDE)
Dataset title: Gephyrin interacts with the K-Cl co-transporter KCC2 to regulate its surface expression and function in cortical neurons
Possible reference: Al Awabdh, S. et al. (2022) Gephyrin Interacts with the K-Cl Cotransporter KCC2 to Regulate Its Surface Expression and Function in Cortical Neurons., J Neurosci, PMID 34810232

PXD022410 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphorylation of Rif1 by Plk1
Possible reference: Benada, J. et al. (2015) Polo-like kinase 1 inhibits DNA damage response during mitosis., Cell Cycle, PMID 25607646

PXD022400 Dataset with its publication pending (from PRIDE)
Dataset title: Venom proteome of the limacodid caterpillar Doratifera vulnerans
Possible reference: Walker, AA. et al. (2021) Production, composition, and mode of action of the painful defensive venom produced by a limacodid caterpillar, Doratifera vulnerans., Proc Natl Acad Sci U S A, PMID 33893140

PXD022343 Dataset with its publication pending (from PRIDE)
Dataset title: A type 2C protein phosphatase activates high-affinity nitrate uptake by directly dephosphorylating NRT2.1 in Arabidopsis
Possible reference: Ohkubo, Y. et al. (2021) A type 2C protein phosphatase activates high-affinity nitrate uptake by dephosphorylating NRT2.1., Nat Plants, PMID 33686225

PXD022215 Dataset with its publication pending (from PRIDE)
Dataset title: Sequences in the cytoplasmic tail of SARS-CoV-2 Spike facilitate expression at the cell surface and syncytia formation
Possible reference: Cattin-Ortol�, J. et al. (2021) Sequences in the cytoplasmic tail of SARS-CoV-2 Spike facilitate expression at the cell surface and syncytia formation., Nat Commun, PMID 34504087

PXD022202 Dataset with its publication pending (from PRIDE)
Dataset title: Mannose and mannobiose specific responses of insect associated cellulolytic Streptomyces.
Possible reference: Ohashi, K. et al. (2021) Mannose- and Mannobiose-Specific Responses of the Insect-Associated Cellulolytic Bacterium Streptomyces sp. Strain SirexAA-E., Appl Environ Microbiol, PMID 33990299

PXD022165 Dataset with its publication pending (from PRIDE)
Dataset title: Proteomic insights into senescence of testicular peritubular cells from a nonhuman primate model
Possible reference: St�ckl, JB. et al. (2020) Proteomic Insights into Senescence of Testicular Peritubular Cells from a Nonhuman Primate Model., Cells, PMID 33213088

PXD022029 Dataset with its publication pending (from PRIDE)
Dataset title: Rhizobium leguminosarum glutathione peroxidase is essential for oxidative stress resistance and efficient nodulation
Possible reference: Hu, A. et al. (2021) Rhizobium leguminosarum Glutathione Peroxidase Is Essential for Oxidative Stress Resistance and Efficient Nodulation., Front Microbiol, PMID 33633710

PXD021959 Dataset with its publication pending (from PRIDE)
Dataset title: Quantitative proteomic analysis to capture the role of heat-accumulated proteins in moss plant acquired thermotolerance
Possible reference: Guihur, A. et al. (2021) Quantitative proteomic analysis to capture the role of heat-accumulated proteins in moss plant acquired thermotolerance., Plant Cell Environ, PMID 33314263

PXD021949 Dataset with its publication pending (from PRIDE)
Dataset title: Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP
Possible reference: Coutu, AN. et al. (2021) Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP., Sci Rep, PMID 33758223

PXD021945 Dataset with its publication pending (from PRIDE)
Dataset title: Spastin recovery in hereditary spastic paraplegia by preventing neddylation-dependent degradation
Possible reference: Sardina, F. et al. (2020) Spastin recovery in hereditary spastic paraplegia by preventing neddylation-dependent degradation., Life Sci Alliance, PMID 33106322

PXD021935 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive Proteomic Profiling of Urinary Exosomes and Identification of Potential Noninvasive Early Biomarkers of Alzheimer’s Disease in 5XFAD Mouse Model
Possible reference: Song, Z. et al. (2020) Comprehensive Proteomic Profiling of Urinary Exosomes and Identification of Potential Non-invasive Early Biomarkers of Alzheimer's Disease in 5XFAD Mouse Model., Front Genet, PMID 33250918

PXD021895 Dataset with its publication pending (from PRIDE)
Dataset title: Hijacking of transcriptional condensates by endogenous retroviruses
Possible reference: Asimi, V. et al. (2022) Hijacking of transcriptional condensates by endogenous retroviruses., Nat Genet, PMID 35864192

PXD021769 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular Vesicles released by Leishmania donovani infected mouse macrophages
Possible reference: Alves-Ferreira, EVC. et al. (2020) Leishmania braziliensis prostaglandin F2α synthase impacts host infection., Parasit Vectors, PMID 31915065

PXD021729 Dataset with its publication pending (from PRIDE)
Dataset title: Tyrosine phosphoproteomics of patient-derived xenografts reveals ephrin type-B receptor 4 tyrosine kinase as novel therapeutic target in pancreatic cancer
Possible reference: Renuse, S. et al. (2021) Tyrosine Phosphoproteomics of Patient-Derived Xenografts Reveals Ephrin Type-B Receptor 4 Tyrosine Kinase as a Therapeutic Target in Pancreatic Cancer., Cancers (Basel), PMID 34298619

PXD021543 Dataset with its publication pending (from PRIDE)
Dataset title: Flavonol-mediated stabilization of efflux complexes regulates polar auxin transport
Possible reference: Teale, WD. et al. (2021) Flavonol-mediated stabilization of PIN efflux complexes regulates polar auxin transport., EMBO J, PMID 33185277

PXD021447 Dataset with its publication pending (from PRIDE)
Dataset title: Restoration of energy homeostasis by SIRT6 extends healthy lifespan
Possible reference: Roichman, A. et al. (2021) Restoration of energy homeostasis by SIRT6 extends healthy lifespan., Nat Commun, PMID 34050173

PXD021413 Dataset with its publication pending (from PRIDE)
Dataset title: Inflammatory Signaling is Regulated by Fucosylation in Metastatic Breast Cancer Cells
Possible reference: Doud, EH. et al. (2020) NF-κB Signaling Is Regulated by Fucosylation in Metastatic Breast Cancer Cells., Biomedicines, PMID 33322811

PXD021395 Dataset with its publication pending (from PRIDE)
Dataset title: Extracellular vesicle proteome of breast cancer patients with and without cognitive impairment following anthracycline-based chemotherapy
Possible reference: Koh, YQ. et al. (2021) Extracellular Vesicle Proteome of Breast Cancer Patients with and Without Cognitive Impairment Following Anthracycline-based Chemotherapy: An Exploratory Study., Biomark Insights, PMID 34103887

PXD021378 (from jPOST)
Dataset title: A Landscape of Ectodomain Shedding by Quantitative Protein Terminomics
Possible reference: Tsumagari, K. et al. (2021) Exploring the landscape of ectodomain shedding by quantitative protein terminomics., iScience, PMID 33796845

PXD021225 Dataset with its publication pending (from jPOST)
Dataset title: Identification of UFM1-binding proteins
Possible reference: Kuang, M. et al. (2026) The UFM1 Conjugation System: A Master Regulator of Cellular Stress Surveillance in Human Disease., Biology (Basel), PMID 41823810

PXD021068 Dataset with its publication pending (from iProX)
Dataset title: Screening and identification of endometrium proteins as novel potential biomarkers
Possible reference: Bae, SJ. et al. (2022) Identification and analysis of novel endometriosis biomarkers via integrative bioinformatics., Front Endocrinol (Lausanne), PMID 36339397

PXD020871 Dataset with its publication pending (from PRIDE)
Dataset title: Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer
Possible reference: Nicolas, AM. et al. (2022) Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer., Cancer Cell, PMID 35120600

PXD020470 Dataset with its publication pending (from PRIDE)
Dataset title: A Co-culture System Reveals a Cross-talk between Alveolar Epithelium and Pulmonary Microvascular Endothelium during SARS-CoV-2 Infection
Possible reference: Wang, P. et al. (2020) A cross-talk between epithelium and endothelium mediates human alveolar-capillary injury during SARS-CoV-2 infection., Cell Death Dis, PMID 33293527

PXD019963 Dataset with its publication pending (from PRIDE)
Dataset title: iTRAQ in proteomic analysis of potential biomarkers in invasive cancer, ductal carcinoma in situ, and mammary fibroadenoma
Possible reference: Wu, H. et al. (2020) Isobaric Tags for Relative and Absolute Quantitation in Proteomic Analysis of Potential Biomarkers in Invasive Cancer, Ductal Carcinoma In Situ, and Mammary Fibroadenoma., Front Oncol, PMID 33194682

PXD019797 Dataset with its publication pending (from jPOST)
Dataset title: A Data-independent Acquisition-based Global Phosphoproteomics System Enables Deep Profiling
Possible reference: Kitata, RB. et al. (2021) A data-independent acquisition-based global phosphoproteomics system enables deep profiling., Nat Commun, PMID 33953186

PXD019795 Dataset with its publication pending (from PRIDE)
Dataset title: Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit
Possible reference: Holder, J. et al. (2020) Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit., Elife, PMID 32869743

PXD019791 Dataset with its publication pending (from PRIDE)
Dataset title: Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit
Possible reference: Holder, J. et al. (2020) Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit., Elife, PMID 32869743

PXD019640 Dataset with its publication pending (from PRIDE)
Dataset title: The pan-HER kinase inhibitor Neratinib modulates plant defense signaling by covalent targeting of an Arabidopsis epoxide hydrolase
Possible reference: Ninck, S. et al. (2023) Chemoproteomics Reveals the Pan-HER Kinase Inhibitor Neratinib To Target an Arabidopsis Epoxide Hydrolase Related to Phytohormone Signaling., ACS Chem Biol, PMID 37115018

PXD019239 Dataset with its publication pending (from PRIDE)
Dataset title: STING mediates lupus via the activation of conventional dendritic cell maturation and plasmacytoid dendritic cell differentiation
Possible reference: Thim-Uam, A. et al. (2020) STING Mediates Lupus via the Activation of Conventional Dendritic Cell Maturation and Plasmacytoid Dendritic Cell Differentiation., iScience, PMID 33083760

PXD019229 no publication (from MassIVE)
Dataset title: EDF1 coordinates cellular responses to ribosome collisions
Possible reference: Sinha, NK. et al. (2020) EDF1 coordinates cellular responses to ribosome collisions., Elife, PMID 32744497

PXD019228 no publication (from MassIVE)
Dataset title: EDF1 coordinates cellular responses to ribosome collisions
Possible reference: Sinha, NK. et al. (2020) EDF1 coordinates cellular responses to ribosome collisions., Elife, PMID 32744497

PXD019225 no publication (from MassIVE)
Dataset title: EDF1 coordinates cellular responses to ribosome collisions
Possible reference: Sinha, NK. et al. (2020) EDF1 coordinates cellular responses to ribosome collisions., Elife, PMID 32744497

PXD019030 Dataset with its publication pending (from PRIDE)
Dataset title: Dietary intervention improves health metrics and life expectancy of the genetically obese Titan mouse
Possible reference: M�ller-Eigner, A. et al. (2022) Dietary intervention improves health metrics and life expectancy of the genetically obese Titan mouse., Commun Biol, PMID 35505192

PXD018803 (from jPOST)
Dataset title: LFQ_TurboID-STING_anti-biotin_antibody
Possible reference: Karunadasa, SS. et al. (2025) Detection and Quantification of Biotinylated Sites for TurboID-Based Proximity Labeling Mass Spectrometry in Arabidopsis., Methods Mol Biol, PMID 40638046

PXD018600 Dataset with its publication pending (from PRIDE)
Dataset title: A Structure-Based Mechanism for DNA Entry into the Cohesin Ring
Possible reference: Higashi, TL. et al. (2020) A Structure-Based Mechanism for DNA Entry into the Cohesin Ring., Mol Cell, PMID 32755595

PXD018397 Dataset with its publication pending (from PRIDE)
Dataset title: Salinity adaptation in the principal arboviral vector Aedes aegypti characterized by larval cuticle changes
Possible reference: Ramasamy, R. et al. (2021) Transcriptomic, proteomic and ultrastructural studies on salinity-tolerant Aedes aegypti in the context of rising sea levels and arboviral disease epidemiology., BMC Genomics, PMID 33836668

PXD018387 Dataset with its publication pending (from PRIDE)
Dataset title: Allosteric HSP70 inhibitors perturb mitochondrial proteostasis and overcome proteasome inhibitor resistance in multiple myeloma
Possible reference: Ferguson, ID. et al. (2022) Allosteric HSP70 inhibitors perturb mitochondrial proteostasis and overcome proteasome inhibitor resistance in multiple myeloma., Cell Chem Biol, PMID 35853457

PXD018380 Dataset with its publication pending (from PRIDE)
Dataset title: Meltome Analysis of Geobacillus thermoleoverans ARTRW1
Possible reference: Oztug, M. et al. (2020) Thermal Proteome Profiling and Meltome Analysis of a Thermophilic Bacterial Strain, Geobacillus thermoleovorans ARTRW1: Toward Industrial Applications., OMICS, PMID 33085568

PXD018268 Dataset with its publication pending (from PRIDE)
Dataset title: Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24
Possible reference: Cao, X. et al. (2021) Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24., Nat Commun, PMID 33479206

PXD018267 Dataset with its publication pending (from PRIDE)
Dataset title: Schwann cell plasticity regulates neuroblastic tumor cell differentiation
Possible reference: Weiss, T. et al. (2016) Proteomics and transcriptomics of peripheral nerve tissue and cells unravel new aspects of the human Schwann cell repair phenotype., Glia, PMID 27545331

PXD018034 Dataset with its publication pending (from PRIDE)
Dataset title: Maturation kinetics of a multiprotein complex revealed by metabolic labeling
Possible reference: Onischenko, E. et al. (2020) Maturation Kinetics of a Multiprotein Complex Revealed by Metabolic Labeling., Cell, PMID 33333025

PXD017771 no publication (from MassIVE)
Dataset title: Age-Related Changes in Hair Shaft Protein Profiling and Genetically Variant Peptides
Possible reference: Plott, TJ. et al. (2020) Age-Related Changes in Hair Shaft Protein Profiling and Genetically Variant Peptides., Forensic Sci Int Genet, PMID 32485593

PXD017696 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive quantitative analysis of the proteome of Leishmania (Viannia) species
Possible reference: Pinho, N. et al. (2020) In-depth quantitative proteomics uncovers specie-specific metabolic programs in Leishmania (Viannia) species., PLoS Negl Trop Dis, PMID 32804927

PXD017490 no publication (from MassIVE)
Dataset title: Absolute quantification of transcription factors reveals principles of gene regulation in erythropoiesis
Possible reference: Palii, CG. et al. (2019) Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate., Cell Stem Cell, PMID 30880026

PXD017367 Dataset with its publication pending (from jPOST)
Dataset title: Soybean under smoke and flooding
Possible reference: Li, X. et al. (2018) Proteomic analysis of the effect of plant-derived smoke on soybean during recovery from flooding stress., J Proteomics, PMID 29704570

PXD017366 no publication (from MassIVE)
Dataset title: Mass spectrometry-based proteomic characterization of cutaneous melanoma ectosomes reveals the presence of cancer-related molecules
Possible reference: Surman, M. et al. (2020) Mass Spectrometry-Based Proteomic Characterization of Cutaneous Melanoma Ectosomes Reveals the Presence of Cancer-Related Molecules., Int J Mol Sci, PMID 32331267

PXD017171 Dataset with its publication pending (from PRIDE)
Dataset title: Comprehensive functional analysis of Escherichia coli ribosomal RNA methyltransferases
Possible reference: Pletnev, P. et al. (2020) Comprehensive Functional Analysis of Escherichia coli Ribosomal RNA Methyltransferases., Front Genet, PMID 32174967

PXD017121 Dataset with its publication pending (from PRIDE)
Dataset title: Global Profiling of the Lysine Crotonylome in Different Pluripotent States
Possible reference: Lv, Y. et al. (2021) Global Profiling of the Lysine Crotonylome in Different Pluripotent States., Genomics Proteomics Bioinformatics, PMID 33746086

PXD016882 Dataset with its publication pending (from PRIDE)
Dataset title: Study of matrix proteins synthesized by DU145 and PC3 prostate cancer cells alone or in co-culture with prostate-derived fibroblasts.
Possible reference: Kim, W. et al. (2014) RUNX1 is essential for mesenchymal stem cell proliferation and myofibroblast differentiation., Proc Natl Acad Sci U S A, PMID 25313057

PXD016729 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of X-linked genes that drive sex differences in murine embryonic stem cells
Possible reference: Genolet, O. et al. (2021) Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach., Genome Biol, PMID 33863351

PXD016581 Dataset with its publication pending (from PRIDE)
Dataset title: Identification of Saliva Proteins of the Whitefly Bemisia tabaci
Possible reference: Huang, HJ. et al. (2021) Identification of salivary proteins in the whitefly Bemisia tabaci by transcriptomic and LC-MS/MS analyses., Insect Sci, PMID 32757245

PXD016356 Dataset with its publication pending (from PRIDE)
Dataset title: MuSC proteomic changes during aging
Possible reference: Pehar, M. et al. (2016) Changes in Protein Expression and Lysine Acetylation Induced by Decreased Glutathione Levels in Astrocytes., Mol Cell Proteomics, PMID 26486419

PXD016225 Dataset with its publication pending (from PRIDE)
Dataset title: Trichodesmium field metaproteomes
Possible reference: Walworth, NG. et al. (2022) Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium., J Proteome Res, PMID 34855411

PXD015471 Dataset with its publication pending (from PRIDE)
Dataset title: The mRNA-binding proteome of proliferating and differentiated muscle cells
Possible reference: Hiller, M. et al. (2020) The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells., Genomics Proteomics Bioinformatics, PMID 33338663

PXD015281 Dataset with its publication pending (from PRIDE)
Dataset title: Phosphoproteomics across the yeast life cycle
Possible reference: Mart�nez-Monta��s, F. et al. (2020) Phosphoproteomic Analysis across the Yeast Life Cycle Reveals Control of Fatty Acyl Chain Length by Phosphorylation of the Fatty Acid Synthase Complex., Cell Rep, PMID 32783946

PXD014905 Dataset with its publication pending (from jPOST)
Dataset title: NC Table S3
Possible reference: Wingrove, JA. et al. (2018) Peripheral blood gene expression signatures which reflect smoking and aspirin exposure are associated with cardiovascular events., BMC Med Genomics, PMID 29329538

PXD014209 Dataset with its publication pending (from iProX)
Dataset title: Brown Algae Extracts inhibit lung cancer cell invasion and migration
Possible reference: Wang, CH. et al. (2019) Dieckol inhibits non-small-cell lung cancer cell proliferation and migration by regulating the PI3K/AKT signaling pathway., J Biochem Mol Toxicol, PMID 31291034

PXD014155 Dataset with its publication pending (from PRIDE)
Dataset title: Evaluation of in-house stabilized trypsin
Possible reference: Gonz�lez-L�pez, NM. et al. (2023) In-house standards derived from doping peptides: Enzymatic and serum stability and degradation profile of GHRP and GHRH-related peptides., Biomed Chromatogr, PMID 37688464

PXD014018 no publication (from MassIVE)
Dataset title: Quantitative proteomic analyses of Chlorella vulgaris NJ-7 and UTEX259
Possible reference: Wang, Y. et al. (2020) Early Stage Adaptation of a Mesophilic Green Alga to Antarctica: Systematic Increases in Abundance of Enzymes and LEA Proteins., Mol Biol Evol, PMID 31794607

PXD013961 Dataset with its publication pending (from PRIDE)
Dataset title: Proteome of L-carnitine-grown Eubacterium limosum ATCC 8486
Possible reference: Picking, JW. et al. (2019) MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation., J Biol Chem, PMID 31341018

PXD013699 no publication (from MassIVE)
Dataset title: iTRAQ-based proteomics for Streptococcus thermophilus ASCC 1275
Possible reference: Wu, Q. et al. (2019) Functional Genomic Analyses of Exopolysaccharide-Producing Streptococcus thermophilus ASCC 1275 in Response to Milk Fermentation Conditions., Front Microbiol, PMID 31507577

PXD013460 Dataset with its publication pending (from PRIDE)
Dataset title: Sex and age specific adaptations of the hippocampal proteome to early-life stress
Possible reference: Eagleson, KL. et al. (2020) Proteomic and mitochondrial adaptations to early-life stress are distinct in juveniles and adults., Neurobiol Stress, PMID 33344706

PXD013272 no publication (from MassIVE)
Dataset title: Paenibacillus larvae exoproteins of ERIC I-IV genotypes
Possible reference: Erban, T. et al. (2019) Comprehensive proteomic analysis of exoproteins expressed by ERIC I, II, III and IV Paenibacillus larvae genotypes reveals a wide range of virulence factors., Virulence, PMID 30957692

PXD012496 no publication (from MassIVE)
Dataset title: The N-cadherin interactome in primary cardiomyocytes as defined by quantitative proximity proteomics
Possible reference: Li, Y. et al. (2019) The N-cadherin interactome in primary cardiomyocytes as defined using quantitative proximity proteomics., J Cell Sci, PMID 30630894

PXD012001 Dataset with its publication pending (from PRIDE)
Dataset title: Systems level analysis of epithelial to mesenchymal transition reveals more alteration in phosphoproteome than proteome and identifies DNAJB4 and CD81 as EMT regulators
Possible reference: Uretmen Kagiali, ZC. et al. (2019) Systems-level Analysis Reveals Multiple Modulators of Epithelial-mesenchymal Transition and Identifies DNAJB4 and CD81 as Novel Metastasis Inducers in Breast Cancer., Mol Cell Proteomics, PMID 31221721

PXD011746 no publication (from MassIVE)
Dataset title: KILchip v1.0 A novel Plasmodium falciparum merozoite protein microarray to facilitate malaria vaccine candidate prioritization
Possible reference: Kamuyu, G. et al. (2018) KILchip v1.0: A Novel Plasmodium falciparum Merozoite Protein Microarray to Facilitate Malaria Vaccine Candidate Prioritization., Front Immunol, PMID 30619257

PXD011352 Dataset with its publication pending (from iProX)
Dataset title: Histone-lysine N-methyltransferase SETD7 is a potential serum biomarker for colorectal cancer patients
Possible reference: Duan, B. et al. (2018) Histone-lysine N-methyltransferase SETD7 is a potential serum biomarker for colorectal cancer patients., EBioMedicine, PMID 30361067

PXD011304 Dataset with its publication pending (from PRIDE)
Dataset title: Macromolecular connectivity landscape of mammalian brain
Possible reference: Pourhaghighi, R. et al. (2020) BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain., Cell Syst, PMID 32325033

PXD011142 Dataset with its publication pending (from PRIDE)
Dataset title: Multi-Omics Analyses Revealed Conserved Aging Signatures in Mice
Possible reference: Tang, X. et al. (2025) Integrative Multi-Omics Analysis Reveals Age-Associated Molecular Mechanisms in SARS-CoV-2 Infection., J Med Virol, PMID 41378745

PXD007973 Dataset with its publication pending (from PRIDE)
Dataset title: Moss proteomes, LC-MS/MS - proteome data analysis
Possible reference: Guihur, A. et al. (2021) Quantitative proteomic analysis to capture the role of heat-accumulated proteins in moss plant acquired thermotolerance., Plant Cell Environ, PMID 33314263

PXD007067 no publication (from MassIVE)
Dataset title: Quantitative proteomics for dcas9 captured proteins
Possible reference: Gao, XD. et al. (2019) Adapting dCas9-APEX2 for subnuclear proteomic profiling., Methods Enzymol, PMID 30691651

PXD006883 Dataset with its publication pending (from PRIDE)
Dataset title: A proteomics analysis of adventitious root formation after leaf removal in lotus (Nelumbo nucifera Gaertn.)
Possible reference: Cheng, L. et al. (2018) A proteomics analysis of adventitious root formation after leaf removal in lotus (Nelumbo nucifera Gaertn.)., Z Naturforsch C J Biosci, PMID 29794259

PXD006843 no publication (from MassIVE)
Dataset title: GeLC-MS/MS of H37Rv and two clinical isolates of Mycobacterium tuberculosis
Possible reference: Heunis, T. et al. (2017) Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates., J Proteome Res, PMID 28820946

PXD006411 Dataset with its publication pending (from MassIVE)
Dataset title: The histone variant macroH2A1 is a BRCA1 ubiquitin ligase substrate
Possible reference: Kim, BJ. et al. (2017) The Histone Variant MacroH2A1 Is a BRCA1�Ubiquitin Ligase Substrate., Cell Rep, PMID 28564596

PXD006150 Dataset with its publication pending (from MassIVE)
Dataset title: Trans-kingdom mimicry underlies ribosome customization by a poxvirus kinase
Possible reference: Jha, S. et al. (2017) Trans-kingdom mimicry underlies ribosome customization by a poxvirus kinase., Nature, PMID 28636603

PXD004677 Dataset with its publication pending (from MassIVE)
Dataset title: Characterization of site-specific N-glycopeptide isoforms of alpha-1-acid glycoprotein from an interlaboratory study using LC-MS/MS
Possible reference: Lee, JY. et al. (2016) Characterization of Site-Specific N-Glycopeptide Isoforms of α-1-Acid Glycoprotein from an Interlaboratory Study Using LC-MS/MS., J Proteome Res, PMID 27760464

PXD004629 Dataset with its publication pending (from PRIDE)
Dataset title: Cancer proteome and metabolite changes linked to SHMT2
Possible reference: Tong, J. et al. (2020) Cancer proteome and metabolite changes linked to SHMT2., PLoS One, PMID 32903271

PXD002497 Dataset with its publication pending (from MassIVE)
Dataset title: Growth condition-dependent cell surface proteome analysis of Enterococcus faecium
Possible reference: Sinnige, JC. et al. (2015) Growth condition-dependent cell surface proteome analysis of Enterococcus faecium., Proteomics, PMID 26316380

Summary of results:
33107 Datasets already with an assoctiated PubMed ID
1 Datasets of status ' Aaron R. Goldman, Benjamin G. Bitler, Zachary Schug, Jose R. Conejo-Garcia, Rugang Zhang, and David W. Speicher. The Primary Effect on the Proteome of ARID1A-Mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post' with no articles found
6 Datasets of status '' with a possible article found
32 Datasets of status '' with no articles found
1 Datasets of status ', Next Generation Sequencing identifies CDH11 and MRC1 as novel translational biomarkers of kidney fibrosis' with no articles found
1 Datasets of status '. . .' with a possible article found
1 Datasets of status '. Endophyte-Promoted Phosphorus Solubilization in Populus. Frontiers in Plant Science (accepted).' with no articles found
1 Datasets of status '. The discovery of a Legionella phage explains a key determinant of human disease. .' with no articles found
1 Datasets of status '. The molecular basis for nuclear pore destruction by a proximity-inducing molecular glue. https://doi.org/10.1016/j.chembiol.2026.04.016.' with no articles found
1 Datasets of status '79) J.G. Meyer, A.K. D?Souza, D.J. Sorensen, M.J. Rardin, A.J. Wolfe, B.W. Gibson, B. Schilling. Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH). J. Amer. Soc.' with no articles found
1 Datasets of status 'A. Katherine Hatstat Hannah D. Ahrendt Matthew W. Foster Leland Mayne M. Arthur Moseley S. Walter Englander Dewey G. McCafferty. Characterization of Small-Molecule-Induced Changes in Parkinson's-Related Trafficking via the Nedd4 Ubiquitin Signaling Cascad' with no articles found
1 Datasets of status 'Acar IE, Willems E, Kersten E, Keizer-Garritsen J, Kragt E, Bakker B, Galesloot TE, Hoyng CB, Fauser S, van Gool AJ, Lechanteur YTE, Koertvely E, Nogoceke E, Gloerich J, de Jonge MI, Lor�s-Motta L, den Hollander AI. Semi-Quantitative Multiplex Profiling o' with no articles found
1 Datasets of status 'Alessio Adamiano Stefania Scialla Francesca Carella Marialuisa Casella Serena Camerini Alessandra Quarta Alexandra Muntiu Francesca Ferrari Alberto Vitali Michele Iafisco Clara Piccirillo. Simultaneous extraction of calcium phosphates and proteins from fi' with no articles found
1 Datasets of status 'Alexander G�nter * , Mohamed Ali Jarboui , Regine Lotte Muehlfriedel and Mathias W Seeliger. Exploration of the visual streak of the Mongolian gerbil as a model for the human central retina. Front. Med. February 2025 (Submitted).' with no articles found
1 Datasets of status 'Alexander S. Dowdell, Maxwell D. Murphy, Christina Azodi, Selene K. Swanson , Laurence Florens, Shiyong Chenac & Wolfram R. Z�ckert. Comprehensive Spatial Analysis of the Borrelia burgdorferi Lipoproteome Reveals a Compartmentalization Bias Toward the B' with a possible article found
1 Datasets of status 'Andrew Frando, Vishant Boradia, Marina Gritsenko, Michael-Claude Beltejar, Le Day, David R. Sherman, Shuyi Ma, Jon M. Jacobs, Christoph Grundner. The Mycobacterium tuberculosis protein O-phosphorylation landscape. bioRxiv. Epub 2022 Feb 17. doi: https://d' with a possible article found
1 Datasets of status 'Angew. Chem. Int. Ed. 2024, e202409220' with no articles found
1 Datasets of status 'Anna Lisa Montemari, Valeria Marzano, Nour Essa, Stefano Levi Mortera, Martina Rossitto, Simone Gardini, Laura Selan, Gianluca Vrenna, Andrea Onetti Muda, Lorenza Putignani, Ersilia Vita Fiscarelli. A shaving proteomic approach to unveil surface proteins ' with no articles found
1 Datasets of status 'Banerjee D, Eng T, Lau AK, Sasaki Y, Wang B, Chen Y, Prahl J-P, Singan VR, Herbert RA, Liu Y, Tanjore D, Petzold CJ, Keasling JD, Mukhopadhyay A. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at sca' with no articles found
1 Datasets of status 'Bhosale SD, Moulder R, Suomi T, et al (2024) Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk. iScience 110048. https://doi.org/https://doi.org/10.1016/j.isci.2024.110048' with a possible article found
1 Datasets of status 'Bleem, Alissa; Kuatsjah, Eugene; Presley, Gerald N.; Hinchen, Daniel J.; Zahn, Michael; Garcia, David C.; Michener, William E.; K�nig, Gerhard; Tornesakis, Konstantinos; Allemann, Marco N.; Giannone, Richard J.; McGeehan, John E.; Beckham, Gregg T.; Miche' with no articles found
1 Datasets of status 'Bonarrigo M, Geisslitz S, Scherf KA, Messina B, Russo G, Sestili F, Masci S. ATI, fructans and predictive assessment of technological quality of Sicilian tetraploid conservation and modern wheat varieties. J Cereal Sci [Internet]. 2025;123:104190. Availab' with no articles found
1 Datasets of status 'Borte�en T, M�ller T, Krijgsveld J. An integrated workflow for quantitative analysis of the newly synthesized proteome. bioRxiv [Internet]. 2023 Jan 1;2023.03.03.530942. Available from: http://biorxiv.org/content/early/2023/03/03/2023.03.03.530942.abstrac' with no articles found
1 Datasets of status 'Brianna Bibel, Elad Elkayam, Steven Silletti, Elizabeth A Komives, and Leemor Joshua-Tor. Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release. eLife (in press).' with no articles found
1 Datasets of status 'Budnik B., Levy E., Harmange G., Slavov N. Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation. https://doi.org/10.1101/102681.' with no articles found
2 Datasets of status 'Caesar LK, Kellogg JJ, Kvalheim OM, Cech RA, Cech NB. Integration of Biochemometrics and Molecular Networking to Identify Antimicrobials in Angelica keiskei. Planta Med. 2018 Jul;84(9-10):721-728. doi: 10.1055/a-0590-5223.' with no articles found
1 Datasets of status 'Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics. Bo Wen, J. Sebastian Paez, Chris Hsu, Daniele Canzani, Alexis Taylor Chang, Nicholas Shulman, Brendan X. MacLean, Matthew D. Berg, Judi' with a possible article found
1 Datasets of status 'Caroline Solazzo, William W. Fitzhugh. Proteomics identify bowhead whale muscle tissue and baleen in cinder residues at a 16th c. Basque whaling site. https://doi.org/10.1016/j.jasrep.2024.104691.' with no articles found
1 Datasets of status 'Chaitanya Dingare, Jenny Yang, Ben Steventon. Mannose is crucial for mesoderm specification and symmetry breaking in gastruloids. https://www.biorxiv.org/content/10.1101/2023.06.05.543730v2.full.' with no articles found
1 Datasets of status 'Chen A, Franks, A & Slavov, N. DART-ID increases single-cell proteome coverage. (submitted).; Chen A, Franks A & Slavov N. DART-ID increases single-cell proteome coverage. biorXiv, DOI: 10.1101/399121. PLOS Comp Bio (submitted).' with a possible article found
1 Datasets of status 'Chen, S., J. L. Baumert, and M. L. Downs. 2025. Quantification, Risk Assessment, and Mitigation of Cashew Allergen Cross-Contact in Shared Roasting Oil Systems. Journal of Food Protection:100678.' with a possible article found
1 Datasets of status 'Chevenier A, Fanuel M, Sokolova E, Latorre DM, Jouanneau D, Jeudy A, et al. Structure, function and catalytic mechanism of the carrageenan-sulfatases from the marine bacterium Zobellia galactanivorans DsijT. Carbohydr Polym. 2025;358:123487' with a possible article found
1 Datasets of status 'Christopher B. Lietz, Thomas Toneff, Charles Mosier, Sonia Podvin, Anthony J. O’Donoghue, Vivian Hook. Phosphopeptidomics Reveals Differential Phosphorylation States and Novel SxE Phosphosite Motifs of Neuropeptides in Dense Core Secretory Vesicles. J. ' with no articles found
1 Datasets of status 'Christopher R. Below ? Oliver M. Bernhardt ? Stephanie Kaspar-Sch�nefeld ? Sander Willems ? Edoardo Coronado ? Ino D. Karemaker ? Bettina Streckenbach ? Monika Pepelnjak ? Luca R�ss ? Sandra Sch�r ? Dennis Trede ? Jonathan R. Krieger ? Tejas Gandhi ? Rola' with a possible article found
1 Datasets of status 'Christopher, et al., submitted' with no articles found
1 Datasets of status 'Corey M. Nemec, Fan Yang, Joshua M. Gilmore, Corinna Hintermair, Yi-Hsuan Ho, Sandra C. Tseng, Martin Heidemann, Ying Zhang, Laurence Florens, Audrey P. Gasch, Dirk Eick, Michael P. Washburn, Gabriele Varani, and Aseem Z. Ansari. Different phosphoisoforms' with no articles found
1 Datasets of status 'Cruz-Mireles N, Os�s-Ruiz M, Derbyshire P, J�gousse C, Ryder LS, Bautista MJ, Eseola AB, Sklenar J, Tang B, Yan X, Ma W, Findlay KC, Were V, MacLean D, Talbot NJ, Menke FLH. The phosphorylation landscape of infection-related development by the rice blast ' with a possible article found
1 Datasets of status 'Cruz-Morales, Pablo, et al. "Biosynthesis of polycyclopropanated high energy biofuels." Joule 6.7 (2022): 1590-1605.' with a possible article found
1 Datasets of status 'Cucina, A., Schmidt, A.L., Di Gianvincenzo, F. et al. Paleoproteomic identification of the species used in fourteenth century gut-skin garments from the archaeological site of Nuulliit, Greenland. Scientific Reports 2024 14(13431). doi: 10.1038/s41598-024' with a possible article found
1 Datasets of status 'D. Salvach�a, A.Z. Werner, I. Pardo, M. Michalska, B.A. Black, B.S. Donohoe, S. Haugen, R. Katahira, S. Notonier, K.J. Ramirez, S.O. Purvine, E.M. Zink, Paul Abraham, R.J. Giannone, S. Poudel, P. Laible, R.L. Hettich, G.T. Beckham. Outer membrane vesicles' with a possible article found
1 Datasets of status 'Dan, Q., Chiu, Y., Lee, N. et al. A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxy acids. Nat Catal 8, 147–161 (2025). https://doi.org/10.1038/s41929-025-01299-5' with no articles found
1 Datasets of status 'Darwinian Evolution of Self-Replicating DNA in a Synthetic Protocell Zhanar Abil, Ana Mar�a Restrepo Sierra, Andreea R. Stan, Am�lie Ch�ne, Alicia del Prado, Miguel de Vega, Yannick Rondelez, Christophe Danelon https://www.nature.com/articles/s41467-024' with no articles found
4467 Datasets of status 'Dataset with its publication pending' with a possible article found
12138 Datasets of status 'Dataset with its publication pending' with no articles found
1 Datasets of status 'Dhamija B, Marathe S, Sawant V, Basu M, Attrish D, Mukherjee D, Kumar S, Pai MGJ, Wad S, Sawant A, Nayak C, Venkatesh KV, Srivastava S, Barthel SR, Purwar R. IL-17A Orchestrates Reactive Oxygen Species/HIF1α-Mediated Metabolic Reprogramming in Psoriasis.' with no articles found
1 Datasets of status 'Donghua Hu, Min Tan, Dongliang Lu, Brian Kleiboeker, Xuejing Liu, Hongsuk Park, Alexxai V. Kravitz, Kooresh I. Shoghi, Yu-Hua Tseng, Babak Razani, Akihiro Ikeda, and Irfan J. Lodhi. TMEM135 Links Peroxisomes to the Regulation of Brown Fat Mitochondrial Fi' with no articles found
1 Datasets of status 'Duriez, et al. (submitted)' with no articles found
1 Datasets of status 'Elias Roihuvuo, Lee Sturgis, Ahmed B. Montaser, Marcin Tabaka, Elliot H. Choi, Deepa Mathew, Anthi-Styliani Makiou, Kristiina M. Huttunen, Krzysztof Palczewski, Frans Vinberg, Henri Leinonen; Presynaptic Changes in Mouse Rod Photoreceptors During Early Re' with no articles found
1 Datasets of status 'Eliza A. Zalis, Austin S. Nuxoll, Sylvie Manuse,G eremy Clair, Lauren C. Radlinski, Brian P. Conlon, Joshua Adkins, Kim Lewis. Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells. mBio 10:e01930-19. doi: 10.1128/mBi' with no articles found
1 Datasets of status 'Evan E. Hubbard, Kevin Reagle, Matthew K. Lui, Maxence Derbez-Morin, Gennifer E. Merrihew, Michael J. MacCoss, Ryan R. Julian, Spontaneous isomerization of tau is most prevalent in Alzheimer’s disease, NeuroMarkers, Volume 3, Issue 2, 2026, 100152, IS' with no articles found
1 Datasets of status 'Gollan PJ, Trotta A, Bajwa AA, Mancini I, Aro E-M. Characterization of the Free and Membrane-Associated Fractions of the Thylakoid Lumen Proteome in Arabidopsis thaliana. Vol. 22, International Journal of Molecular Sciences . 2021.' with no articles found
1 Datasets of status 'Gonz�lez-G�mez, P., Echeverria, V., Estades, C.F., Perez, J.H., Krause, J.S., Sabat, P., Li, J., K�ltz, D., Wingfield, J.C. Proteome and endocrine traits in relattion to timing of stages of the annual cycle and body condition in seasonal and aseasonal env' with no articles found
1 Datasets of status 'Graaf, et al.' with a possible article found
1 Datasets of status 'Hana Antonicka, Zhen-Yuan Lin, Alexandre Janer, Mari J. Aaltonen, Woranontee Weraarpachai, Anne-Claude Gingras, Eric A. Shoubridge. A high-density human mitochondrial proximity interaction network. Cell Metabolism (pre-acceptance).' with no articles found
1 Datasets of status 'Hartman, K.; Steiner, G.; Siegel, M.; Looney, C.M.; Hickling, T.P.; Bray-French, K.; Springer, S.; Marban-Doran, C.; Ducret, A. Expanding the MAPPs Assay to Accommodate MHC-II Pan Receptors for Improved Predictability of Potential T Cell Epitopes. accep' with no articles found
1 Datasets of status 'Hempel, B.-F.; Damm, M.; G��men, B.; Karis, M.; Oguz, M.A.; Nalbantsoy, A.; S�ssmuth, R.D. Comparative Venomics of the Vipera ammodytes transcaucasiana and Vipera ammodytes montandoni from Turkey Provides Insights into Kinship. Toxins 2018, 10 (1), 23. do' with a possible article found
1 Datasets of status 'Hillestad Nel T, Peters C, Korzow Richter K, Henshilwood C, van Niekerk K, Douka K. Peptide mass fingerprinting as a tool to assess micromammal biodiversity in Pleistocene South Africa: The case of Klipdrift Shelter. Quat. Sci. Rev. 2023 Dec; 322; 108380.' with no articles found
1 Datasets of status 'Ho, T.C., Blackburn, K., Goshe, M.B., and Williamson, J.D. Identification of multiple proteins whose interaction with mannitol dehydrogenase is induced by salicylic acid: Implications for unconventional secretion. Proteomics, [O1] DOI: 10.1002/pmic.202100' with no articles found
1 Datasets of status 'Huwa, N., Sch�nenberger, R., & Groh, K. J. (2025). Development and application of a targeted phosphoproteomics method for analysing the mTOR pathway dynamics in zebrafish PAC2 cell line. Journal of Proteomics, 319, 105469.' with a possible article found
1 Datasets of status 'Ivan Avilov, Yehor Horokhovskyi, Pooja Mehta, Luisa Welp, Jasmin Jakobi, Mingfang Cai, Aleksander Orzechowski, Henning Urlaub, Juliane Liepe and Peter Lenart. Phosphoproteomic identification of Mos-MAPK targets in meiotic cell cycle and asymmetric divisio' with no articles found
1 Datasets of status 'J. Li, B.B. Levitan, S. Gomez-Jimenez and D. Kültz. Development of a gill assay library for ecological proteomics of threespine sticklebacks (Gasterosteus aculeatus). Mol. Cell. Proteomics (2018) in press.' with no articles found
4 Datasets of status 'Jean-Philippe Lambert, Sarah Picaud, Takao Fujisawa, Huayun Hou, Pavel Savitsky, Liis Uusk�la-Reimand, Gagan D. Gupta, Hala Abdouni, Zhen-Yuan Lin, Monika Tucholska, James D.R. Knight, Beatriz Gonzalez-Badillo, Nicole St-Denis, Joseph A. Newman, Manuel St' with no articles found
1 Datasets of status 'Jihye, et al. (submitted)' with no articles found
1 Datasets of status 'Jinglin L. Xie, Iryna Bohovych, Erin O.Y. Wong, Jean-Philippe Lambert, Anne-Claude Gingras, Oleh Khalimonchuk, Leah E. Cowen and Michelle D. Leach. Ydj1 governs fungal morphogenesis and stress response, and facilitates mitochondrial protein import via Mas' with no articles found
1 Datasets of status 'John D. Lapek, Jr., Mary K Lewinski, Jacob M Wozniak, John Guatelli, and David J Gonzalez. Quantitative temporal viromics of an inducible HIV-1 model yields insight to global host targets and phospho-dynamics associated with Vpr. Mol Cell Proteomics mcp.M' with no articles found
1 Datasets of status 'Josiah Hardesty, Le Day, Jeffrey Warner, Dennis Warner, Marina Gritsenko, Aliya Asghar, Andrew Stolz, Timothy Morgan, Craig McClain, Jon Jacobs, Irina Kirpich. Hepatic Protein and Phosphoprotein Signatures of Alcohol-Associated Cirrhosis and Hepatitis. Am' with a possible article found
1 Datasets of status 'Journal of the World Aquaculture Society: Volume 56, Issue 6' with no articles found
1 Datasets of status 'Justin Sanders, Bo Wen, Paul Rudnick, Rich Johnson, Christine C. Wu, Sewoong Oh, Michael J. MacCoss, William Stafford Noble A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data bioRxiv 2024.06.03.597251; doi: h' with no articles found
3 Datasets of status 'Kai-Ting Fan, Aaron K. Rendahl, Wen-Ping Chen, Dana M. Freund, William M. Gray, Jerry D. Cohen, and Adrian D. Hegeman. Proteome scale-protein turnover analysis using high resolution mass spectrometric data from stable-isotope labeled plants. J. Proteome R' with no articles found
1 Datasets of status 'Kala M Dodson, Erica M Periandri, A Yadav, M Lopes, AJ Barfield, A Ola, FN de Luna Vitorino, C Cearlock, BA Garcia, CA Hill, SE Maloney, G Egervari. ACSS2 mediates prenatal alcohol exposure-related morphological and behavioral phenotypes. Neurobiology of ' with a possible article found
1 Datasets of status 'Kankuri E, Finckenberg P, Leinonen J, Tarkia M, Bj�rk S, Purhonen J, Kallij�rvi J, Kankainen M, Soliymani R, Lalowski M, Mervaala E. Altered acylcarnitine metabolism and inflexible mitochondrial fuel utilization characterize the loss of neonatal myocardia' with no articles found
1 Datasets of status 'Kaouthar Louati, Fatma Kolsi, Manel Mellouli, Hanen Louati, Rania Zribi, Rim Kallel, Mahdi Borni, Yassine Gdoura, Leila Sellami Hakim, Amina Maalej, Sirine Choura, Mohamed Chamkha, Sami Sayadi, Basma Mnif, Zouheir Khemakhem, Tahya Sellami Boudawara, Moham' with no articles found
1 Datasets of status 'Kaouthar Louati,* Amina Maalej, Fatma Kolsi, Rim Kallel, Yassine Gdoura, Mahdi Borni, Leila Sellami Hakim, Rania Zribi, Sirine Choura, Sami Sayadi, Mohamed Chamkha, Basma Mnif, Zouheir Khemakhem, Tahya Sellami Boudawara, Mohamed Zaher Boudawara, Abderrahm' with no articles found
1 Datasets of status 'Kathryn Wolhuter, Lijiang Ma, Nicole S Bryce, Osvaldo Contreras, Natalie Mellett, Ling Zhong, Chris Thekkedam, Corey Giles, Richard P Harvey, Thomas Hennessy, Chris Fouracre, David Bradley, Peter J Meikle, Johan L M Bj�rkegren, Jason C Kovacic. Multi-omic' with no articles found
1 Datasets of status 'Kegley, N. R., Ito, A., Williamson, D. B., McArdle, C. C., and Haltiwanger, R. S. Marfan syndrome variation of the POGLUT2 and POGLUT3 consensus sequence can produce aberrant fibrillin-1 O-glucosylation. Journal of Biological Chemistry' with a possible article found
1 Datasets of status 'Kevin W. Cormier, Brett Larsen, Anne-Claude Gingras, James R. Woodgett. Interactomes of Glycogen Synthase Kinase-3 Isoforms. J. Proteome Res. 2023 (in preparation).' with no articles found
1 Datasets of status 'Kopylov, et al., submitted' with no articles found
1 Datasets of status 'Kuchaříková H, Dobrovolná P, Lochmanová G, Zdráhal Z. Trimethylacetic anhydride-based derivatization facilitates quantification of histone marks at the MS1 level. Mol Cell Proteomics [Internet]. 2021;100114. Available from: https://www.sciencedirect' with no articles found
1 Datasets of status 'Lacroix, et al. (submitted)' with no articles found
1 Datasets of status 'Lauer, S.M., Gasse, J., Krizsan, A. et al. The proline-rich antimicrobial peptide Api137 disrupts large ribosomal subunit assembly and induces misfolding. Nat Commun 16, 567 (2025). https://doi.org/10.1038/s41467-025-55836-8' with no articles found
1 Datasets of status 'Lexhaller B, Colgrave ML, Scherf KA. Characterization and relative quantitation of wheat, rye and barley gluten protein types by LC-MS/MS. Frontiers in Plant Science. 2019;10:1530' with no articles found
1 Datasets of status 'Li et al., submitted' with no articles found
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