PXD061601

PXD061601 is an original dataset announced via ProteomeXchange.

Title	An Integrated Workflow for Analysis of Multiple Protein Post-Translational Modifications
Description	Investigating multiple protein post-translational modifications (PTMs) is critical for unraveling the complexities of protein regulation and the dynamic interplay among PTMs, a growing focus in proteomics. However, simultaneous analysis of diverse PTMs remains a significant technical challenge, as existing workflows struggle to balance throughput, sensitivity, and reproducibility, particularly with limited amount of samples. To address these limitations, we present the first multi-PTM workflow termed MoSAIC, integrating co-enrichment strategies, multiplexing, fractionation, hybrid data acquisition, and unified data analysis, optimized for clinically relevant biological samples. This approach targets phosphorylation, glycosylation, acetylation, and ubiquitination, enabling comprehensive and simultaneous interrogation of these modifications. Compared to conventional methodologies, our strategy reduced total instrument time while identifying more PTM-specific peptides. By leveraging fractionation and tandem mass tag (TMT) labeling, we achieved concurrent identification and quantification of PTM-specific peptides from the same sample, enhancing throughput and data consistency. This robust workflow addresses key limitations in multi-PTM proteomics, providing a cost-effective and efficient platform to advance biological and clinical research.
HostingRepository	PRIDE
AnnounceDate	2026-02-16
AnnouncementXML	Submission_2026-02-15_20:06:44.386.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yuanwei Xu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	ubiquitination signature dipeptidyl lysine; phosphorylated residue; acetylated residue; complex glycosylation
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-08 02:47:24	ID requested
⏵ 1	2026-02-15 20:06:45	announced

Xu Y, Chen L, Lih TM, Hu Y, Zhang H, MoSAIC: An Integrated and Modular Workflow for Confident Analysis of Protein Post-Translational Modification Landscapes. Mol Cell Proteomics, 25(2):101502(2026) [pubmed]

10.1016/j.mcpro.2025.101502;

submitter keyword: LC-MS/MS, DIA, TMT, PTM, PDX, DDA

Hui Zhang
contact affiliation	Professor of Pathology, Oncology, and Chemical and Biomolecular Engineering Director of Mass Spectrometry Core Facility, Center for Biomarker Discovery and Translation Johns Hopkins University 400 N. Broadway Street, Smith Building, Room 4011, Baltimore, MD 21231
contact email	huizhang@jhu.edu
lab head
Yuanwei Xu
contact affiliation	Johns Hopkins University
contact email	yxu105@jh.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD061601

PRIDE project URI

• PRIDE
  1. PXD061601
     1. Label: PRIDE project
     2. Name: An Integrated Workflow for Analysis of Multiple Protein Post-Translational Modifications