PXD059305

PXD059305 is an original dataset announced via ProteomeXchange.

Title	Dimethylpiperidine Cross-linker DPST: Enhanced Enrichment and Quantitative Analysis of In Vivo Protein Complexes from Limited Samples
Description	In vivo cross-linking mass spectrometry (XL-MS) enables proteome-wide characterization of protein complexes in live cells. However, current XL-MS methods face significant sample loss during enrichment, limiting their application to small sample quantities, and suffer from low reproducibility (20%-40%), hindering precise quantification. To address these challenges, we developed a novel membrane-permeable cross-linker, 2,6-dimethylpiperidine disuccinimidyl tridecanoate (DPST). The dimethylpiperidinyl group in DPST enables efficient cross-linked peptide enrichment via a one-step TMT antibody approach, eliminating sample loss from multi-step processes and allowing analysis with as few as 1E4 cells. Furthermore, DPST facilitates isotopic labeling (DPST-H/L), enabling light and heavy labeling of cross-linked samples at the cellular level, which reduces inaccuracies from multi-step preparations. This generates reporter ions for precise MS2 quantification, improving the signal-to-noise ratio without increasing spectral complexity. Using DPST (H/L), we successfully analyzed cross-links in primary neurons from single fetal mice and quantified transient and weak interactions, such as between hnRNPA2B1 and MKI67 in dynamic LLPS environments, further validated by biological analysis. Additionally, DPST’s design supports multiple isotopic labeling configurations (e.g., 6-plex, 10-plex). Therefore, our approach provides a powerful tool for both qualitative and quantitative XL-MS analysis of living systems, advancing proteomics and biomedical research even with limited sample quantities.
HostingRepository	iProX
AnnounceDate	2024-12-30
AnnouncementXML	Submission_2025-04-02_21:00:36.722.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jing Chen
SpeciesList	scientific name: Bos taurus; NCBI TaxID: 9913; scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-29 22:05:32	ID requested
⏵ 1	2025-04-02 21:00:37	announced

Dataset with its publication pending

submitter keyword: Chemistry Cross-linking,Mass Spectrometry,Protein-protein Interactions,Protein Structures,Quantitative Analysis

Lihua Zhang
contact affiliation	Dalian Institute of Chemical Physics, Chinese Academy of Sciences
contact email	lihuazhang@dicp.ac.cn
lab head
Jing Chen
contact affiliation	Dalian Institute of Chemical Physics, Chinese Academy of Sciences
contact email	chenj1810@dicp.ac.cn
dataset submitter

iProX dataset URI