PXD083162-1

PXD083162 is an original dataset announced via ProteomeXchange.

Title	In Vivo Chemical Cross-Linking Coupled with Reversed-Phase Co-Fractionation Mass Spectrometry Enables Protein Complex Analysis
Description	Understanding protein–protein interactions (PPIs) and the architecture of protein complexes is essential for elucidating cellular functions and drug action mechanisms. Co-fractionation mass spectrometry (CF–MS) has emerged as an effective tool for ana-lyzing protein complexes under near-native conditions; however, its resolution and structural fidelity are often compromised by complex dissociation during biochemical processing. Here, we present an analytical strategy that integrates in vivo formalde-hyde cross-linking with reversed-phase co-fractionation mass spectrometry (XL–RP–CF–MS) to identify protein complexes in living cells. Cross-linking stabilizes native interactions, preserving complex integrity during denaturing separation. Reversed-phase liquid chromatography provides high-resolution, reproducible fractionation, enabling robust detection of co-elution pat-terns. Applying this platform to RS4;11 leukemia cells, we identified 5,983 proteins and detected 1,753 CORUM complexes together with 487 high-confidence EPIC-predicted assemblies. The workflow also demonstrated excellent quantitative perfor-mance, exhibiting highly linear correlations between chromatographic peak areas and protein loading (R² = 0.9972) as well as between MS signal intensities and loading amounts (R² = 0.9467). This strategy enables sensitive and physiologically relevant identification of protein complexes, offering a reliable approach for characterizing the composition of potential protein assem-blies within specific biological systems.
HostingRepository	iProX
AnnounceDate	2026-08-23
AnnouncementXML	Submission_2026-08-25_18:16:01.352.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liuqing She
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2026-08-25 18:15:06	ID requested
⏵ 1	2026-08-25 18:16:01	announced

Dataset with its publication pending

submitter keyword: co-fractionation mass spectrometry, reversed-phase liquid chromatography, data-independent acquisition, proteomics, protein complex

Wei Liu
contact affiliation	Fudan University
contact email	wliu21@m.fudan.edu.cn
lab head
Liuqing She
contact affiliation	Fudan University
contact email	24110220059@m.fudan.edu.cn
dataset submitter

iProX dataset URI