PXD068962-1

PXD068962 is an original dataset announced via ProteomeXchange.

Title	Quantitative Native Proteomics by Capillary Zone Electrophoresis-Mass Spectrometry
Description	Accurately measuring protein complex dynamics (i.e., composition and/or abundance changes) in cells is vital for advancing fundamental and translational research. In this work, we present a pilot study establishing capillary zone electrophoresis (CZE)-mass spectrometry (MS) based quantitative native proteomics to determine significant changes in protein complex abundance during the transition from logarithmic to stationary phase growth in Escherichia coli. The approach integrates (1) efficient and fast native-state CZE-MS to obtain the mass and signal intensity of protein complexes for label-free quantification, (2) in-source collision-induced dissociation, enabling informative fragmentation that reveals oligomeric states, and (3) denatured top-down proteomics for the identification of proteoforms, which form the protein complexes. We revealed differentially expressed protein complexes during the growth of Escherichia coli. For example, the glutamate decarboxylase beta hexamer (~317 kDa) exhibits a significantly higher abundance at the stationary phase, which aligns with its biological function. This work represents the first quantitative native proteomics study using online native CZE-MS.
HostingRepository	PRIDE
AnnounceDate	2025-12-08
AnnouncementXML	Submission_2025-12-07_16:07:51.257.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fei FANG
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF; Q Exactive UHMR

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-29 07:31:26	ID requested
⏵ 1	2025-12-07 16:07:52	announced

10.1021/acs.analchem.5c06099;

Fang F, Sun L, Quantitative Native Proteomics by Capillary Zone Electrophoresis-Mass Spectrometry. Anal Chem, 97(46):25385-25390(2025) [pubmed]

submitter keyword: capillary zone electrophoresis-mass spectrometry,quantitative native proteomics

Liangliang Sun
contact affiliation	Michigan State University
contact email	lsun@chemistry.msu.edu
lab head
Fei FANG
contact affiliation	Michigan State University
contact email	fiona.dicp@outlook.com
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/2025/12/PXD068962

PRIDE project URI

• PRIDE
  1. PXD068962
     1. Label: PRIDE project
     2. Name: Quantitative Native Proteomics by Capillary Zone Electrophoresis-Mass Spectrometry