PXD059108

PXD059108 is an original dataset announced via ProteomeXchange.

Title	CE-MS Top Down Proteomics Multi-lab Study
Description	A single gene can give rise to multiple functionally distinct forms of protein molecules, called proteoforms, originating from gene mutations, RNA alternative splicing, polymorphisms, and post-translational modifications (PTMs). It is essential to characterize proteins in a proteoform-specific manner to improve our understanding of their role in health and disease. Mass spectrometry (MS)-based top-down proteomics (TDP) has emerged as a powerful tool for the characterization of proteoforms by coupling high-efficiency liquid-phase separation techniques to high-resolution MS and tandem MS (MS/MS). Capillary zone electrophoresis (CZE)-MS is one such separation technique offering unique advantages compared to conventional liquid chromatography (LC)-MS methods, including highly efficient separations of proteoforms based on electrophoretic mobility (µep), minimal sample and solvent consumption, high sensitivity for proteoform detection, and ease of predicting proteoforms’ µep. In this work, research teams from around the world joined forces to validate the robustness and reproducibility of CZE-MS for TDP in both simple and complex model proteoform mixtures, comparing its performance with state-of-the-art LC-MS methods. This study encompasses a full spectrum of commercially available CE-MS interfaces and CE and MS instrumentation amenable to TDP analysis. We provide a repository of CZE-MS methods and detailed experimental protocols for robust, reproducible, and sensitive CE-MS-based TDP analysis that were evaluated by several laboratories. We expect this study will offer the proteomics community an informative resource of ready-to-use experimental CE-MS techniques and a better understanding of the CZE-MS approach and its potential in TDP, which together will accelerate the broad adoption of CZE-MS in protein and proteoform research.
HostingRepository	PRIDE
AnnounceDate	2025-12-18
AnnouncementXML	Submission_2025-12-18_11:44:01.518.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Noah Gould
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932;
ModificationList	monomethylated residue; acetylated residue
Instrument	Orbitrap Eclipse; Q Exactive HF; timsTOF Pro; Orbitrap Fusion Lumos; timsTOF fleX; Q Exactive UHMR; 6560 Q-TOF LC/MS; Orbitrap Exploris 240; 6230A Time-of-Flight LC/MS; maXis

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-20 14:42:55	ID requested
⏵ 1	2025-12-18 11:44:02	announced

Dataset with its publication pending

submitter keyword: CE-MS, Top Down Proteomics, CE, MS

Alexander R. Ivanov
contact affiliation	Barnett Institute of Chemical and Biological Analysis and Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, USA.
contact email	a.ivanov@northeastern.edu
lab head
Noah Gould
contact affiliation	Northeastern University
contact email	gould.n@northeastern.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/2025/12/PXD059108

PRIDE project URI

• PRIDE
  1. PXD059108
     1. Label: PRIDE project
     2. Name: CE-MS Top Down Proteomics Multi-lab Study