PXD062702

PXD062702 is an original dataset announced via ProteomeXchange.

Title	Live Electrophoresis-Correlative AI Democratizes Single-cell Mass Spectrometry Proteomics
Description	The goal of this project was to deepen proteome coverage on broadly accessible mass spectrometers. We developed electrophoresis-correlative (Eco) ion sorting mass spectrometry (MS) on a decade-old quadrupole orbitrap mass spectrometer (Q Exactive Plus, Thermo). Artificial intelligence (AI) was adapted (CHIMERYS, Thermo) to process the chimeric tandem mass spectra . The strategy was tested, configured, and validated on 1 ng to 250 pg of the HeLa proteome digest. Within a 15-min effective separation window, 1,758 proteins were identified cumulatively from single-cell equivalent proteome amounts (~250 pg). As demonstration, Eco-AI was deployed to profile the proteomic state of dorsal and ventral cell lineages in blastula stage (stage 8) Xenopus laevis embryos. 1,524 proteins were identified from n = 16 single cells. The quantitative protein profiles revealed emerging cell heterogeneity during differentiation.
HostingRepository	PRIDE
AnnounceDate	2025-08-16
AnnouncementXML	Submission_2025-08-16_02:35:27.809.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Peter Nemes
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-07 17:54:20	ID requested
⏵ 1	2025-08-16 02:35:28	announced

10.1002/ANIE.202510692;

submitter keyword: Single-cell proteomics, mass spectrometry, artificial intelligence, capillary electrophoresis

Peter Nemes
contact affiliation	University of Maryland, College Park
contact email	nemes@umd.edu
lab head
Peter Nemes
contact affiliation	University of Maryland, College Park
contact email	nemes@umd.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/2025/08/PXD062702

PRIDE project URI

• PRIDE
  1. PXD062702
     1. Label: PRIDE project
     2. Name: Live Electrophoresis-Correlative AI Democratizes Single-cell Mass Spectrometry Proteomics