PXD053023

PXD053023 is an original dataset announced via ProteomeXchange.

Title	Electrophoresis-Correlative Framing of Ion Mobility Deepens Single-Cell Mass Spectrometry Proteomics
Description	This project developed electrophoresis-correlative (Eco) mass spectrometry (MS) to measure the proteome of single cells on a trapped ion mobility mass spectrometer (timsTOF PRO). Eco-MS identified 962 protein groups in a <20 min of electrophoresing a single-HeLa-cell-equivalent (~200 pg) proteome amount. Match-between-runs improved this number to 2,139 protein groups on the same dataset. We demonstrate the approach to measure the proteome of single cells in X. laevis embryos at stage 8 (blastula). Single cells were isolated from the animal cap and their proteomes digested on a fluorosilane-coated microplate. Less than 4% of the available single-cell proteome was analyzed on a custom-built capillary electrophoresis (CE) platform under classical and Eco-driven ddaPASEF. Eco-MS returned ~51% of more protein groups than the control, identifying 1,157 proteins from N = 9 different single cells (biological replicates) of the animal cap. Eco-MS deepens the detectable coverage of the single-cell proteome using ddaPASEF on a timsTOF MS.
HostingRepository	PRIDE
AnnounceDate	2025-02-06
AnnouncementXML	Submission_2025-02-06_07:44:14.529.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	timsTOF

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-11 12:16:32	ID requested
⏵ 1	2025-02-06 07:44:14	announced

10.1016/J.MCPRO.2024.100892;

submitter keyword: proteomics, Xenopus laevis, mass spectrometry,Single cell, capillary electrophoresis

Peter Nemes
contact affiliation	Department of Chemistry & Biochemistry, University of Maryland at 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/2025/02/PXD053023

PRIDE project URI

• PRIDE
  1. PXD053023
     1. Label: PRIDE project
     2. Name: Electrophoresis-Correlative Framing of Ion Mobility Deepens Single-Cell Mass Spectrometry Proteomics