PXD063566

PXD063566 is an original dataset announced via ProteomeXchange.

Title	Subcellular Mass Spectrometry Reveals Proteome Remodeling in an Asymmetrically Dividing (Frog) Embryonic Stem Cell
Description	This project enhanced discovery subcellular proteomics sensitivity by integrating diaPASEF with capillary electrophoresis mass spectrometry (CE-MS). The method was developed, tested, and validated on ~200 pg of the HeLa proteome digest, ~80% of the total proteome of a single cell. Reproducible identification of at least 1,000 proteins marked robust performance to explore subcellular proteome heterogeneity as the dorsal-animal (D1) cell divides asymmetrically in the Xenopus laevis embryo to establish the D11 and D12 descendants in the 16-cell embryo. The label-free quantification (LFQ) values were normalized to compare equal proteome amounts. Relative quantification of the proteomes revealed molecular differences between the future D11 and future D12 poles of the D1 cell and the offspring cells. Functional experiments ventralizing the fertilized embryo using ultraviolet (UV) light revealed corroborated the proteome profiles and helped decipher the origin of the gradients in the context of dorsal-ventral patterning.
HostingRepository	PRIDE
AnnounceDate	2026-01-10
AnnouncementXML	Submission_2026-01-09_17:23:01.876.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Peter Nemes
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: NEWT:8355;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-02 11:28:09	ID requested
⏵ 1	2026-01-09 17:23:02	announced

10.1073/PNAS.2518372123;

submitter keyword: proteomics, mass spectrometry, differentiation, profiling,Single cell, asymmetric division, capillary electrophoresis, diaPASEF, quantification

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/2026/01/PXD063566

PRIDE project URI

• PRIDE
  1. PXD063566
     1. Label: PRIDE project
     2. Name: Subcellular Mass Spectrometry Reveals Proteome Remodeling in an Asymmetrically Dividing (Frog) Embryonic Stem Cell