PXD055942-1

PXD055942 is an original dataset announced via ProteomeXchange.

Title	An Atlas of Proteome and Phosphoproteome Turnover Across Mouse Tissues and Brain Regions
Description	Understanding how different mammalian tissues are regulated is central to biology. Since the same proteins often appear in multiple tissues, protein abundance, turnover, and post-translational modifications, like phosphorylation, are key factors that determine tissue-specific proteome properties. However, these properties are challenging to study comprehensively across tissues and remain poorly understood. Here, we present Turnover-PPT, a comprehensive resource mapping the abundance and lifetime of 11,000 proteins and 40,000 phosphosites across eight mouse tissues and various brain regions, using advanced proteomics and stable isotope labeling. We identified tissue-specific short- and long-lived proteins, revealing strong correlations between interacting protein lifetimes and differences between unmodified/phosphorylated peptide pairs. Notably, we discovered that peroxisomes are regulated by protein turnover across tissues, and that phosphorylation impacts the stability of key proteins in the brain such as Tau and α-synuclein. Turnover-PPT provides new fundamental insights into protein stability, tissue dynamics, and the role of protein phosphorylation.
HostingRepository	PRIDE
AnnounceDate	2025-03-12
AnnouncementXML	Submission_2025-03-11_23:06:08.611.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wenxue Li
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	phosphorylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-17 08:14:59	ID requested
⏵ 1	2025-03-11 23:06:09	announced

10.1016/J.CELL.2025.02.021;

submitter keyword: brain region, TMTpro, pSILAC, DIA, phosphoproteome,Mouse tissue, protein turnover, proteome

yansheng liu
contact affiliation	yale cancer biology institute
contact email	yansheng.liu@yale.edu
lab head
Wenxue Li
contact affiliation	Yale University
contact email	wenxue.li@yale.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/2025/03/PXD055942

PRIDE project URI

• PRIDE
  1. PXD055942
     1. Label: PRIDE project
     2. Name: An Atlas of Proteome and Phosphoproteome Turnover Across Mouse Tissues and Brain Regions