PXD060168

PXD060168 is an original dataset announced via ProteomeXchange.

Title	Isotopic labeling-enabled Chemical Proteomic Analysis Revealed Structural and Functional Features of Allysine Modifications in Mammalian Cells and Tissues
Description	In this study, we reported the application of a streamlined chemical proteomic workflow with heavy isotopic labeling that enables system-wide enrichment and site-specific identification of allysine as well as other carbonylated peptides such as peptides containing glutamic semialdehyde derived from oxidative damage of arginine and proline with high confidence in cultured human cells and mouse tissues. The streamlined workflow led to the identification of 434 allysine sites on 349 proteins in human 293T and HCT116 cells and 317 allysine sites on 157 proteins in mouse muscle tissues without any treatment of oxidative stress-inducing chemical reagent. We identified 48 histone allysine sites including 38 sites on core histones in human 293T cells, many of which overlapped with well-characterized histone acetylation and methylation epigenetic marks. Bioinformatic analysis revealed notable characteristics of the amino acid preferences of allysine flanking sequences and significant depletion of allysine sites in the protein secondary structures in human cells. Pathway analysis showed that allysine substrates were involved in diverse cellular processes including translation, protein folding and RNA processing in human cells and were enriched with muscle contractile fiber proteins and metabolic enzymes in mouse muscle tissue. Thus, our integrated chemical proteomic analysis revealed structural and functional features of allysine targets under regular growth conditions in mammalian cells and tissues.
HostingRepository	PRIDE
AnnounceDate	2025-04-29
AnnouncementXML	Submission_2025-04-29_01:59:06.605.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yue Chen
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	L-allysine; acetylated residue; glutamyl semialdehyde
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-24 11:17:41	ID requested
1	2025-04-22 14:33:21	announced
⏵ 2	2025-04-29 01:59:07	announced	2025-04-29: Updated project metadata.

10.1021/ACS.ANALCHEM.5C00660;

submitter keyword: carbonylation, lysyl oxidase, chemical proteomics, isotopic labeling,allysine

Yue Chen
contact affiliation	University of Minnesota
contact email	yuechen@umn.edu
lab head
Yue Chen
contact affiliation	University of Minnesota
contact email	ychen2001@yahoo.com
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/2025/04/PXD060168

PRIDE project URI

• PRIDE
  1. PXD060168
     1. Label: PRIDE project
     2. Name: Isotopic labeling-enabled Chemical Proteomic Analysis Revealed Structural and Functional Features of Allysine Modifications in Mammalian Cells and Tissues