⮝ Full datasets listing

PXD060168

PXD060168 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIsotopic labeling-enabled Chemical Proteomic Analysis Revealed Structural and Functional Features of Allysine Modifications in Mammalian Cells and Tissues
DescriptionIn 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.
HostingRepositoryPRIDE
AnnounceDate2025-04-29
AnnouncementXMLSubmission_2025-04-29_01:59:06.605.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterYue Chen
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListL-allysine; acetylated residue; glutamyl semialdehyde
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02025-01-24 11:17:41ID requested
12025-04-22 14:33:21announced
22025-04-29 01:59:07announced2025-04-29: Updated project metadata.
Publication List
10.1021/ACS.ANALCHEM.5C00660;
Keyword List
submitter keyword: carbonylation, lysyl oxidase, chemical proteomics, isotopic labeling,allysine
Contact List
Yue Chen
contact affiliationUniversity of Minnesota
contact emailyuechen@umn.edu
lab head
Yue Chen
contact affiliationUniversity of Minnesota
contact emailychen2001@yahoo.com
dataset submitter
Full Dataset Link List
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
Repository Record List
[ + ]