PXD010176

PXD010176 is an original dataset announced via ProteomeXchange.

Title	TCellXTalk enables the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells
Description	Protein function is regulated by post-translational modifications (PTMs) that may act individually or interact with others in a phenomenon termed PTM cross-talk. Multiple databases have been dedicated to PTMs, including recent initiatives oriented to the in silico prediction of PTM interactions. The study of PTM cross-talk ultimately requires experimental evidence about whether certain PTMs co-exist in a single protein molecule. However, available resources do not assist researchers in the experimental detection of co-modified peptides. Here we present TCellXTalk, a comprehensive database of phosphorylation, ubiquitination and acetylation sites in human T cells that supports the experimental detection of co-modified peptides using targeted or directed mass spectrometry. We demonstrate the efficacy of TCellXTalk and the strategy presented here in a proof of concept experiment that enabled the identification and quantification of 15 co-modified (phosphorylated and ubiquitinated) peptides in CD3 proteins of the T-cell receptor complex. To our knowledge, these are the first co-modified peptide sequences described in this widely studied cell type. Furthermore, quantitative data showed distinct dynamics of co-modified peptides upon T cell activation, demonstrating differential regulation of co-occurring PTMs in this biological context. Overall, TCellXTalk enables the experimental detection of co-modified peptides in human T cells and puts forward a novel and generic strategy for the study of PTM cross-talk.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:46:19.656.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Montserrat Carrascal
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitination signature dipeptidyl lysine; phosphorylated residue; acetylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2018-06-21 02:29:08	ID requested
1	2018-09-19 03:54:36	announced
⏵ 2	2024-10-22 04:46:20	announced	2024-10-22: Updated project metadata.

Casanovas A, Gallardo Ó, Carrascal M, Abian J, TCellXTalk facilitates the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells. Bioinformatics, 35(8):1404-1413(2019) [pubmed]

10.1093/bioinformatics/bty805;

ProteomeXchange project tag: Chromosome-centric Human Proteome Project (C-HPP), Human Proteome Project

curator keyword: Biological

submitter keyword: PTMs,cross-talk, TCR activation, T cells

Montserrat Carrascal
contact affiliation	CSIC/UAB Proteomics Facility. IIBB-CSIC, IDIBAPS. Barcelona, Spain.
contact email	montserrat.carrascal.csic@uab.cat
lab head
Montserrat Carrascal
contact affiliation	IIBB-CSIC
contact email	montserrat.carrascal.csic@uab.cat
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/2018/09/PXD010176

PRIDE project URI

• PRIDE
  1. PXD010176
     1. Label: PRIDE project
     2. Name: TCellXTalk enables the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells