{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,14]],"date-time":"2025-10-14T20:10:32Z","timestamp":1760472632979,"version":"3.37.3"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2018,9,13]],"date-time":"2018-09-13T00:00:00Z","timestamp":1536796800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Spanish Ministry of Economy and Competitiveness","award":["BIO2013-46492-R"],"award-info":[{"award-number":["BIO2013-46492-R"]}]},{"name":"Beatriu de Pin\u00f3s Fellowship","award":["2014 BP-B 00168"],"award-info":[{"award-number":["2014 BP-B 00168"]}]},{"name":"Cell Lines of the Institute of Health Carlos III","award":["PT13\/0001\/0008","PT17\/0019\/0008"],"award-info":[{"award-number":["PT13\/0001\/0008","PT17\/0019\/0008"]}]},{"DOI":"10.13039\/501100004587","name":"ISCIII","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>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 towards the in silico prediction of PTM interactions. The study of PTM cross-talk ultimately requires experimental evidence about whether certain PTMs coexist in a single protein molecule. However, available resources do not assist researchers in the experimental detection of co-modified peptides.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Herein, 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 from 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 for co-modified peptides upon T cell activation, demonstrating differential regulation of co-occurring PTMs in this biological context. Overall, TCellXTalk facilitates 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TCellXTalk is available at https:\/\/www.tcellxtalk.org. Source Code is available at https:\/\/bitbucket.org\/lp-csic-uab\/tcellxtalk.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty805","type":"journal-article","created":{"date-parts":[[2018,9,12]],"date-time":"2018-09-12T19:24:16Z","timestamp":1536780256000},"page":"1404-1413","source":"Crossref","is-referenced-by-count":2,"title":["TCellXTalk facilitates the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5986-4258","authenticated-orcid":false,"given":"Albert","family":"Casanovas","sequence":"first","affiliation":[{"name":"Proteomics Laboratory CSIC\/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC\/IDIBAPS), Barcelona, Spain"},{"name":"Autonomous University of Barcelona, E-08193 Bellaterra, Spain"}]},{"given":"\u00d3scar","family":"Gallardo","sequence":"additional","affiliation":[{"name":"Proteomics Laboratory CSIC\/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC\/IDIBAPS), Barcelona, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0205-2176","authenticated-orcid":false,"given":"Montserrat","family":"Carrascal","sequence":"additional","affiliation":[{"name":"Proteomics Laboratory CSIC\/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC\/IDIBAPS), Barcelona, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2823-5429","authenticated-orcid":false,"given":"Joaquin","family":"Abian","sequence":"additional","affiliation":[{"name":"Proteomics Laboratory CSIC\/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC\/IDIBAPS), Barcelona, Spain"},{"name":"Autonomous University of Barcelona, E-08193 Bellaterra, Spain"}]}],"member":"286","published-online":{"date-parts":[[2018,9,13]]},"reference":[{"key":"2023012808150268400_bty805-B1","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/nchembio.2576","article-title":"How many human proteoforms are there?","volume":"14","author":"Aebersold","year":"2018","journal-title":"Nat. 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