{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T18:58:34Z","timestamp":1732042714604},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T00:00:00Z","timestamp":1683158400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["12B7123N","G010023N","G028821N","1SE3722"],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012331","name":"Agentschap Innoveren en Ondernemen","doi-asserted-by":"publisher","award":["HBC.2020.2205"],"id":[{"id":"10.13039\/100012331","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union's Horizon 2020 Programme","award":["823839"]},{"name":"Ghent University Concerted Research Action","award":["BOF21\/GOA\/033"]},{"name":"Spanish Ministry of Science, Innovation and Universities","award":["PID2020-115092GB-I00"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"Abstract<\/jats:title>\n Interest in the use of machine learning for peptide fragmentation spectrum prediction has been strongly on the rise over the past years, especially for applications in challenging proteomics identification workflows such as immunopeptidomics and the full-proteome identification of data independent acquisition spectra. Since its inception, the MS\u00b2PIP peptide spectrum predictor has been widely used for various downstream applications, mostly thanks to its accuracy, ease-of-use, and broad applicability. We here present a thoroughly updated version of the MS\u00b2PIP web server, which includes new and more performant prediction models for both tryptic- and non-tryptic peptides, for immunopeptides, and for CID-fragmented TMT-labeled peptides. Additionally, we have also added new functionality to greatly facilitate the generation of proteome-wide predicted spectral libraries, requiring only a FASTA protein file as input. These libraries also include retention time predictions from DeepLC. Moreover, we now provide pre-built and ready-to-download spectral libraries for various model organisms in multiple DIA-compatible spectral library formats. Besides upgrading the back-end models, the user experience on the MS\u00b2PIP web server is thus also greatly enhanced, extending its applicability to new domains, including immunopeptidomics and MS3-based TMT quantification experiments. MS\u00b2PIP is freely available at https:\/\/iomics.ugent.be\/ms2pip\/.<\/jats:p>","DOI":"10.1093\/nar\/gkad335","type":"journal-article","created":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T12:28:14Z","timestamp":1683203294000},"page":"W338-W342","source":"Crossref","is-referenced-by-count":13,"title":["Updated MS\u00b2PIP web server supports cutting-edge proteomics applications"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-9376-1399","authenticated-orcid":false,"given":"Arthur","family":"Declercq","sequence":"first","affiliation":[{"name":"VIB-UGent Center for Medical Biotechnology , VIB, Belgium"},{"name":"Department of Biomolecular Medicine, Ghent University , Belgium"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-6807-7029","authenticated-orcid":false,"given":"Robbin","family":"Bouwmeester","sequence":"additional","affiliation":[{"name":"VIB-UGent Center for Medical Biotechnology , VIB, Belgium"},{"name":"Department of Biomolecular Medicine, Ghent University , Belgium"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-8150-6203","authenticated-orcid":false,"given":"Cristina","family":"Chiva","sequence":"additional","affiliation":[{"name":"Proteomics Unit, Universitat Pompeu Fabra , 08003 , Barcelona , Spain"},{"name":"Proteomics Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST) , 08003, Barcelona , Spain"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-6506-7714","authenticated-orcid":false,"given":"Eduard","family":"Sabid\u00f3","sequence":"additional","affiliation":[{"name":"Proteomics Unit, Universitat Pompeu Fabra , 08003 , Barcelona , Spain"},{"name":"Proteomics Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST) , 08003, Barcelona , Spain"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-5066-6263","authenticated-orcid":false,"given":"Aur\u00e9lie","family":"Hirschler","sequence":"additional","affiliation":[{"name":"Laboratoire de Spectrom\u00e9trie de Masse BioOrganique (LSMBO) , Universit\u00e9 de Strasbourg, CNRS, France"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-0079-319X","authenticated-orcid":false,"given":"Christine","family":"Carapito","sequence":"additional","affiliation":[{"name":"Laboratoire de Spectrom\u00e9trie de Masse BioOrganique (LSMBO) , Universit\u00e9 de Strasbourg, CNRS, France"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-4277-658X","authenticated-orcid":false,"given":"Lennart","family":"Martens","sequence":"additional","affiliation":[{"name":"VIB-UGent Center for Medical Biotechnology , VIB, Belgium"},{"name":"Department of Biomolecular Medicine, Ghent University , Belgium"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-8349-3370","authenticated-orcid":false,"given":"Sven","family":"Degroeve","sequence":"additional","affiliation":[{"name":"VIB-UGent Center for Medical Biotechnology , VIB, Belgium"},{"name":"Department of Biomolecular Medicine, Ghent University , Belgium"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-1679-1711","authenticated-orcid":false,"given":"Ralf","family":"Gabriels","sequence":"additional","affiliation":[{"name":"VIB-UGent Center for Medical Biotechnology , VIB, Belgium"},{"name":"Department of Biomolecular Medicine, Ghent University , Belgium"}]}],"member":"286","published-online":{"date-parts":[[2023,5,4]]},"reference":[{"key":"2023070504573917200_B1","doi-asserted-by":"crossref","first-page":"e1700464","DOI":"10.1002\/pmic.201700464","article-title":"In immunopeptidomics we need a sniper instead of a shotgun","volume":"18","author":"Faridi","year":"2018","journal-title":"Proteomics"},{"key":"2023070504573917200_B2","doi-asserted-by":"crossref","first-page":"4045","DOI":"10.1021\/pr100230q","article-title":"Undesirable charge-enhancement of isobaric tagged phosphopeptides leads to reduced identification efficiency","volume":"9","author":"Thingholm","year":"2010","journal-title":"J. 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Proteome Res."},{"key":"2023070504573917200_B4","doi-asserted-by":"crossref","first-page":"1900351","DOI":"10.1002\/pmic.201900351","article-title":"The age of data-driven proteomics: how machine learning enables novel workflows","volume":"20","author":"Bouwmeester","year":"2020","journal-title":"Proteomics"},{"key":"2023070504573917200_B5","doi-asserted-by":"crossref","first-page":"3199","DOI":"10.1093\/bioinformatics\/btt544","article-title":"MS2PIP: a tool for MS\/MS peak intensity prediction","volume":"29","author":"Degroeve","year":"2013","journal-title":"Bioinformatics"},{"key":"2023070504573917200_B6","doi-asserted-by":"crossref","first-page":"W326","DOI":"10.1093\/nar\/gkv542","article-title":"MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation","volume":"43","author":"Degroeve","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2023070504573917200_B7","doi-asserted-by":"crossref","first-page":"W295","DOI":"10.1093\/nar\/gkz299","article-title":"Updated MS2PIP web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques","volume":"47","author":"Gabriels","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023070504573917200_B8","doi-asserted-by":"crossref","first-page":"5243","DOI":"10.1093\/bioinformatics\/btz383","article-title":"Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions","volume":"35","author":"Silva","year":"2019","journal-title":"Bioinformatics"},{"key":"2023070504573917200_B9","doi-asserted-by":"crossref","first-page":"100266","DOI":"10.1016\/j.mcpro.2022.100266","article-title":"MS2Rescore: data-driven rescoring dramatically boosts immunopeptide identification rates","volume":"21","author":"Declercq","year":"2022","journal-title":"Mol. 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