{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T01:36:11Z","timestamp":1782783371116,"version":"3.54.5"},"reference-count":43,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,11,5]],"date-time":"2019-11-05T00:00:00Z","timestamp":1572912000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["WT101477MA"],"award-info":[{"award-number":["WT101477MA"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["208391\/Z\/17\/Z"],"award-info":[{"award-number":["208391\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/N022440\/1"],"award-info":[{"award-number":["BB\/N022440\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/N022432\/1"],"award-info":[{"award-number":["BB\/N022432\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/P024599\/1"],"award-info":[{"award-number":["BB\/P024599\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R24 GM127667-01"],"award-info":[{"award-number":["R24 GM127667-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 GM103551"],"award-info":[{"award-number":["R01 GM103551"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 GM121696"],"award-info":[{"award-number":["R01 GM121696"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U54 HG008097"],"award-info":[{"award-number":["U54 HG008097"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U01DK121289"],"award-info":[{"award-number":["U01DK121289"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01GM087221"],"award-info":[{"award-number":["R01GM087221"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R24GM127667"],"award-info":[{"award-number":["R24GM127667"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U54EB020406"],"award-info":[{"award-number":["U54EB020406"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["5P41GM103484-07"],"award-info":[{"award-number":["5P41GM103484-07"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R24GM127667"],"award-info":[{"award-number":["R24GM127667"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"H2020 EU EPIC-XS","award":["823839"],"award-info":[{"award-number":["823839"]}]},{"name":"ELIXIR"},{"DOI":"10.13039\/100000049","name":"NIA","doi-asserted-by":"publisher","award":["U19AG02312"],"award-info":[{"award-number":["U19AG02312"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100003187","name":"NSF","doi-asserted-by":"publisher","award":["1922871"],"award-info":[{"award-number":["1922871"]}],"id":[{"id":"10.13039\/100003187","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100003187","name":"NSF","doi-asserted-by":"publisher","award":["1933311"],"award-info":[{"award-number":["1933311"]}],"id":[{"id":"10.13039\/100003187","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002855","name":"MOST","doi-asserted-by":"publisher","award":["2016YFB0201702"],"award-info":[{"award-number":["2016YFB0201702"]}],"id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002855","name":"MOST","doi-asserted-by":"publisher","award":["2016YFC0901701"],"award-info":[{"award-number":["2016YFC0901701"]}],"id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007812","name":"University of Washington","doi-asserted-by":"publisher","award":["UWPR95794"],"award-info":[{"award-number":["UWPR95794"]}],"id":[{"id":"10.13039\/100007812","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ABI 1759980"],"award-info":[{"award-number":["ABI 1759980"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004696","name":"National Bioscience Database Center","doi-asserted-by":"publisher","award":["18063028"],"award-info":[{"award-number":["18063028"]}],"id":[{"id":"10.13039\/501100004696","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The ProteomeXchange (PX) consortium of proteomics resources (http:\/\/www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14\u00a0100 datasets had been submitted to PX resources since 2012, and from those, more than 9\u00a0500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including \u2018big data\u2019 approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.<\/jats:p>","DOI":"10.1093\/nar\/gkz984","type":"journal-article","created":{"date-parts":[[2019,10,14]],"date-time":"2019-10-14T19:28:47Z","timestamp":1571081327000},"source":"Crossref","is-referenced-by-count":311,"title":["The ProteomeXchange consortium in 2020: enabling \u2018big data\u2019 approaches in proteomics"],"prefix":"10.1093","author":[{"given":"Eric W","family":"Deutsch","sequence":"first","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuno","family":"Bandeira","sequence":"additional","affiliation":[{"name":"Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"},{"name":"Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"},{"name":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vagisha","family":"Sharma","sequence":"additional","affiliation":[{"name":"University of Washington, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasset","family":"Perez-Riverol","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy J","family":"Carver","sequence":"additional","affiliation":[{"name":"Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"},{"name":"Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"},{"name":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deepti J","family":"Kundu","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Garc\u00eda-Seisdedos","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew F","family":"Jarnuczak","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suresh","family":"Hewapathirana","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin S","family":"Pullman","sequence":"additional","affiliation":[{"name":"Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"},{"name":"Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"},{"name":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie","family":"Wertz","sequence":"additional","affiliation":[{"name":"Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"},{"name":"Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"},{"name":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi","family":"Sun","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shin","family":"Kawano","sequence":"additional","affiliation":[{"name":"Faculty of Contemporary Society, Toyama University of International Studies, Toyama 930\u20131292, Japan"},{"name":"Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba 277\u20130871, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shujiro","family":"Okuda","sequence":"additional","affiliation":[{"name":"Niigata University Graduate School of Medical and Dental Sciences, Niigata 951\u20138510, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Watanabe","sequence":"additional","affiliation":[{"name":"Niigata University Graduate School of Medical and Dental Sciences, Niigata 951\u20138510, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8479-0262","authenticated-orcid":false,"given":"Henning","family":"Hermjakob","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"},{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences\u00a0(Beijing), Beijing Institute of Life Omics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brendan","family":"MacLean","sequence":"additional","affiliation":[{"name":"University of Washington, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael J","family":"MacCoss","sequence":"additional","affiliation":[{"name":"University of Washington, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunping","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences\u00a0(Beijing), Beijing Institute of Life Omics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasushi","family":"Ishihama","sequence":"additional","affiliation":[{"name":"Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606\u20138501, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3905-4335","authenticated-orcid":false,"given":"Juan A","family":"Vizca\u00edno","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,11,5]]},"reference":[{"key":"2019110500060218300_B1","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/nbt.2839","article-title":"ProteomeXchange provides globally coordinated proteomics data submission and dissemination","volume":"32","author":"Vizcaino","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2019110500060218300_B2","doi-asserted-by":"crossref","first-page":"D1100","DOI":"10.1093\/nar\/gkw936","article-title":"The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition","volume":"45","author":"Deutsch","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B3","doi-asserted-by":"crossref","first-page":"D442","DOI":"10.1093\/nar\/gky1106","article-title":"The PRIDE database and related tools and resources in 2019: improving support for quantification data","volume":"47","author":"Perez-Riverol","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B4","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1002\/pmic.201100515","article-title":"PASSEL: the PeptideAtlas SRMexperiment library","volume":"12","author":"Farrah","year":"2012","journal-title":"Proteomics"},{"key":"2019110500060218300_B5","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1038\/embor.2008.56","article-title":"PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows","volume":"9","author":"Deutsch","year":"2008","journal-title":"EMBO Rep."},{"key":"2019110500060218300_B6","doi-asserted-by":"crossref","first-page":"D1218","DOI":"10.1093\/nar\/gky899","article-title":"The jPOST environment: an integrated proteomics data repository and database","volume":"47","author":"Moriya","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B7","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1093\/jamia\/ocv001","article-title":"Development of data representation standards by the human proteome organization proteomics standards initiative","volume":"22","author":"Deutsch","year":"2015","journal-title":"J. Am. Med. Inform. Assoc."},{"key":"2019110500060218300_B8","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1021\/acs.jproteome.7b00370","article-title":"Proteomics standards initiative: Fifteen years of progress and future work","volume":"16","author":"Deutsch","year":"2017","journal-title":"J. Proteome Res."},{"key":"2019110500060218300_B9","doi-asserted-by":"crossref","first-page":"2903","DOI":"10.1093\/bioinformatics\/btv250","article-title":"ms-data-core-api: an open-source, metadata-oriented library for computational proteomics","volume":"31","author":"Perez-Riverol","year":"2015","journal-title":"Bioinformatics"},{"key":"2019110500060218300_B10","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1074\/mcp.O115.050229","article-title":"PRIDe inspector toolsuite: Moving toward a universal visualization tool for proteomics data standard formats and quality assessment of proteomexchange datasets","volume":"15","author":"Perez-Riverol","year":"2016","journal-title":"Mol. Cell. Proteomics"},{"key":"2019110500060218300_B11","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/nbt.3597","article-title":"Sharing and community curation of mass spectrometry data with global natural products social molecular networking","volume":"34","author":"Wang","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2019110500060218300_B12","doi-asserted-by":"crossref","first-page":"D1211","DOI":"10.1093\/nar\/gky869","article-title":"iProX: an integrated proteome resource","volume":"47","author":"Ma","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B13","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1074\/mcp.RA117.000543","article-title":"Panorama public: a public repository for quantitative data sets processed in skyline","volume":"17","author":"Sharma","year":"2018","journal-title":"Mol. Cell. Proteomics"},{"key":"2019110500060218300_B14","doi-asserted-by":"crossref","first-page":"M111 014381","DOI":"10.1074\/mcp.M111.014381","article-title":"The mzIdentML data standard for mass spectrometry-based proteomics results","volume":"11","author":"Jones","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"2019110500060218300_B15","doi-asserted-by":"crossref","first-page":"2765","DOI":"10.1074\/mcp.O113.036681","article-title":"The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience","volume":"13","author":"Griss","year":"2014","journal-title":"Mol. Cell. Proteomics"},{"key":"2019110500060218300_B16","doi-asserted-by":"crossref","DOI":"10.1002\/mas.21540","article-title":"The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics","author":"Pino","year":"2017","journal-title":"Mass Spectrom. Rev."},{"key":"2019110500060218300_B17","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1038\/nbt.3790","article-title":"Discovering and linking public omics data sets using the Omics Discovery Index","volume":"35","author":"Perez-Riverol","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"2019110500060218300_B18","doi-asserted-by":"crossref","first-page":"3512","DOI":"10.1038\/s41467-019-11461-w","article-title":"Quantifying the impact of public omics data","volume":"10","author":"Perez-Riverol","year":"2019","journal-title":"Nat Commun."},{"key":"2019110500060218300_B19","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"The UniProt Consortium","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B20","doi-asserted-by":"crossref","first-page":"D745","DOI":"10.1093\/nar\/gky1113","article-title":"Ensembl 2019","volume":"47","author":"Cunningham","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B21","doi-asserted-by":"crossref","first-page":"D246","DOI":"10.1093\/nar\/gkx1158","article-title":"Expression Atlas: gene and protein expression across multiple studies and organisms","volume":"46","author":"Papatheodorou","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B22","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1016\/j.cels.2018.08.004","article-title":"Assembling the Community-Scale discoverable human proteome","volume":"7","author":"Wang","year":"2018","journal-title":"Cell Syst."},{"key":"2019110500060218300_B23","doi-asserted-by":"crossref","first-page":"4227","DOI":"10.1021\/acs.jproteome.8b00496","article-title":"ProteinExplorer: a repository-scale resource for exploration of protein detection in public mass spectrometry data sets","volume":"17","author":"Pullman","year":"2018","journal-title":"J. Proteome Res."},{"key":"2019110500060218300_B24","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"2019110500060218300_B25","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1002\/pmic.201500295","article-title":"Exploring the potential of public proteomics data","volume":"16","author":"Vaudel","year":"2016","journal-title":"Proteomics"},{"key":"2019110500060218300_B26","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/j.tibs.2017.01.001","article-title":"A golden age for working with public proteomics data","volume":"42","author":"Martens","year":"2017","journal-title":"Trends Biochem. Sci."},{"key":"2019110500060218300_B27","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/nmeth.3902","article-title":"Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets","volume":"13","author":"Griss","year":"2016","journal-title":"Nat. Methods"},{"key":"2019110500060218300_B28","doi-asserted-by":"crossref","first-page":"4299","DOI":"10.1021\/acs.jproteome.7b00467","article-title":"The human plasma proteome draft of 2017: building on the human plasma peptideatlas from mass spectrometry and complementary assays","volume":"16","author":"Schwenk","year":"2017","journal-title":"J. Proteome Res."},{"key":"2019110500060218300_B29","doi-asserted-by":"crossref","first-page":"3961","DOI":"10.1021\/acs.jproteome.6b00392","article-title":"Human proteome project mass spectrometry data interpretation guidelines 2.1","volume":"15","author":"Deutsch","year":"2016","journal-title":"J. Proteome Res."},{"key":"2019110500060218300_B30","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1038\/s41592-019-0426-7","article-title":"Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning","volume":"16","author":"Gessulat","year":"2019","journal-title":"Nat. Methods"},{"key":"2019110500060218300_B31","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/s41592-019-0427-6","article-title":"High-quality MS\/MS spectrum prediction for data-dependent and data-independent acquisition data analysis","volume":"16","author":"Tiwary","year":"2019","journal-title":"Nat. Methods"},{"key":"2019110500060218300_B32","doi-asserted-by":"crossref","first-page":"W295","DOI":"10.1093\/nar\/gkz299","article-title":"Updated MS(2)PIP web server delivers fast and accurate MS(2) peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques","volume":"47","author":"Gabriels","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B33","doi-asserted-by":"crossref","first-page":"D177","DOI":"10.1093\/nar\/gkw1062","article-title":"The neXtProt knowledgebase on human proteins: 2017 update","volume":"45","author":"Gaudet","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B34","doi-asserted-by":"crossref","first-page":"D853","DOI":"10.1093\/nar\/gky1095","article-title":"The UCSC Genome Browser database: 2019 update","volume":"47","author":"Haeussler","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B35","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s13059-017-1377-x","article-title":"The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data","volume":"19","author":"Menschaert","year":"2018","journal-title":"Genome Biol."},{"key":"2019110500060218300_B36","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1021\/pr049882h","article-title":"Open source system for analyzing, validating, and storing protein identification data","volume":"3","author":"Craig","year":"2004","journal-title":"J. Proteome Res."},{"key":"2019110500060218300_B37","doi-asserted-by":"crossref","first-page":"D1271","DOI":"10.1093\/nar\/gkx1029","article-title":"ProteomicsDB","volume":"46","author":"Schmidt","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B38","doi-asserted-by":"crossref","first-page":"D135","DOI":"10.1093\/nar\/gky1031","article-title":"LNCipedia 5: towards a reference set of human long non-coding RNAs","volume":"47","author":"Volders","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B39","doi-asserted-by":"crossref","first-page":"D497","DOI":"10.1093\/nar\/gkx1130","article-title":"An update on sORFs.org: a repository of small ORFs identified by ribosome profiling","volume":"46","author":"Olexiouk","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B40","doi-asserted-by":"crossref","first-page":"D1237","DOI":"10.1093\/nar\/gkx664","article-title":"The SysteMHC Atlas project","volume":"46","author":"Shao","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B41","first-page":"D403","article-title":"OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes","volume":"47","author":"Brunet","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B42","doi-asserted-by":"crossref","first-page":"W599","DOI":"10.1093\/nar\/gkv382","article-title":"Introducing the PRIDE Archive RESTful web services","volume":"43","author":"Reisinger","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2019110500060218300_B43","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/nbt.3109","article-title":"PeptideShaker enables reanalysis of MS-derived proteomics data sets","volume":"33","author":"Vaudel","year":"2015","journal-title":"Nat. Biotechnol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz984\/30376219\/gkz984.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz984\/30376219\/gkz984.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,24]],"date-time":"2021-01-24T20:23:15Z","timestamp":1611519795000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gkz984\/5612546"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11,5]]},"references-count":43,"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz984","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,11,5]]},"article-number":"gkz984"}}