{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T05:10:10Z","timestamp":1784351410486,"version":"3.55.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,12,6]],"date-time":"2021-12-06T00:00:00Z","timestamp":1638748800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Key Research Program of China","award":["2020YFE0202200"],"award-info":[{"award-number":["2020YFE0202200"]}]},{"name":"Innovation special zone","award":["18-163-15-ZT-001-006-07"],"award-info":[{"award-number":["18-163-15-ZT-001-006-07"]}]},{"name":"Program for Guangdong Introducing Innovative and Entrepreneurial Teams","award":["2016ZT06D211"],"award-info":[{"award-number":["2016ZT06D211"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U1811461"],"award-info":[{"award-number":["U1811461"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["16CXZ027"],"award-info":[{"award-number":["16CXZ027"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The rapid development of proteomics studies has resulted in large volumes of experimental data. The emergence of big data platform provides the opportunity to handle these large amounts of data. The integrated proteome resource, iProX (https:\/\/www.iprox.cn), which was initiated in 2017, has been greatly improved with an up-to-date big data platform implemented in 2021. Here, we describe the main iProX developments since its first publication in Nucleic Acids Research in 2019. First, a hyper-converged architecture with high scalability supports the submission process. A hadoop cluster can store large amounts of proteomics datasets, and a distributed, RESTful-styled Elastic Search engine can query millions of records within one second. Also, several new features, including the Universal Spectrum Identifier (USI) mechanism proposed by ProteomeXchange,\u00a0RESTful Web Service API, and a high-efficiency reanalysis pipeline, have been added to iProX for better open data sharing. By the end of August 2021, 1526 datasets had been submitted to iProX, reaching a total data volume of 92.42TB. With the implementation of the big data platform, iProX can support PB-level data storage, hundreds of billions of spectra records, and second-level latency service capabilities that meet the requirements of the fast growing field of proteomics.<\/jats:p>","DOI":"10.1093\/nar\/gkab1081","type":"journal-article","created":{"date-parts":[[2021,10,22]],"date-time":"2021-10-22T11:58:09Z","timestamp":1634903889000},"page":"D1522-D1527","source":"Crossref","is-referenced-by-count":963,"title":["iProX in 2021: connecting proteomics data sharing with big data"],"prefix":"10.1093","volume":"50","author":[{"given":"Tao","family":"Chen","sequence":"first","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8934-922X","authenticated-orcid":false,"given":"Jie","family":"Ma","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiguang","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou\u00a026469, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nong","family":"Xiao","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou\u00a026469, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yutong","family":"Lu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou\u00a026469, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinjin","family":"Fu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou\u00a026469, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyuan","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mansheng","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Songfeng","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xue","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongsheng","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuchu","family":"He","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8479-0262","authenticated-orcid":false,"given":"Henning","family":"Hermjakob","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"},{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7320-7411","authenticated-orcid":false,"given":"Yunping","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing\u00a0102206, China"},{"name":"Basic Medical School, Anhui Medical University, Anhui\u00a0230032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,12,6]]},"reference":[{"key":"2022010507401063200_B1","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/498255a","article-title":"Biology: the big challenges of big data","volume":"498","author":"Marx","year":"2013","journal-title":"Nature"},{"key":"2022010507401063200_B2","doi-asserted-by":"crossref","first-page":"e47381","DOI":"10.7554\/eLife.47381","article-title":"The challenges of big data biology","volume":"8","author":"Leonelli","year":"2019","journal-title":"Elife"},{"key":"2022010507401063200_B3","first-page":"D1145","article-title":"The ProteomeXchange consortium in 2020: enabling \u2018big data\u2019 approaches in proteomics","volume":"48","author":"Deutsch","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507401063200_B4","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":"Vizca\u00edno","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2022010507401063200_B5","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":"2022010507401063200_B6","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":"2022010507401063200_B7","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":"2022010507401063200_B8","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":"2022010507401063200_B9","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":"2022010507401063200_B10","doi-asserted-by":"crossref","first-page":"D1202","DOI":"10.1093\/nar\/gkx807","article-title":"The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics","volume":"46","author":"Brenes","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022010507401063200_B11","first-page":"96","article-title":"The application of Hadoop in structural bioinformatics","volume":"21","author":"Alnasir","year":"2018","journal-title":"Brief. Bioinform."},{"key":"2022010507401063200_B12","first-page":"1","article-title":"A framework for social media data analytics using Elasticsearch and Kibana","author":"Shah","year":"2018","journal-title":"Wireless Netw"},{"key":"2022010507401063200_B13","doi-asserted-by":"crossref","first-page":"1994","DOI":"10.1109\/TCBB.2019.2915811","article-title":"Enabling Massive XML-Based biological data management in HBase","volume":"17","author":"Liu","year":"2020","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"2022010507401063200_B14","doi-asserted-by":"crossref","first-page":"3388","DOI":"10.1021\/acs.jproteome.1c00096","article-title":"Universal spectrum explorer: a standalone (web-)application for cross-resource spectrum comparison","volume":"20","author":"Schmidt","year":"2021","journal-title":"J. Proteome Res."},{"key":"2022010507401063200_B15","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1038\/s41592-021-01184-6","article-title":"Universal Spectrum Identifier for mass spectra","volume":"18","author":"Deutsch","year":"2021","journal-title":"Nat. Methods"},{"key":"2022010507401063200_B16","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":"2022010507401063200_B17","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":"2022010507401063200_B18","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1038\/s41586-019-0987-8","article-title":"Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma","volume":"567","author":"Jiang","year":"2019","journal-title":"Nature"},{"key":"2022010507401063200_B19","doi-asserted-by":"crossref","first-page":"100071","DOI":"10.1016\/j.mcpro.2021.100071","article-title":"Data management of sensitive human proteomics data: current practices, recommendations, and perspectives for the future","volume":"20","author":"Bandeira","year":"2021","journal-title":"Mol. Cell. Proteomics"},{"key":"2022010507401063200_B20","doi-asserted-by":"crossref","first-page":"100046","DOI":"10.1016\/j.mcpro.2021.100046","article-title":"Ethical principles, constraints and opportunities in clinical proteomics","volume":"20","author":"Mann","year":"2021","journal-title":"Mol. Cell. Proteomics"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D1522\/42058424\/gkab1081.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D1522\/42058424\/gkab1081.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T08:18:17Z","timestamp":1641370697000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D1522\/6454291"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,6]]},"references-count":20,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,12,6]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab1081","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,12,6]]}}}