The ProteomeXchange consortium at 10 years: 2023 update.

Autor:	Deutsch EW; Institute for Systems Biology, Seattle WA 98109, USA., Bandeira N; Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.; Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA., Perez-Riverol Y; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK., Sharma V; University of Washington, Seattle, WA 98195, USA., Carver JJ; Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.; Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA., Mendoza L; Institute for Systems Biology, Seattle WA 98109, USA., Kundu DJ; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK., Wang S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK., Bandla C; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK., Kamatchinathan S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK., Hewapathirana S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK., Pullman BS; Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.; Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA., Wertz J; Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.; Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA., Sun Z; Institute for Systems Biology, Seattle WA 98109, USA., Kawano S; Faculty of Contemporary Society, Toyama University of International Studies, Toyama 930-1292, Japan.; Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba 277-0871, Japan.; School of Frontier Engineering, Kitasato University, Sagamihara 252-0373, Japan., Okuda S; Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan., Watanabe Y; Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan., MacLean B; University of Washington, Seattle, WA 98195, USA., MacCoss MJ; University of Washington, Seattle, WA 98195, USA., Zhu Y; Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China., Ishihama Y; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan., Vizcaíno JA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2023 Jan 06; Vol. 51 (D1), pp. D1539-D1548.
DOI:	10.1093/nar/gkac1040
Abstrakt:	Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data. (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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