{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T09:44:39Z","timestamp":1792143879364,"version":"4.4.0"},"publisher-location":"New York, NY","reference-count":16,"publisher":"Springer US","isbn-type":[{"value":"9781071655184","type":"print"},{"value":"9781071655191","type":"electronic"}],"license":[{"start":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T00:00:00Z","timestamp":1792108800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T00:00:00Z","timestamp":1792108800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2027]]},"DOI":"10.1007\/978-1-0716-5519-1_2","type":"book-chapter","created":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T03:45:41Z","timestamp":1792122341000},"page":"17-28","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Standardized Annotation of Quantitative Proteomics Datasets Using SDRF-Proteomics"],"prefix":"10.1007","author":[{"given":"Lev","family":"Levitsky","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tine","family":"Claeys","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veit","family":"Schw\u00e4mmle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,16]]},"reference":[{"key":"2_CR1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-26111-3","volume":"12","author":"C Dai","year":"2021","unstructured":"Dai C, F\u00fcllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P et al. (2021) A proteomics sample metadata representation for multiomics integration and big data analysis. Nat Commun 12: 5854","journal-title":"Nat Commun"},{"key":"2_CR2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-489","volume":"7","author":"TF Rayner","year":"2006","unstructured":"Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E et al. (2006) A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinform 7: 489","journal-title":"BMC Bioinform"},{"key":"2_CR3","doi-asserted-by":"publisher","unstructured":"Johnson D, Batista D, Cochrane K, Davey RP, Etuk A, Gonzalez-Beltran A et al (2021) ISA API: an open platform for interoperable life science experimental metadata. Gigascience 10.\u2002https:\/\/doi.org\/10.1093\/gigascience\/giab060","DOI":"10.1093\/gigascience\/giab060"},{"key":"2_CR4","doi-asserted-by":"publisher","first-page":"1603","DOI":"10.1038\/s41592-024-02343-1","volume":"21","author":"C Dai","year":"2024","unstructured":"Dai C, Pfeuffer J, Wang H, Zheng P, K\u00e4ll L, Sachsenberg T et al. (2024) quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data. Nat Methods 21:1603\u20131607","journal-title":"Nat Methods"},{"key":"2_CR5","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1021\/acs.jproteome.3c00636","volume":"23","author":"D Bouyssi\u00e9","year":"2024","unstructured":"Bouyssi\u00e9 D, Alt\u0131ner P, Capella-Gutierrez S, Fern\u00e1ndez JM, Hagemeijer YP, Horvatovich P et al. (2024) WOMBAT-P: benchmarking label-free proteomics data analysis workflows. J Proteome Res 23:418\u2013429","journal-title":"J Proteome Res"},{"key":"2_CR6","doi-asserted-by":"publisher","first-page":"2915","DOI":"10.1038\/s41596-024-01000-3","volume":"19","author":"D Kohler","year":"2024","unstructured":"Kohler D, Staniak M, Yu F, Nesvizhskii AI, Vitek O (2024) An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing. Nat Protoc 19:2915\u20132938","journal-title":"Nat Protoc"},{"key":"2_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-025-64089-4","volume":"16","author":"W Viegener","year":"2025","unstructured":"Viegener W, Urazbakhtin S, Ferretti D, Cox J, Xiao J (2025) Facilitating analysis and dissemination of proteomics data through metadata integration in MaxQuant. Nat Commun 16:1\u20135","journal-title":"Nat Commun"},{"key":"2_CR8","doi-asserted-by":"publisher","first-page":"4010","DOI":"10.1038\/s41467-026-70118-7","volume":"17","author":"H-Y Chang","year":"2026","unstructured":"Chang H-Y, Deng Y, Li R, Avtonomov D, Wen B, Haynes SE, et al. (2026) Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform. Nat Commun 17:4010. https:\/\/doi.org\/10.1038\/s41467-026-70118-7","journal-title":"Nat Commun"},{"key":"2_CR9","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkae1011","volume":"53","author":"Y Perez-Riverol","year":"2025","unstructured":"Perez-Riverol Y, Bandla C, Kundu DJ, Kamatchinathan S, Bai J, Hewapathirana S et al. (2025) The PRIDE database at 20 years: 2025 update. Nucleic Acids Res 53:D543\u2013D553","journal-title":"Nucleic Acids Res"},{"key":"2_CR10","doi-asserted-by":"publisher","first-page":"bat009","DOI":"10.1093\/database\/bat009","volume":"2013","author":"G Mayer","year":"2013","unstructured":"Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz P-A, Deutsch EW et al. (2013) The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford) 2013:bat009","journal-title":"Database (Oxford)"},{"key":"2_CR11","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.1002\/pmic.200300744","volume":"4","author":"DM Creasy","year":"2004","unstructured":"Creasy DM, Cottrell JS (2004) Unimod: protein modifications for mass spectrometry. Proteomics 4:1534\u20131536","journal-title":"Proteomics"},{"key":"2_CR12","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1093\/bioinformatics\/btq099","volume":"26","author":"J Malone","year":"2010","unstructured":"Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N et al. (2010) Modeling sample variables with an experimental factor ontology. Bioinformatics 26:1112\u20131118","journal-title":"Bioinformatics"},{"key":"2_CR13","doi-asserted-by":"publisher","DOI":"10.1038\/sdata.2016.18","volume":"3","author":"MD Wilkinson","year":"2016","unstructured":"Wilkinson MD, Dumontier M, Aalbersberg IJJ, Appleton G, Axton M, Baak A et al. (2016) The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3: 160018","journal-title":"Sci Data"},{"key":"2_CR14","doi-asserted-by":"publisher","first-page":"D1539","DOI":"10.1093\/nar\/gkac1040","volume":"51","author":"EW Deutsch","year":"2023","unstructured":"Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L et al. (2023) The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res 51:D1539\u2013D1548","journal-title":"Nucleic Acids Res"},{"key":"2_CR15","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-42543-5","volume":"14","author":"T Claeys","year":"2023","unstructured":"Claeys T, Van Den Bossche T, Perez-Riverol Y, Gevaert K, Vizca\u00edno JA, Martens L (2023) lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation. Nat Commun 14: 6743","journal-title":"Nat Commun"},{"key":"2_CR16","doi-asserted-by":"publisher","first-page":"106121","DOI":"10.1016\/j.dib.2020.106121","volume":"32","author":"B Rivera","year":"2020","unstructured":"Rivera B, Leyva A, Portela MM, Moratorio G, Moreno P, Dur\u00e1n R et al. (2020) Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: detection of viral proteins and host\u2019s biological processes altered by the infection. Data Brief 32:106121","journal-title":"Data Brief"}],"container-title":["Methods in Molecular Biology","Bioinformatics for Mass Spectrometry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-5519-1_2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T08:52:31Z","timestamp":1792140751000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/chapter\/10.1007\/978-1-0716-5519-1_2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,16]]},"ISBN":["9781071655184","9781071655191"],"references-count":16,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-5519-1_2","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,16]]},"assertion":[{"value":"16 October 2026","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"The authors declare no conflicts of interest that are relevant to the content of this chapter.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of Interest"}}]}}