{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T20:13:18Z","timestamp":1760645598113},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":2907,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Mass spectrometry-based proteomics stands to gain from additional analysis of its data, but its large, complex datasets make demands on speed and memory usage requiring special consideration from scripting languages. The software library \u2018mspire\u2019\u2014developed in the Ruby programming language\u2014offers quick and memory-efficient readers for standard xml proteomics formats, converters for intermediate file types in typical proteomics spectral-identification work flows (including the Bioworks .srf format), and modules for the calculation of peptide false identification rates.<\/jats:p>\n               <jats:p>Availability: Freely available at http:\/\/mspire.rubyforge.org. Additional data models, usage information, and methods available at http:\/\/bioinformatics.icmb.utexas.edu\/mspire<\/jats:p>\n               <jats:p>Contact: \u00a0marcotte@icmb.utexas.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn513","type":"journal-article","created":{"date-parts":[[2008,10,18]],"date-time":"2008-10-18T00:13:50Z","timestamp":1224288830000},"page":"2796-2797","source":"Crossref","is-referenced-by-count":20,"title":["mspire: mass spectrometry proteomics in Ruby"],"prefix":"10.1093","volume":"24","author":[{"given":"John T.","family":"Prince","sequence":"first","affiliation":[{"name":"1 Institute for Cellular and Molecular Biology, 2Center for Systems and Synthetic Biology and 3Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA"},{"name":"1 Institute for Cellular and Molecular Biology, 2Center for Systems and Synthetic Biology and 3Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edward M.","family":"Marcotte","sequence":"additional","affiliation":[{"name":"1 Institute for Cellular and Molecular Biology, 2Center for Systems and Synthetic Biology and 3Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA"},{"name":"1 Institute for Cellular and Molecular Biology, 2Center for Systems and Synthetic Biology and 3Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA"},{"name":"1 Institute for Cellular and Molecular Biology, 2Center for Systems and Synthetic Biology and 3Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,10,16]]},"reference":[{"key":"2023020212240190900_B1","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1021\/pr0504236","article-title":"InSilicoSpectro: an open-source proteomics library","volume":"5","author":"Colinge","year":"2006","journal-title":"J. Proteome Res."},{"key":"2023020212240190900_B2","doi-asserted-by":"crossref","first-page":"D655","DOI":"10.1093\/nar\/gkj040","article-title":"The PeptideAtlas project","volume":"34","author":"Desiere","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023020212240190900_B3","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1093\/bioinformatics\/btl573","article-title":"ProteomeCommons.org IO framework: reading and writing multiple proteomics data formats","volume":"23","author":"Falkner","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020212240190900_B4","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1038\/nmeth1113","article-title":"Semi-supervised learning for peptide identification from shotgun proteomics datasets","volume":"4","author":"Kall","year":"2007","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/23\/2796\/49055789\/bioinformatics_24_23_2796.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/23\/2796\/49055789\/bioinformatics_24_23_2796.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T12:25:22Z","timestamp":1675340722000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/23\/2796\/180173"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,10,16]]},"references-count":4,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2008,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn513","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,12,1]]},"published":{"date-parts":[[2008,10,16]]}}}