{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T09:52:24Z","timestamp":1774432344313,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The IRMa toolbox provides an interactive application to assist in the validation of Mascot\u00ae search results. It allows automatic filtering of Mascot\u00ae identification results as well as manual confirmation or rejection of individual PSM (a match between a fragmentation mass spectrum and a peptide). Dynamic grouping and coherence of information are maintained by the software in real time. Validated results can be exported under various forms, including an identification database (MSIdb). This allows biologists to compile search results from a whole study in a unique repository in order to provide a summarized view of their project. IRMa also features a fully automated version that can be used in a high-throughput pipeline. Given filter parameters, it can delete hits with no significant PSM, regroup hits identified by the same peptide(s) and export the result to the specified format without user intervention.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/biodev.extra.cea.fr\/docs\/irma (java 1.5 or higher needed)<\/jats:p>\n               <jats:p>Contact: \u00a0christophe.bruley@cea.fr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp301","type":"journal-article","created":{"date-parts":[[2009,5,7]],"date-time":"2009-05-07T00:44:24Z","timestamp":1241657064000},"page":"1980-1981","source":"Crossref","is-referenced-by-count":110,"title":["A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa"],"prefix":"10.1093","volume":"25","author":[{"given":"V\u00e9ronique","family":"Dupierris","sequence":"first","affiliation":[{"name":"1 Fondation Rh\u00f4ne-Alpes Futur, 89 rue Bellecombe, 69003 Lyon and 2 CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Prot\u00e9omes, INSERM, U880, Universit\u00e9 Joseph Fourier, Grenoble F-38054, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe","family":"Masselon","sequence":"additional","affiliation":[{"name":"1 Fondation Rh\u00f4ne-Alpes Futur, 89 rue Bellecombe, 69003 Lyon and 2 CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Prot\u00e9omes, INSERM, U880, Universit\u00e9 Joseph Fourier, Grenoble F-38054, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Magali","family":"Court","sequence":"additional","affiliation":[{"name":"1 Fondation Rh\u00f4ne-Alpes Futur, 89 rue Bellecombe, 69003 Lyon and 2 CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Prot\u00e9omes, INSERM, U880, Universit\u00e9 Joseph Fourier, Grenoble F-38054, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sylvie","family":"Kieffer-Jaquinod","sequence":"additional","affiliation":[{"name":"1 Fondation Rh\u00f4ne-Alpes Futur, 89 rue Bellecombe, 69003 Lyon and 2 CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Prot\u00e9omes, INSERM, U880, Universit\u00e9 Joseph Fourier, Grenoble F-38054, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe","family":"Bruley","sequence":"additional","affiliation":[{"name":"1 Fondation Rh\u00f4ne-Alpes Futur, 89 rue Bellecombe, 69003 Lyon and 2 CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Prot\u00e9omes, INSERM, U880, Universit\u00e9 Joseph Fourier, Grenoble F-38054, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,5,6]]},"reference":[{"key":"2023013112100112200_B1","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1038\/nature01511","article-title":"Mass spectrometry-based proteomics","volume":"422","author":"Aebersold","year":"2003","journal-title":"Nature"},{"key":"2023013112100112200_B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1074\/mcp.R300012-MCP200","article-title":"Protein identification by mass spectrometry: issues to be considered","volume":"3","author":"Baldwin","year":"2004","journal-title":"Mol. 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Today"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/15\/1980\/48994532\/bioinformatics_25_15_1980.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/15\/1980\/48994532\/bioinformatics_25_15_1980.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:39:21Z","timestamp":1675190361000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/15\/1980\/211492"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,5,6]]},"references-count":4,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2009,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp301","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,8,1]]},"published":{"date-parts":[[2009,5,6]]}}}