{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:01:55Z","timestamp":1761058915768},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We report a software scheme for automated diagnosis of liquid chromatography tandem mass spectrometry (LC-MS\/MS) system performance. The proposed software scheme provides a robust framework for establishing automated diagnosis of LC-MS\/MS system performance for a variety of instruments and experiments. This schematic consists of four main software components: (i) data conversion, (ii) peptide identification, (iii) LC retention time analysis and (iv) system performance evaluation. The implementation of a standard approach for assessing LC-MS\/MS system performance enables researchers to apply reliable metrics to assess their workflows performance over different batch experiments. Furthermore, the results from system diagnosis can provide feedback to the workflow to stop batch analysis if system performance falls below prescribed thresholds. A basic implementation of the approach based on the MassMatrix database search and LC retention time analysis programs is presented.<\/jats:p>\n               <jats:p>Availability: An open source implementation of the LC-MS\/MS system diagnosis software based on the MassMatrix database search program is freely available to non-commercial users and can be downloaded at www.massmatrix.net.<\/jats:p>\n               <jats:p>Contact: \u00a0huaxu@uic.edu; freitas.5@osu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp155","type":"journal-article","created":{"date-parts":[[2009,3,21]],"date-time":"2009-03-21T01:29:56Z","timestamp":1237598996000},"page":"1341-1343","source":"Crossref","is-referenced-by-count":18,"title":["Automated diagnosis of LC-MS\/MS performance"],"prefix":"10.1093","volume":"25","author":[{"given":"Hua","family":"Xu","sequence":"first","affiliation":[{"name":"1 Proteomics and Informatics Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, IL 60612 and 2Department of Molecular Virology, Immunology and Medical Genetics, the Ohio State University, Columbus, OH 43210, USA"}]},{"given":"Michael A.","family":"Freitas","sequence":"additional","affiliation":[{"name":"1 Proteomics and Informatics Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, IL 60612 and 2Department of Molecular Virology, Immunology and Medical Genetics, the Ohio State University, Columbus, OH 43210, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,3,20]]},"reference":[{"key":"2023013110284560400_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":"2023013110284560400_B2","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1002\/prca.200600771","article-title":"Clinical proteomics: a need to define the field and to begin to set adequate standards","volume":"1","author":"Mischak","year":"2007","journal-title":"Proteomics Clin. 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Proteome Res."},{"key":"2023013110284560400_B7","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1186\/1471-2105-9-347","article-title":"A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time","volume":"9","author":"Xu","year":"2008","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/10\/1341\/48988715\/bioinformatics_25_10_1341.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/10\/1341\/48988715\/bioinformatics_25_10_1341.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:31:22Z","timestamp":1675189882000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/10\/1341\/270609"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,3,20]]},"references-count":7,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2009,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp155","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,5,15]]},"published":{"date-parts":[[2009,3,20]]}}}