{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:02:30Z","timestamp":1761058950010},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":2626,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput protein identification experiments based on tandem mass spectrometry (MS\/MS) often suffer from low sensitivity and low-confidence protein identifications. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other evidence to suggest that a protein is present and confidence in individual protein identification can be updated accordingly.<\/jats:p>\n               <jats:p>Results: We develop a method that analyzes MS\/MS experiments in the larger context of the biological processes active in a cell. Our method, MSNet, improves protein identification in shotgun proteomics experiments by considering information on functional associations from a gene functional network. MSNet substantially increases the number of proteins identified in the sample at a given error rate. We identify 8\u201329% more proteins than the original MS experiment when applied to yeast grown in different experimental conditions analyzed on different MS\/MS instruments, and 37% more proteins in a human sample. We validate up to 94% of our identifications in yeast by presence in ground-truth reference sets.<\/jats:p>\n               <jats:p>Availability and Implementation: Software and datasets are available at http:\/\/aug.csres.utexas.edu\/msnet<\/jats:p>\n               <jats:p>Contact: \u00a0miranker@cs.utexas.edu, marcotte@icmb.utexas.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp461","type":"journal-article","created":{"date-parts":[[2009,7,25]],"date-time":"2009-07-25T00:59:00Z","timestamp":1248483540000},"page":"2955-2961","source":"Crossref","is-referenced-by-count":34,"title":["Mining gene functional networks to improve mass-spectrometry-based protein identification"],"prefix":"10.1093","volume":"25","author":[{"given":"Smriti R.","family":"Ramakrishnan","sequence":"first","affiliation":[{"name":"1 Department of Computer Sciences, 1 University Station C0500, 2Department of Chemistry and Biochemistry & Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, 2500 Speedway, The University of Texas at Austin, Austin, TX 78712 and 3Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Christine","family":"Vogel","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 1 University Station C0500, 2Department of Chemistry and Biochemistry & Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, 2500 Speedway, The University of Texas at Austin, Austin, TX 78712 and 3Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Taejoon","family":"Kwon","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 1 University Station C0500, 2Department of Chemistry and Biochemistry & Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, 2500 Speedway, The University of Texas at Austin, Austin, TX 78712 and 3Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Luiz O.","family":"Penalva","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 1 University Station C0500, 2Department of Chemistry and Biochemistry & Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, 2500 Speedway, The University of Texas at Austin, Austin, TX 78712 and 3Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Edward M.","family":"Marcotte","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 1 University Station C0500, 2Department of Chemistry and Biochemistry & Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, 2500 Speedway, The University of Texas at Austin, Austin, TX 78712 and 3Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Daniel P.","family":"Miranker","sequence":"additional","affiliation":[{"name":"1 Department of Computer Sciences, 1 University Station C0500, 2Department of Chemistry and Biochemistry & Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, 2500 Speedway, The University of Texas at Austin, Austin, TX 78712 and 3Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,7,24]]},"reference":[{"key":"2023013112153287000_B1","doi-asserted-by":"crossref","first-page":"2502","DOI":"10.1093\/bioinformatics\/btg363","article-title":"Characterizing gene sets with FuncAssociate","volume":"19","author":"Berriz","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013112153287000_B2","doi-asserted-by":"crossref","first-page":"R35","DOI":"10.1186\/gb-2004-5-5-r35","article-title":"Prolinks: a database of protein functional linkages derived from coevolution","volume":"5","author":"Bowers","year":"2004","journal-title":"Genome Biol."},{"key":"2023013112153287000_B3","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1038\/nbt1300","article-title":"A high-quality catalog of the Drosophila melanogaster proteome","volume":"25","author":"Brunner","year":"2007","journal-title":"Nat. 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