{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T20:14:30Z","timestamp":1760645670645},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"22","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: Database searching is the major peptide identification method in shotgun proteomics. It searches tandem mass spectrometry (MS\/MS) spectra against a protein database to identify target peptides. The success of such a database searching method relies on a scoring algorithm that can evaluate the quality of peptide-spectrum matches (PSMs) accurately. However, current scoring algorithms frequently generate inaccurate assignments due to variations and noises in the MS\/MS spectra. To address this issue, we like to improve peptide identification by using additional information from other data sources.<\/jats:p>\n               <jats:p>Results: Single-stage MS data is complementary to MS\/MS data in the sense that it provides broader mass coverage but less sequence information. In this article, we show that single-stage MS data can be used to re-rank PSMs. The proposed method explores a linear combination of scores between MS and MS\/MS data to perform re-ranking. Experimental results on real data show that such a re-ranking strategy improves the identification performance significantly.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/bioinformatics.ust.hk\/ReRankPSMwMS1.rar<\/jats:p>\n               <jats:p>Contact: \u00a0eezyhe@ust.hk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp501","type":"journal-article","created":{"date-parts":[[2009,8,19]],"date-time":"2009-08-19T03:03:10Z","timestamp":1250650990000},"page":"2969-2974","source":"Crossref","is-referenced-by-count":6,"title":["Improving peptide identification with single-stage mass spectrum peaks"],"prefix":"10.1093","volume":"25","author":[{"given":"Zengyou","family":"He","sequence":"first","affiliation":[{"name":"Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China"}]},{"given":"Weichuan","family":"Yu","sequence":"additional","affiliation":[{"name":"Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China"}]}],"member":"286","published-online":{"date-parts":[[2009,8,18]]},"reference":[{"key":"2023013112151374100_B1","doi-asserted-by":"crossref","first-page":"i416","DOI":"10.1093\/bioinformatics\/btn184","article-title":"Multi-spectra peptide sequencing and its applications to multistage mass spectrometry","volume":"24","author":"Bandeira","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112151374100_B2","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1093\/bioinformatics\/bth092","article-title":"Tandem: matching proteins with tandem mass spectra","volume":"20","author":"Craig","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013112151374100_B3","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1287\/mnsc.38.5.645","article-title":"Multiple criteria decision making, multiattribute utility theory: the next ten years","volume":"38","author":"Dyer","year":"1992","journal-title":"Manage. 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