{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,13]],"date-time":"2024-06-13T09:46:46Z","timestamp":1718272006471},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,7,1]]},"abstract":"Abstract<\/jats:title>\n Motivation: Tandem mass spectrometry (MS\/MS) has been routinely used in proteomics studies. Post-translational modification (PTM) identification is a challenging problem in tandem mass spectral analysis.<\/jats:p>\n Results: In this article, we define two scoring functions for identifying peptides\/proteins with PTMs from MS\/MS spectra: match scores and diagonal scores, as well as two spectral identification problems based on the two scores. We propose several index-based algorithms for the two problems. Both theoretical and experimental analyses show that the index-based algorithms significantly improve on speed when compared with existing algorithms.<\/jats:p>\n Contact: \u00a0xil018@cs.ucsd.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts244","type":"journal-article","created":{"date-parts":[[2012,4,28]],"date-time":"2012-04-28T03:49:15Z","timestamp":1335584955000},"page":"1692-1697","source":"Crossref","is-referenced-by-count":11,"title":["Speeding up tandem mass spectral identification using indexes"],"prefix":"10.1093","volume":"28","author":[{"given":"Xiaowen","family":"Liu","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and Engineering, University of California, San Diego, California, 92093, USA and 2Department of Information Engineering, University of Padova, Padova 35131, Italy"}]},{"given":"Alessandro","family":"Mammana","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, University of California, San Diego, California, 92093, USA and 2Department of Information Engineering, University of Padova, Padova 35131, Italy"}]},{"given":"Vineet","family":"Bafna","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, University of California, San Diego, California, 92093, USA and 2Department of Information Engineering, University of Padova, Padova 35131, Italy"}]}],"member":"286","published-online":{"date-parts":[[2012,4,27]]},"reference":[{"issue":"Suppl. 1","key":"2023012512380406000_B1","doi-asserted-by":"crossref","first-page":"S13","DOI":"10.1093\/bioinformatics\/17.suppl_1.S13","article-title":"SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database","volume":"17","author":"Bafna","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012512380406000_B2","doi-asserted-by":"crossref","first-page":"4422","DOI":"10.1021\/pr800400q","article-title":"Improved sequence tag generation method for peptide identification in tandem mass spectrometry","volume":"7","author":"Cao","year":"2008","journal-title":"J. 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