{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T17:42:42Z","timestamp":1762623762541,"version":"3.37.3"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"17","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation : There is a growing trend for biomedical researchers to extract evidence and draw conclusions from mass spectrometry based proteomics experiments, the cornerstone of which is peptide identification. Inaccurate assignments of peptide identification confidence thus may have far-reaching and adverse consequences. Although some peptide identification methods report accurate statistics, they have been limited to certain types of scoring function. The extreme value statistics based method, while more general in the scoring functions it allows, demands accurate parameter estimates and requires, at least in its original design, excessive computational resources. Improving the parameter estimate accuracy and reducing the computational cost for this method has two advantages: it provides another feasible route to accurate significance assessment, and it could provide reliable statistics for scoring functions yet to be developed.<\/jats:p><jats:p>Results : We have formulated and implemented an efficient algorithm for calculating the extreme value statistics for peptide identification applicable to various scoring functions, bypassing the need for searching large random databases.<\/jats:p><jats:p>Availability and Implementation : The source code, implemented in C\u2009++\u2009on a linux system, is available for download at ftp:\/\/ftp.ncbi.nlm.nih.gov\/pub\/qmbp\/qmbp_ms\/RAId\/RAId_Linux_64Bit<\/jats:p><jats:p>Contact: \u00a0yyu@ncbi.nlm.nih.gov<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw225","type":"journal-article","created":{"date-parts":[[2016,4,30]],"date-time":"2016-04-30T01:35:22Z","timestamp":1461980122000},"page":"2642-2649","source":"Crossref","is-referenced-by-count":7,"title":["Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution"],"prefix":"10.1093","volume":"32","author":[{"given":"Gelio","family":"Alves","sequence":"first","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}]},{"given":"Yi-Kuo","family":"Yu","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,6,29]]},"reference":[{"key":"2023020112585296700_btw225-B1","doi-asserted-by":"crossref","first-page":"6538","DOI":"10.1016\/j.physa.2008.08.024","article-title":"Statistical characterization of a 1D random potential problem \u2013 with applications in score statistics of MS-based peptide sequencing","volume":"387","author":"Alves","year":"2008","journal-title":"Physica A"},{"key":"2023020112585296700_btw225-B2","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1093\/bioinformatics\/btu717","article-title":"Mass spectrometry-based protein identification with accurate statistical significance assignment","volume":"31","author":"Alves","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020112585296700_btw225-B3","doi-asserted-by":"crossref","first-page":"26.","DOI":"10.1186\/1745-6150-2-26","article-title":"Calibrating E-values for MS2 database search methods","volume":"2","author":"Alves","year":"2007","journal-title":"Biol. 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