{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T08:52:53Z","timestamp":1758703973846},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2017,3,2]],"date-time":"2017-03-02T00:00:00Z","timestamp":1488412800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The mapping of amino acid sequences is an essential task in bioinformatics. Notably, the mapping of peptide sequences on a proteome is required for the post-processing of proteomics results. However, this step can quickly become a bottleneck when working with extensive numbers of peptides or large protein sequence databases. Here, we present PeptideMapper, a novel amino acid sequence mapper for both peptide sequences and de novo sequencing identification results. By taking advantage of the latest advances in pattern matching, PeptideMapper achieves unprecedented performance (i.e. up to 1000\u00d7 faster than state-of-the-art software) in terms of memory footprint and execution speed, with regards to both the indexing and the querying of protein sequence databases.<\/jats:p>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>PeptideMapper is implemented in the open source Java CompOmics framework under the permissive Apache 2.0 license https:\/\/github.com\/compomics\/compomics-utilities.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx122","type":"journal-article","created":{"date-parts":[[2017,3,1]],"date-time":"2017-03-01T20:48:26Z","timestamp":1488401306000},"page":"2042-2044","source":"Crossref","is-referenced-by-count":14,"title":["PeptideMapper: efficient and versatile amino acid sequence and tag mapping"],"prefix":"10.1093","volume":"33","author":[{"given":"Dominik","family":"Kopczynski","sequence":"first","affiliation":[{"name":"Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V, Dortmund, Germany"}]},{"given":"Harald","family":"Barsnes","sequence":"additional","affiliation":[{"name":"Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway"},{"name":"Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway"}]},{"given":"P\u00e5l R","family":"Nj\u00f8lstad","sequence":"additional","affiliation":[{"name":"KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway"},{"name":"Department of Pediatrics, Haukeland University Hospital, Bergen, Norway"}]},{"given":"Albert","family":"Sickmann","sequence":"additional","affiliation":[{"name":"Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V, Dortmund, Germany"},{"name":"College of Physical Sciences, University of Aberdeen, Old Aberdeen, UK"},{"name":"Medizinische Fakult\u00e4t, Ruhr-Universit\u00e4t Bochum, Bochum, Germany"}]},{"given":"Marc","family":"Vaudel","sequence":"additional","affiliation":[{"name":"KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway"},{"name":"Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway"}]},{"given":"Robert","family":"Ahrends","sequence":"additional","affiliation":[{"name":"Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V, Dortmund, Germany"}]}],"member":"286","published-online":{"date-parts":[[2017,3,2]]},"reference":[{"key":"2023020206005576100_btx122-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-12-70","article-title":"compomics-utilities: an open-source Java library for computational proteomics","volume":"12","author":"Barsnes","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020206005576100_btx122-B2","author":"Burrows","year":"1994"},{"key":"2023020206005576100_btx122-B3","doi-asserted-by":"crossref","first-page":"2808","DOI":"10.1093\/bioinformatics\/btt484","article-title":"A fast peptide match service for UniProt knowledgebase","volume":"29","author":"Chen","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020206005576100_btx122-B4","doi-asserted-by":"crossref","first-page":"e29","DOI":"10.1093\/nar\/gku1283","article-title":"PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration","volume":"43","author":"Crapp\u00e9","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020206005576100_btx122-B5","doi-asserted-by":"crossref","first-page":"1716","DOI":"10.1021\/pr900850m","article-title":"TagRecon: high-throughput mutation identification through sequence tagging","volume":"9","author":"Dasari","year":"2010","journal-title":"J. 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Proteome Res"},{"key":"2023020206005576100_btx122-B14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0082981","article-title":"Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture","volume":"8","author":"Tanca","year":"2013","journal-title":"PLoS ONE"},{"key":"2023020206005576100_btx122-B15","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1586\/epr.12.51","article-title":"Current methods for global proteome identification","volume":"9","author":"Vaudel","year":"2012","journal-title":"Exp. Rev. Proteomics"},{"key":"2023020206005576100_btx122-B16","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/nbt.3109","article-title":"PeptideShaker enables reanalysis of MS-derived proteomics data sets","volume":"33","author":"Vaudel","year":"2015","journal-title":"Nat. Biotechnol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/13\/2042\/49040321\/bioinformatics_33_13_2042.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/13\/2042\/49040321\/bioinformatics_33_13_2042.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:01:17Z","timestamp":1675317677000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/13\/2042\/3059929"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,3,2]]},"references-count":16,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2017,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx122","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,7,1]]},"published":{"date-parts":[[2017,3,2]]}}}