{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T22:37:53Z","timestamp":1772750273385,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The central proteomics facilities pipeline (CPFP) provides identification, validation, and quantitation of peptides and proteins from LC-MS\/MS datasets through an easy to use web interface. It is the first analysis pipeline targeted specifically at the needs of proteomics core facilities, reducing the data analysis load on staff, and allowing facility clients to easily access and work with their data. Identification of peptides is performed using multiple search engines, their output combined and validated using state-of-the-art techniques for improved results. Cluster execution of jobs allows analysis capacity to be increased easily as demand grows.<\/jats:p>\n               <jats:p>Availability: Released under the Common Development and Distribution License at http:\/\/cpfp.sourceforge.net\/. Demonstration available at https:\/\/cpfp-master.molbiol.ox.ac.uk\/cpfp_demo<\/jats:p>\n               <jats:p>Contact: \u00a0dctrud@ccmp.ox.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq081","type":"journal-article","created":{"date-parts":[[2010,2,27]],"date-time":"2010-02-27T01:13:51Z","timestamp":1267233231000},"page":"1131-1132","source":"Crossref","is-referenced-by-count":95,"title":["CPFP: a central proteomics facilities pipeline"],"prefix":"10.1093","volume":"26","author":[{"given":"David C.","family":"Trudgian","sequence":"first","affiliation":[{"name":"1 Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, 2 Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK"},{"name":"1 Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, 2 Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK"}]},{"given":"Benjamin","family":"Thomas","sequence":"additional","affiliation":[{"name":"1 Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, 2 Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK"}]},{"given":"Simon J.","family":"McGowan","sequence":"additional","affiliation":[{"name":"1 Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, 2 Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK"}]},{"given":"Benedikt M.","family":"Kessler","sequence":"additional","affiliation":[{"name":"1 Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, 2 Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK"}]},{"given":"Mogjiborahman","family":"Salek","sequence":"additional","affiliation":[{"name":"1 Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, 2 Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK"}]},{"given":"Oreste","family":"Acuto","sequence":"additional","affiliation":[{"name":"1 Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, 2 Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK"}]}],"member":"286","published-online":{"date-parts":[[2010,2,25]]},"reference":[{"key":"2023012508072827200_B1","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":"2023012508072827200_B2","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1002\/pmic.200300744","article-title":"Unimod: protein modifications for mass spectrometry","volume":"4","author":"Creasy","year":"2004","journal-title":"Proteomics"},{"key":"2023012508072827200_B3","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nmeth1019","article-title":"Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry","volume":"4","author":"Elias","year":"2007","journal-title":"Nat. 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