{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T04:30:26Z","timestamp":1761539426578},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We describe an integrative software platform, Prequips, for comparative proteomics-based systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)-based proteomics as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein abundances to external tools often used in systems biology studies.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/prequips.sourceforge.net<\/jats:p>\n               <jats:p>Contact: \u00a0dhhwang@postech.ac.kr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp005","type":"journal-article","created":{"date-parts":[[2009,1,8]],"date-time":"2009-01-08T01:24:23Z","timestamp":1231377863000},"page":"682-683","source":"Crossref","is-referenced-by-count":12,"title":["Prequips\u2014an extensible software platform for integration, visualization and analysis of LC-MS\/MS proteomics data"],"prefix":"10.1093","volume":"25","author":[{"given":"Nils","family":"Gehlenborg","sequence":"first","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Yan","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inyoul Y.","family":"Lee","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hyuntae","family":"Yoo","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kay","family":"Nieselt","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daehee","family":"Hwang","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruedi","family":"Aebersold","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leroy","family":"Hood","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics T\u00fcbingen, University of T\u00fcbingen, T\u00fcbingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,1,6]]},"reference":[{"key":"2023013110110982500_B1","doi-asserted-by":"crossref","first-page":"5383","DOI":"10.1021\/ac025747h","article-title":"Empirical statistical model to estimate the accuracy of peptide identifications made by MS\/MS and database search","volume":"74","author":"Keller","year":"2002","journal-title":"Anal. Chem."},{"key":"2023013110110982500_B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/msb4100024","article-title":"A uniform proteomics MS\/MS analysis platform utilizing open XML formats","volume":"1","author":"Keller","year":"2005","journal-title":"Mol. Syst. Biol."},{"key":"2023013110110982500_B3","doi-asserted-by":"crossref","first-page":"3856","DOI":"10.1021\/ac035375s","article-title":"A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectroscopy","volume":"76","author":"Li","year":"2004","journal-title":"Anal. Chem."},{"key":"2023013110110982500_B4","doi-asserted-by":"crossref","first-page":"374","DOI":"10.2144\/03342mt01","article-title":"TM4: a free, open-source system for microarray data management and analysis","volume":"34","author":"Saeed","year":"2003","journal-title":"Biotechniques"},{"key":"2023013110110982500_B5","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1186\/1471-2105-7-176","article-title":"The gaggle: an open-source software system for integrating bioinformatics software and data sources","volume":"7","author":"Shannon","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013110110982500_B6","doi-asserted-by":"crossref","first-page":"2138","DOI":"10.1074\/mcp.M700498-MCP200","article-title":"An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures","volume":"7","author":"Schmidt","year":"2008","journal-title":"Mol. Cell. Proteomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/5\/682\/48983762\/bioinformatics_25_5_682.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/5\/682\/48983762\/bioinformatics_25_5_682.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T19:47:49Z","timestamp":1675194469000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/5\/682\/182599"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1,6]]},"references-count":6,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2009,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp005","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,3,1]]},"published":{"date-parts":[[2009,1,6]]}}}