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The community of proteomic researchers has been generating openly available software infrastructure for systematic proteomic data analyses and data management for the past several years. The Computational Proteomics Analysis System (CPAS) integrates many of these efforts into a single Web-based platform for mining liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic experiments. CPAS incorporates several tools currently used in proteomic analysis, including the X! Tandem search engine and the PeptideProphet and ProteinProphet data mining tools. These tools and others are integrated into a single application built on the open-source LabKey platform, an extensible architecture for developing high-throughput biological applications. The CPAS analysis pipeline acts on data in standardized file formats, so that researchers may use CPAS with other search engines, including Mascot or SEQUEST, that follow a standardized procedure for reporting search engine results. All components of the CPAS toolkit are freely available at http://cpas.fhcrc.org.
Myers T, Law W, Eng JK, McIntosh M. Installation and use of the Computational Proteomics Analysis System (CPAS). Curr Protoc Bioinformatics. 2007 June; Chapter 13: Unit 13.5.