title: Installation and use of LabKey Server for proteomics.
abstract: LabKey Server (formerly CPAS, the Computational Proteomics Analysis System) provides a Web-based platform for mining data from liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic experiments. This open source platform supports systematic proteomic analyses and secure data management, integration, and sharing. LabKey Server incorporates several tools currently used in proteomic analysis, including the X! Tandem search engine, the ProteoWizard toolkit, and the PeptideProphet and ProteinProphet data mining tools. These tools and others are integrated into LabKey Server, which provides an extensible architecture for developing high-throughput biological applications. The LabKey Server analysis pipeline acts on data in standardized file formats, so that researchers may use LabKey Server with other search engines, including Mascot or SEQUEST, that follow a standardized format for reporting search engine results. Supported builds of LabKey Server are freely available at http://www.labkey.com/. Documentation and source code are available under the Apache License 2.0 at http://www.labkey.org.
authors.affiliation: LabKey Software, Seattle, Washington.
authors.forename: Joshua
authors.initials: J
authors.lastname: Eckels
authors.affiliation: LabKey Software, Seattle, Washington.
authors.forename: Peter
authors.initials: P
authors.lastname: Hussey
authors.affiliation: LabKey Software, Seattle, Washington.
authors.forename: Elizabeth K
authors.initials: EK
authors.lastname: Nelson
authors.affiliation: LabKey Software, Seattle, Washington.
authors.forename: Tamra
authors.initials: T
authors.lastname: Myers
authors.affiliation: LabKey Software, Seattle, Washington.
authors.forename: Adam
authors.initials: A
authors.lastname: Rauch
authors.affiliation: LabKey Software, Seattle, Washington.
authors.forename: Matthew
authors.initials: M
authors.lastname: Bellew
authors.affiliation: LabKey Software, Seattle, Washington.
authors.forename: Brian
authors.initials: B
authors.lastname: Connolly
authors.affiliation: Marsha Rivkin Center for Ovarian Cancer Research, Seattle, Washington.
authors.forename: Wendy
authors.initials: W
authors.lastname: Law
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington.
authors.forename: Jimmy K
authors.initials: JK
authors.lastname: Eng
authors.affiliation: Departments of Medicine and Biomedical Engineering, University of Southern California Center for Applied Molecular Medicine, Los Angeles, California.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Katz
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Martin
authors.initials: M
authors.lastname: McIntosh
authors.affiliation: Departments of Medicine and Biomedical Engineering, University of Southern California Center for Applied Molecular Medicine, Los Angeles, California.|Department of Radiology, Stanford University, Stanford, California.
authors.forename: Parag
authors.initials: P
authors.lastname: Mallick
authors.affiliation: LabKey Software, Seattle, Washington.
authors.forename: Mark
authors.initials: M
authors.lastname: Igra
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods; D057225:Data Mining; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D012984:Software