UNIT 13.5 Installation and Use of LabKey Server for Proteomics
Published Online: 1 DEC 2011
Copyright © 2011 by John Wiley & Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
How to Cite
Eckels, J., Hussey, P., Nelson, E. K., Myers, T., Rauch, A., Bellew, M., Connolly, B., Law, W., Eng, J. K., Katz, J., McIntosh, M., Mallick, P. and Igra, M. 2011. Installation and Use of LabKey Server for Proteomics. Current Protocols in Bioinformatics. 36:13.5.1–13.5.25.
- Published Online: 1 DEC 2011
- Published Print: DEC 2011
LabKey Server (formerly CPAS, the Computational Proteomics Analysis System) provides a Web-based platform for mining data from liquid chromatographytandem 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. Curr. Protoc. Bioinform. 36:13.5.1-13.5.25. © 2011 by John Wiley & Sons, Inc.
Keywords: liquid chromatography; mass spectrometry; proteomics; data analysis; protein identification