UNIT 13.5 Installation and Use of LabKey Server for Proteomics

  1. Joshua Eckels1,
  2. Peter Hussey1,
  3. Elizabeth K. Nelson1,
  4. Tamra Myers1,
  5. Adam Rauch1,
  6. Matthew Bellew1,
  7. Brian Connolly1,
  8. Wendy Law2,
  9. Jimmy K. Eng3,
  10. Jonathan Katz4,
  11. Martin McIntosh5,
  12. Parag Mallick4,6,
  13. Mark Igra1

Published Online: 1 DEC 2011

DOI: 10.1002/0471250953.bi1305s36

Current Protocols in Bioinformatics

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. 36:13.5:13.5.1–13.5.25.

Author Information

  1. 1

    LabKey Software, Seattle, Washington

  2. 2

    Marsha Rivkin Center for Ovarian Cancer Research, Seattle, Washington

  3. 3

    Department of Genome Sciences, University of Washington, Seattle, Washington

  4. 4

    Departments of Medicine and Biomedical Engineering, University of Southern California Center for Applied Molecular Medicine, Los Angeles, California

  5. 5

    Fred Hutchinson Cancer Research Center, Seattle, Washington

  6. 6

    Department of Radiology, Stanford University, Stanford, California

Publication History

  1. Published Online: 1 DEC 2011
  2. Published Print: DEC 2011


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. Curr. Protoc. Bioinform. 36:13.5.1-13.5.25. © 2011 by John Wiley & Sons, Inc.


  • liquid chromatography;
  • mass spectrometry;
  • proteomics;
  • data analysis;
  • protein identification