Installation and Use of LabKey Server for Proteomics

Joshua Eckels1, Peter Hussey1, Elizabeth K. Nelson1, Tamra Myers1, Adam Rauch1, Matthew Bellew1, Brian Connolly1, Wendy Law2, Jimmy K. Eng3, Jonathan Katz4, Martin McIntosh5, Parag Mallick6, Mark Igra1

1 LabKey Software, Seattle, Washington, 2 Marsha Rivkin Center for Ovarian Cancer Research, Seattle, Washington, 3 Department of Genome Sciences, University of Washington, Seattle, Washington, 4 Departments of Medicine and Biomedical Engineering, University of Southern California Center for Applied Molecular Medicine, Los Angeles, California, 5 Fred Hutchinson Cancer Research Center, Seattle, Washington, 6 Department of Radiology, Stanford University, Stanford, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.5
DOI:  10.1002/0471250953.bi1305s36
Online Posting Date:  December, 2011
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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 Documentation and source code are available under the Apache License 2.0 at 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

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Table of Contents

  • Introduction
  • Basic Protocol 1: Search Tandem Mass Spectrometry Data
  • Basic Protocol 2: Viewing and Analyzing MS/MS Data in LabKey Server
  • Support Protocol 1: Install and Configure LabKey Server
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

   Craig, R. and Beavis, R.C. 2004. TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 20:1466‐1467.
   Eng, J. K., McCormack, A.L., and Yates, J.R. 3rd. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5:976‐989.
   Han, D.K., Eng, J., Zhou, H., and Aebersold, R. 2001. Quantitative profiling of differentiation‐induced microsomal proteins using isotope‐coded affinity tags and mass spectrometry. Nat. Biotechnol. 19:946‐951.
   Keller, A., Nesvizhskii, A.I., Kolker, E., and Aebersold, R. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74:5383‐5392.
   Keller, A., Eng, J., Zhang, N., Li, X.J., and Aebersold, R. 2005. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 1:2005.0017.
   MacLean, B., Eng, J.K., Beavis, R.C., and McIntosh, M. 2006. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 22:2830‐2832.
   Nelson, E.K., Piehler, B., Eckels, J., Rauch, A., Bellew, M., Hussey, P., Ramsay, S., Nathe, C., Lum, K., Krouse, K., Stearns, D., Connolly, B., Skillman, T., and Igra, M. 2011. LabKey server: An open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics 12:71.
   Nesvizhskii, A.I., Keller, A., Kolker, E., and Aebersold, R. 2003. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646‐4658.
   Perkins, D.N., Pappin, D.J., Creasy, D.M., and Cottrell, J.S. 1999. Probability‐based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 18:3551‐3567.
   Rauch, A., Bellew, M., Eng, J., Fitzgibbon, M., Holzman, T., Hussey, P., Igra, M., MacLean, B., Lin, C.W., Detter, A., Fang, R., Faca, V., Gafken, P., Zhang, H., Whiteaker, J., States, D., Hanash, S., Paulovich, A., and McIntosh, M. 2006. Computational Proteomics Analysis System (CPAS): An extensible, open‐source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J. Proteome Res. 5:112‐121.
Internet Resources
  The LabKey Software Foundation site provides source code, documentation and community support forums for LabKey Server.
  The LabKey Software site provides installers for LabKey Server and related components. LabKey Software develops LabKey Server.
  LabKey Software's hosting site provides free, limited‐time accounts for trial usage of LabKey Server.
  The Institute for Systems Biology distributes a variety of proteomics tools, including XPRESS, PeptideProphet, ProteinProphet, and many mzXML conversion tools.
  Open source software for matching tandem mass spectra with peptide sequences.
  The Fred Hutchinson Cancer Research Center's Computational Proteomics Laboratory (CPL) instance of LabKey Server.
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