Installation and Use of LabKey Server for Proteomics

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.

[1]  R. Aebersold,et al.  A statistical model for identifying proteins by tandem mass spectrometry. , 2003, Analytical chemistry.

[2]  Alexey I Nesvizhskii,et al.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.

[3]  R. Aebersold,et al.  A uniform proteomics MS/MS analysis platform utilizing open XML file formats , 2005, Molecular systems biology.

[4]  Robertson Craig,et al.  TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.

[5]  Adam Rauch,et al.  Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. , 2006, Journal of proteome research.

[6]  Adam Rauch,et al.  LabKey Server: An open source platform for scientific data integration, analysis and collaboration , 2011, BMC Bioinformatics.

[7]  R. Aebersold,et al.  Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry , 2001, Nature Biotechnology.

[8]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[9]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[10]  Brendan MacLean,et al.  General framework for developing and evaluating database scoring algorithms using the TANDEM search engine , 2006, Bioinform..