LabKey CPAS Overview 
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LabKey Server's Proteomics tools (formerly the Computational Proteomics Analysis System, "CPAS") provide a web-based system for managing, analyzing, and sharing high volumes of tandem mass spectrometry data. It employs open-source tools provided by the Trans Proteomic Pipeline, developed by the Institute for Systems Biology.

Searches are performed against FASTA sequence databases using the X! Tandem search engine or, optionally, the Sequest or Mascot engines. Once the experimental data has been searched and scored, results are analyzed by PeptideProphet and ProteinProphet. You can configure LabKey to also perform XPRESS or Q3 quantitation analyses on the scored results.

Analyzed results can be dynamically displayed, enabling you to filter, sort, customize, compare, and export experiment runs. You can share data securely with collaborators inside or outside your organization, with fine-grained control over permissions.

A data pipeline imports and processes MS/MS data from raw and mzXML data files. The pipeline searches the data file for peptides using the X!Tandem search engine against the specified FASTA database. Once the data has been searched and scored (using X! Tandem scoring or a pluggable scoring algorithm), the pipeline optionally runs PeptideProphet, ProteinProphet, and XPRESS quantitation analyses on the search results.

The data pipeline can also load results that have been processed externally by some other programs. For example, it can load quantitation data processed by Q3.

LabKey Server powers proteomics repositories at the following institutions:

Documentation Topics

Integrated Tools

CPAS Team 


  • Martin McIntosh, FHCRC
  • Jimmy Eng, FHCRC
  • Samir Hanash, FHCRC
  • Parag Mallick, Cedars-Sinai
  • Phillip Gafken, FHCRC

Funding Institutions


  • Josh Eckels, LabKey Software
  • Matthew Fitzgibbon, FHCRC
  • Peter Hussey, LabKey Software
  • Brendan MacLean, University of Washington
  • Damon May, FHCRC
  • Bill Nelson, University of Kentucky
  • Adam Rauch, LabKey Software
  • Chee-Hong Wong, FHCRC