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 a peptide search tool such as X! Tandem, Sequest, Mascot, or Comet. Once the spectra have been searched and scored, results are typically analyzed by validation tools PeptideProphet and ProteinProphet. You can also configure LabKey to perform quantitation analyses on the scored results, using XPRESS or Q3.

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.

Documentation Topics

• Proteomics Tutorial
• Work with MS2 Data
• Loading Public Protein Annotation Files
• Using Custom Protein Annotations
• Using ProteinProphet
• Using Quantitation Tools
• Protein Expression Matrix Assay
• Link Protein Expression Data with Annotations
• Spectra Counts
• MS1
• Proteomics Team
• Panorama - Targeted Proteomics - Panorama is a LabKey Server module that provides tools for targeted proteomics experiments

Proteomics Installations

LabKey Server powers proteomics repositories at the following institutions:

• Fred Hutchinson Cancer Research Center
• Harvard Partners
• USC Center for Applied Molecular Medicine
• Stanford Canary Center for Cancer Early Detection
• Mallick Lab at Stanford University
• University of Washington
• Molecular Imaging Program at Stanford, and others

Integrated Tools