Proteomics solutions built with LabKey Server provide a comprehensive system for processing, analyzing, storing and sharing high volumes of mass spectrometry data.

The LabKey Server platform works exceptionally well for research teams and organizations that need a system to process, analyze, store and securely share high volumes of mass spectrometry data.

LabKey Server incorporates a robust data pipeline for importing and processing mass spectrometry  data from raw and mzXML data files. The pipeline manages the chain of processing steps needed to infer protein identifications and expression levels from the output of a mass spec machine. The pipeline integrates with leading search engines including X!Tandem™, Mascot™, and Sequest™. The pipeline also integrates PeptideProphet™, ProteinProphet™ , and XPRESS™, all components of the Trans Proteomic Pipeline™ from the Institute for Systems Biology.

For analysis, LabKey Server displays the search results from one or many runs in your web browser, enabling you to filter, sort, customize, compare, and export experimental runs. You can share data securely with collaborators inside or outside your organization while exercising fine-grained control over permissions.

Today, LabKey Server powers proteomics repositories at the Fred Hutchinson Cancer Research Center, Cedars-Sinai Medical Center, the University of Washington and many others, where it is central to efforts to identify predictive biomarkers for cancer.

LabKey's proteomics features, also known collectively as CPAS (for Computational Proteomics Analysis System) are caBIG™ compatible.

Proteomics Solution Components

Proteomics Core

LabKey Server easily manages tandem mass spectrometry analyses using a variety of popular search engines including Mascot™, Sequest™, and X-Tandem™. Peakaboo and msInspect are included for analyzing precursor ion spectra, and msconvert from the ProteoWizard project is included for converting raw output files from the mass spectrometer into standard XML formats.

Collaboration Tools

LabKey Server provides tools for sharing information and ideas on public and private webs. It includes a wiki for sharing dynamic content, a message board for online discussions and an issue tracker for workflow management.

Administration and Installation Tools

LabKey Server provides fine-grained control over project structures and user permissions. Administrators can add specialized tools to customized projects and folders.

Developers

The LabKey Software Foundation provides the LabKey Developer Community Forum for programmers who seek to customize or extend LabKey Server.