Mass Spectrometry

Process, analyze, store and share high volumes of mass spectrometry data

LabKey Server provides a data pipeline for importing and processing mass spectrometry data from raw and mzXML data files. This pipeline manages the chain of processing steps needed to infer protein identifications and expression levels from the output of a mass spec machine. It integrates with leading search engines, including X!Tandem™, Mascot™, and Sequest™, and components of the Trans Proteomic Pipeline™, such as PeptideProphet™, ProteinProphet™ , and XPRESS™.

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.

Learn more about mass spectrometry support in the LabKey documentation.

The system can act as a secure repository, allowing you to aggregate curated results, explore hypotheses using historical data, and integrate with other kinds of data.  The Panorama module of LabKey Server supports users who need a repository tailored for targeted proteomics assays and integration into Skyline workflows.  For assistance in using Panorama, consider the Panorama Partners Program.

Proteomics Core

LabKey Server 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.

LabKey in Action

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

Get Started with LabKey

Interested in learning more about LabKey? Contact us and the LabKey team will work with you to understand your needs and determine how LabKey would best fit your research.