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LabKey Server provides a broad range of tools for research using mass spectrometry techniques, including:

Targeted Mass Spectrometry

  • Panorama - a web-based collaboration tool for Skyline targeted mass spectrometry documents
  • Automating instrument quality control / system suitability
  • Support for small molecule experiments


Discovery Proteomics

  • Managing, analyzing, and sharing high volumes of tandem mass spectrometry data, employing open-source tools provided by the Trans Proteomic Pipeline, developed by the Institute for Systems Biology
  • Searches against FASTA sequence databases using tools such as X! Tandem, Sequest, Mascot, or Comet
  • Analysis by PeptideProphet and ProteinProphet
  • Quantitation analysis on scored results using XPRESS and Q3


  • Discovery Proteomics - Protein database searching, analysis and collaboration for discovery proteomics experiments.


Mass Spectrometry Installations

LabKey Server powers proteomics repositories at the following institutions:

Proteomics Team


  • Mike MacCoss, University of Washington
  • Brendan MacLean, University of Washington
  • Phillip Gafken, FHCRC
  • Jimmy Eng, University of Washington
  • Parag Mallick, Stanford University
Funding Institutions Development
  • Josh Eckels, LabKey
  • Cory Nathe, LabKey
  • Adam Rauch, LabKey
  • Vagisha Sharma, University of Washington
  • Kaipo Tamura, University of Washington
  • Yuval Boss, University of Washington

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