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

Documentation

• Panorama: Targeted Mass Spectrometry - Web-based collaboration for Skyline documents.
• Resources on PanoramaWeb - See tutorials, video demonstrations, and published experiments on PanoramaWeb.org.

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

Documentation

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

Demo

• MS2 Demo

Mass Spectrometry Installations

LabKey Server powers proteomics repositories at the following institutions:

• Fred Hutchinson Cancer Research Center
• Harvard Partners HealthCare
• 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

Proteomics Team

Scientific

• Mike MacCoss, University of Washington
• Brendan MacLean, University of Washington
• Phillip Gafken, FHCRC
• Jimmy Eng, University of Washington
• Parag Mallick, Stanford University

• National Cancer Institute

• Josh Eckels, LabKey
• Cory Nathe, LabKey
• Adam Rauch, LabKey
• Vagisha Sharma, University of Washington
• Kaipo Tamura, University of Washington
• Yuval Boss, University of Washington