[Panorama - Targeted Proteomics] [Discovery Proteomics Tutorial] [MS2 Demo]

LabKey Server provides a broad range of mass spec tools, including:

Targeted Mass Spec

  • Panorama - a web-based collaboration tool for Skyline targeted proteomics
  • Automating instrument quality control / system suitability
  • Small molecules

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
A data processing pipeline can be configured to apply a series of tools in sequence: for example, after importing MS2 data from raw and mzXML data files, it can search the files for peptides using the X!Tandem search engine against a specified FASTA database. Once the data has been searched and scored, the pipeline optionally runs PeptideProphet, ProteinProphet, or XPRESS quantitation analyses on the search results.

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.

Documentation Topics

Mass Spectrometry Installations

LabKey Server powers proteomics repositories at the following institutions:


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