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Comet is an open source sequence search engine for tandem mass spectrometry. It is developed and maintained by the University of Washington. Detailed information and source and binary downloads can be obtained at the Comet project on Sourceforge.

The Comet analysis pipeline will automatically run Comet and the Trans-Proteomic Pipeline, and import the results into the database for viewing and further analysis.

LabKey Server currently supports Comet version 2013.02 rev. 0.

In order for LabKey Server to successfully run Comet, it needs to be installed in the directory pointed to by the "Pipeline tools directory" setting (in (Admin) > Site > Admin Console > Settings > Configuration > Site Settings). If you are running Comet on a remote pipeline server instead of the web server, it needs to be in the "toolsDirectory" under "appProperties" in pipelineConfig.xml (see Enterprise Pipeline with ActiveMQ for more details).

Configure Comet Defaults

To configure the Comet default parameters:

  • Go to the MS2 Dashboard.
  • In the Data Pipeline panel, click Setup.
  • Under Comet specific settings, click Set defaults.
  • Edit the XML configuration file using the Comet parameter reference.

You can override these defaults when you specify a run protocol for your experiment.

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