crux comet [options] <input spectra> <database_name>


This command searches a protein database with a set of spectra, assigning peptide sequences to the observed spectra. This search engine was developed by Jimmy Eng at the University of Washington Proteomics Resource.

Although its history goes back two decades, the Comet search engine was first made publicly available in August 2012 on SourceForge. Comet is multithreaded and supports multiple input and output formats.

"Comet: an open source tandem mass spectrometry sequence database search tool." Eng JK, Jahan TA, Hoopmann MR. Proteomics. 2012 Nov 12. doi: 10.1002/pmic201200439



The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created: