...It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases.
Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab-delimited text, Percolator pin, SQT, and pepXML
Documentation and project website: http://comet-ms.sourceforge.net