Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. 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, and ms2 files. Supported output formats are .out, SQT, and pepXML Documentation and project website: http://comet-ms.sourceforge.net
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