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Welcome to the Comet project!

Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool released under the Apache 2.0 license.

Searching uninterpreted tandem mass spectra of peptides against sequence databases is the most common method used to identify peptides and proteins. Since this method was first developed in 1993, many commercial, free, and open source tools have been created over the years that accomplish this task. Although its history goes back two decades, the Comet search engine was first made publicly available in August 2012 on SourceForge under the Apache License, version 2.0. The repository was migrated to GitHub in September 2021.

Comet is multithreaded, supports multiple input and output formats, and binaries are available for both Windows and Linux operating systems. Note that Comet is just a single command line binary that performs MS/MS database search. It takes in spectra in various supported input formats, using the MSToolkit C++ library, and writes .pep.xml, .pin, .sqt and/or .txt files. You will need some other support tool(s) to actually make use of Comet results. Unless you specifically know that you want to use the standalone Comet command line binary available from this repository, you should start with one of the many proteomics software suites that Comet is integrated into.


I know you’re smart. But everyone here is smart. Smart isn’t enough. The kind of people I want on my research team are those who will help everyone feel happy to be here. Randy Pausch, The Last Lecture