Welcome to the Comet project!

com·et   noun   \ˈkä-mət\

»  a celestial body wth a fuzzy head of ice and dust and characteristic long tail
»  a common variety of fancy goldfish with a deep, forked tail
»  an open source tandem mass spectrometry (MS/MS) sequence database search tool

Comet MS/MS

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. 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 does MS/MS database search. It takes in spectra in some supported input format and writes out .pep.xml, .pin.xml, .sqt and/or .out files. You will need some other support tool(s) to actually make use of Comet results.


  • A Deeper Look into Comet - Implementation and Features. Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ. J Am Soc Mass Spectrom. 2015 Jun 27. doi: 10.1007/s13361-015-1179-x
  • Comet: an open source tandem mass spectrometry sequence database search tool. Eng JK, Jahan TA, Hoopmann MR. Proteomics. 2012 Nov 12. doi: 10.1002/pmic.201200439