Support:

• Comet's Google group. Post your questions, problems, and feature requests here.
• If you would rather not post to this public forum, feel free to e-mail me directly (jke000 at gmail dot com or engj at uw dot edu).

To run Comet, you need one or more input spectral files in mzXML, mzML, mgf, or ms2/cms2 formats and a comet.params file. Then issue a command such as:

• comet.exe input.mzXML
• comet.exe input.mzML
• comet.exe input.mgf
• comet.exe input.ms2
• comet.exe *.ms2 multiple inputs supported

• 2020/12/01: Terminal modification masses.
• 2019/11/04: Quick analysis on search times vs. number of search threads.
• 2019/08/20: Misc. notes on indexed database and real-time search support
• 2019/03/14: Misc. notes on Comet's decoy peptides
• 2017/10/05: Parameter settings for isotopic/isobaric labeling (iTRAQ, TMT, SILAC)
• 2017/09/06: Parameter settings for 15N (and 13C) heavy search
• 2016/06/13: Information I will need when you report a problem/bug
• 2016/03/09: high res vs. low res fragmention comparison on Q Exactive data
• 2016/01/01: Comet parameters info and suggested high-res/low-res settings