Comet Notes

Support

• The main support venue is via 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.com or engj at uw.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

Miscellaneous Notes

• 2024/10/01: Comet fragment ion index
• 2023/06/13: Linux compile issues
• 2022/02/28: Searching Thermo RAW files supported only under Windows
• 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 decoy peptides
• 2017/10/05: Parameter settings for isotopic/isobaric labeling (iTRAQ, TMT, SILAC)
• 2017/09/06: Parameter settings for N15 (and C13) 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