Search parameters (2014.01)

Comet search parameters are defined here. These are valid for Comet version 2014.01.x.

Parameters for all versions of Comet can be found here.
Entries marked with an * are new parameters.
Entries marked with an ** are redefined compared to previous release.

To generate a comet.params file appropriate for your Comet binary, issue the command "comet -p".
Example comet.params files (primary differences are the MS and MS/MS mass tolerance settings):
●  comet.params.low-low for low res MS1 and low res MS2 e.g. ion trap
●  comet.params.high-low high res MS1 and low res MS2 e.g. Velos-Orbitrap
●  comet.params.high-high high res MS1 and high res MS2 e.g. Q Exactive or Q-Tof

Here's a link to all parameter descriptions on a single web page.


CPU threads


Search enzyme

Fragment ions


mzXML/mzML parameters

Misc. parameters

Spectral processing

Variable modifications

Static modifications