Search parameters (2023.01)

Comet search parameters are defined here. These are valid for Comet version 2023.01.X.

Parameters for all versions of Comet can be found here. Entries marked with an * are new parameters. Entries marked with an ** are modified parameters.

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

Search parameters (2023.01)

Database

CPU threads

Masses

Search enzyme

Fragment ions

Output

mzXML/mzML parameters

Misc. parameters

Spectral processing

Variable modifications

Static modifications