Search parameters (2024.02)

Comet search parameters are defined here. These are valid for Comet version 2024.02.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

Database

CPU threads

num_threads

Masses

Search enzyme

Fragment ions

Fragment-ion index

Output

mzXML/mzML parameters

Misc. parameters

clip_nterm_aa
clip_nterm_methionine
decoy_prefix
digest_mass_range
equal_I_and_L
mass_offsets
max_duplicate_proteins
max_fragment_charge
max_index_runtime
max_precursor_charge
minimum_xcorr
num_results
nucleotide_reading_frame
output_suffix
peff_verbose_output
peptide_length_range
precursor_NL_ions
skip_researching
spectrum_batch_size
text_file_extension
explicit_deltacn
old_mods_encoding
export_additional_pepxml_scores
resolve_fullpaths
pinfile_protein_delimiter
set_X_residue aka set_A_residue through set_Z_residue