# comet_version 2019.01 rev. 5
# Comet MS/MS search engine parameters file.
# Everything following the '#' symbol is treated as a comment.
database_name = uniprot-SP_human_CRAP_fwbw_mrgd.fasta
decoy_search = 0
num_threads = 1
peptide_mass_tolerance = 30
peptide_mass_units = 2
mass_type_parent = 1
mass_type_fragment = 1
precursor_tolerance_type = 0
isotope_error = 0
search_enzyme_number = 1
num_enzyme_termini = 2
allowed_missed_cleavage = 0
variable_mod01 = 15.9949 M 0 5 -1 0 0
variable_mod02 = 0.0 X 0 3 -1 0 0
variable_mod03 = 0.0 X 0 3 -1 0 0
variable_mod04 = 0.0 X 0 3 -1 0 0
variable_mod05 = 0.0 X 0 3 -1 0 0
variable_mod06 = 0.0 X 0 3 -1 0 0
variable_mod07 = 0.0 X 0 3 -1 0 0
variable_mod08 = 0.0 X 0 3 -1 0 0
variable_mod09 = 0.0 X 0 3 -1 0 0
max_variable_mods_in_peptide = 5
require_variable_mod = 0
fragment_bin_tol = 0.02
fragment_bin_offset = 0
theoretical_fragment_ions = 0
use_A_ions = 0
use_B_ions = 1
use_C_ions = 0
use_X_ions = 0
use_Y_ions = 1
use_Z_ions = 0
use_NL_ions = 0
output_sqtstream = 0
output_sqtfile = 0
output_txtfile = 0
output_pepxmlfile = 1
output_percolatorfile = 0
output_outfiles = 0
print_expect_score = 1
num_output_lines = 1
show_fragment_ions = 0
sample_enzyme_number = 1
scan_range = 0 0
precursor_charge = 0 0
override_charge = 3
ms_level = 2
activation_method = ALL
digest_mass_range = 600 5000
num_results = 100
skip_researching = 1
max_fragment_charge = 3
max_precursor_charge = 5
nucleotide_reading_frame = 0
clip_nterm_methionine = 0
spectrum_batch_size = 20000
decoy_prefix = --decoysearch-not-used--
output_suffix = 
mass_offsets = 0.0
minimum_peaks = 10
minimum_intensity = 0
remove_precursor_peak = 0
remove_precursor_tolerance = 1.5
clear_mz_range = 0 0
add_C_cysteine = 57.0215
[COMET_ENZYME_INFO]
0.  No_enzyme              0      -           -
1.  Trypsin                1      KR          P
2.  Trypsin/P              1      KR          -
3.  Lys_C                  1      K           P
4.  Lys_N                  0      K           -
5.  Arg_C                  1      R           P
6.  Asp_N                  0      D           -
7.  CNBr                   1      M           -
8.  Glu_C                  1      DE          P
9.  PepsinA                1      FL          P
10. Chymotrypsin           1      FWYL        P