num_threads = 8
precursor_mass_tolerance = 500.00
precursor_mass_lower = -20
precursor_mass_upper = 20
precursor_mass_units = 1
precursor_true_tolerance = 20
precursor_true_units = 1
fragment_mass_tolerance = 0.02
fragment_mass_units = 1
isotope_error = 0/1/2
mass_offsets = 0
shifted_ions = 0
shifted_ions_exclude_ranges = (-1.5,3.5)
search_enzyme_name = Trypsin
search_enzyme_cutafter = KR
search_enzyme_butnotafter = P
num_enzyme_termini = 2
allowed_missed_cleavage = 4
clip_nTerm_M = 1
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
# variable_mod_03 = 79.96633 STY
variable_mod_04 = -17.02650 nQnC
# variable_mod_05 = -18.01060 nE
allow_multiple_variable_mods_on_residue = 1
max_variable_mods_per_mod = 3
max_variable_mods_combinations = 5000
output_file_extension = pepXML
output_format = pepXML
output_report_topN = 30
output_max_expect = 30.0
precursor_charge = 2 6
override_charge = 0
digest_min_length = 6
digest_max_length = 50
digest_mass_range = 500.0 5000.0
max_fragment_charge = 2
track_zero_topN = 0
zero_bin_accept_expect = 0
zero_bin_mult_expect = 1
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 100
min_fragments_modelling = 3
min_matched_fragments = 4
minimum_ratio = 0.01
clear_mz_range = 0.0 0.0
add_Cterm_peptide = 0.000000
add_Nterm_peptide = 0.000000
add_Cterm_protein = 0.000000
add_Nterm_protein = 0.000000
add_G_glycine = 0.000000
add_A_alanine = 0.000000
add_S_serine = 0.000000
add_P_proline = 0.000000
add_V_valine = 0.000000
add_T_threonine = 0.000000
# add_C_cysteine = 57.021464
add_L_leucine = 0.000000
add_I_isoleucine = 0.000000
add_N_asparagine = 0.000000
add_D_aspartic_acid = 0.000000
add_Q_glutamine = 0.000000
add_K_lysine = 0.000000
add_E_glutamic_acid = 0.000000
add_M_methionine = 0.000000
add_H_histidine = 0.000000
add_F_phenylalanine = 0.000000
add_R_arginine = 0.000000
add_Y_tyrosine = 0.000000
add_W_tryptophan = 0.000000
add_B_user_amino_acid = 0.000000
add_J_user_amino_acid = 0.000000
add_O_user_amino_acid = 0.000000
add_U_user_amino_acid = 0.000000
add_X_user_amino_acid = 0.000000
add_Z_user_amino_acid = 0.000000
database_name = E:\msgf\RefSeq_Protein_FASTA_9606_20150610.revCat.fasta
fragpipe_ram = 28
variable_mod_06 = 0.98402 dN