public static string CometParamsToFileContents(CometParams options)
{
var configFile = new StringWriter();
configFile.WriteLine("# comet_version 2013.02 rev. 1");
configFile.WriteLine("# Comet MS/MS search engine parameters file.");
configFile.WriteLine("# Everything following the '#' symbol is treated as a comment.");
configFile.WriteLine("");
configFile.WriteLine("decoy_search = 1 # 0=no (default), 1=concatenated search, 2=separate search");
configFile.WriteLine("");
configFile.WriteLine("num_threads = 0 # 0=poll CPU to set num threads; else specify num threads directly (max 64)");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# masses");
configFile.WriteLine("#");
configFile.WriteLine("peptide_mass_tolerance = {0}", options.PrecursorTolerance.ToString(CultureInfo.InvariantCulture));
configFile.WriteLine("peptide_mass_units = {0} # 0=amu, 1=mmu, 2=ppm", options.PrecursorUnit);
configFile.WriteLine("mass_type_parent = 1 # 0=average masses, 1=monoisotopic masses");
configFile.WriteLine("mass_type_fragment = 1 # 0=average masses, 1=monoisotopic masses");
configFile.WriteLine("precursor_tolerance_type = 1 # 0=MH+ (default), 1=precursor m/z");
configFile.WriteLine("isotope_error = 1 # 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling)");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# search enzyme");
configFile.WriteLine("#");
configFile.WriteLine("search_enzyme_number = {0} # choose from list at end of this params file", options.CleavageAgent);
configFile.WriteLine("num_enzyme_termini = {0} # valid values are 1 (semi-digested), 2 (fully digested, default), 8 N-term, 9 C-term", options.Specificity);
configFile.WriteLine("allowed_missed_cleavage = {0} # maximum value is 5; for enzyme search", options.MaxMissedCleavages);
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# Up to 6 variable modifications are supported");
configFile.WriteLine("# format: <mass> <residues> <0=variable/1=binary> <max mods per a peptide>");
configFile.WriteLine("# e.g. 79.966331 STY 0 3");
configFile.WriteLine("#");
for (var x = 1; x <= 6; x++)
{
if (options.DynamicModifications.Count >= x)
{
configFile.WriteLine("variable_mod{0} = {1} {2} 0 3", x, options.DynamicModifications[x - 1].MassChange.ToString(CultureInfo.InvariantCulture),
options.DynamicModifications[x - 1].Residue);
}
else
{
configFile.WriteLine("variable_mod{0} = 0.0 X 0 3", x);
}
}
configFile.WriteLine("max_variable_mods_in_peptide = {0}", options.MaxMods);
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# fragment ions");
configFile.WriteLine("#");
configFile.WriteLine("# ion trap ms/ms: 1.0005 tolerance, 0.4 offset (mono masses), theoretical_fragment_ions = 1");
configFile.WriteLine("# high res ms/ms: 0.02 tolerance, 0.0 offset (mono masses), theoretical_fragment_ions = 0");
configFile.WriteLine("#");
configFile.WriteLine("fragment_bin_tol = {0} # binning to use on fragment ions", options.FragmentBinTolerance.ToString(CultureInfo.InvariantCulture));
configFile.WriteLine("fragment_bin_offset = {0} # offset position to start the binning (0.0 to 1.0)", options.FragmentBinOffset.ToString(CultureInfo.InvariantCulture));
configFile.WriteLine("theoretical_fragment_ions = 0 # 0=default peak shape, 1=M peak only");
configFile.WriteLine("use_A_ions = 0");
configFile.WriteLine("use_B_ions = 1");
configFile.WriteLine("use_C_ions = 0");
configFile.WriteLine("use_X_ions = 0");
configFile.WriteLine("use_Y_ions = 1");
configFile.WriteLine("use_Z_ions = 0");
configFile.WriteLine("use_NL_ions = 1 # 0=no, 1=yes to consider NH3/H2O neutral loss peaks");
configFile.WriteLine("use_sparse_matrix = 1");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# output");
configFile.WriteLine("#");
configFile.WriteLine("output_sqtstream = 0 # 0=no, 1=yes write sqt to standard output");
configFile.WriteLine("output_sqtfile = 0 # 0=no, 1=yes write sqt file");
configFile.WriteLine("output_txtfile = 0 # 0=no, 1=yes write tab-delimited txt file");
configFile.WriteLine("output_pepxmlfile = 1 # 0=no, 1=yes write pep.xml file");
configFile.WriteLine("output_pinxmlfile = 0 # 0=no, 1=yes write pin.xml file");
configFile.WriteLine("output_outfiles = 0 # 0=no, 1=yes write .out files");
configFile.WriteLine("print_expect_score = 1 # 0=no, 1=yes to replace Sp with expect in out & sqt");
configFile.WriteLine("num_output_lines = 5 # num peptide results to show");
configFile.WriteLine("show_fragment_ions = 0 # 0=no, 1=yes for out files only");
configFile.WriteLine("output_suffix = {0}", options.OutputSuffix);
configFile.WriteLine("");
configFile.WriteLine("sample_enzyme_number = 1 # Sample enzyme which is possibly different than the one applied to the search.");
configFile.WriteLine(" # Used to calculate NTT & NMC in pepXML output (default=1 for trypsin).");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# mzXML parameters");
configFile.WriteLine("#");
configFile.WriteLine("scan_range = 0 0 # start and scan scan range to search; 0 as 1st entry ignores parameter");
configFile.WriteLine("precursor_charge = 0 0 # precursor charge range to analyze; does not override mzXML charge; 0 as 1st entry ignores parameter");
configFile.WriteLine("ms_level = 2 # MS level to analyze, valid are levels 2 (default) or 3");
configFile.WriteLine("activation_method = ALL # activation method; used if activation method set; allowed ALL, CID, ECD, ETD, PQD, HCD, IRMPD");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# misc parameters");
configFile.WriteLine("#");
configFile.WriteLine("digest_mass_range = 600.0 5000.0 # MH+ peptide mass range to analyze");
configFile.WriteLine("num_results = 5 # number of search hits to store internally");
configFile.WriteLine("skip_researching = 1 # for '.out' file output only, 0=search everything again (default), 1=don't search if .out exists");
configFile.WriteLine("max_fragment_charge = 3 # set maximum fragment charge state to analyze (allowed max 5)");
configFile.WriteLine("max_precursor_charge = 6 # set maximum precursor charge state to analyze (allowed max 9)");
configFile.WriteLine("nucleotide_reading_frame = 0 # 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six");
configFile.WriteLine("clip_nterm_methionine = 0 # 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine");
configFile.WriteLine("spectrum_batch_size = 8000 # max. # of spectra to search at a time; 0 to search the entire scan range in one loop");
configFile.WriteLine("decoy_prefix = XXX_ # decoy entries are denoted by this string which is pre-pended to each protein accession");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# spectral processing");
configFile.WriteLine("#");
configFile.WriteLine("minimum_peaks = 10 # required minimum number of peaks in spectrum to search");
configFile.WriteLine("minimum_intensity = 0 # minimum intensity value to read in");
configFile.WriteLine("remove_precursor_peak = 0 # 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD)");
configFile.WriteLine("remove_precursor_tolerance = 1.5 # +- Da tolerance for precursor removal");
configFile.WriteLine("clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# additional modifications");
configFile.WriteLine("#");
configFile.WriteLine("");
configFile.WriteLine("variable_C_terminus = 0.0");
configFile.WriteLine("variable_N_terminus = 0.0");
configFile.WriteLine("variable_C_terminus_distance = -1 # -1=all peptides, 0=protein terminus, 1-N = maximum offset from C-terminus");
configFile.WriteLine("variable_N_terminus_distance = -1 # -1=all peptides, 0=protein terminus, 1-N = maximum offset from N-terminus");
configFile.WriteLine("");
configFile.WriteLine("add_Cterm_peptide = 0.0");
configFile.WriteLine("add_Nterm_peptide = 0.0");
configFile.WriteLine("add_Cterm_protein = 0.0");
configFile.WriteLine("add_Nterm_protein = 0.0");
configFile.WriteLine("");
configFile.WriteLine("add_G_glycine = 0.0000 # added to G - avg. 57.0513, mono. 57.02146");
configFile.WriteLine("add_A_alanine = 0.0000 # added to A - avg. 71.0779, mono. 71.03711");
configFile.WriteLine("add_S_serine = 0.0000 # added to S - avg. 87.0773, mono. 87.03203");
configFile.WriteLine("add_P_proline = 0.0000 # added to P - avg. 97.1152, mono. 97.05276");
configFile.WriteLine("add_V_valine = 0.0000 # added to V - avg. 99.1311, mono. 99.06841");
configFile.WriteLine("add_T_threonine = 0.0000 # added to T - avg. 101.1038, mono. 101.04768");
configFile.WriteLine("add_C_cysteine = {0} # added to C - avg. 103.1429, mono. 103.00918", options.StaticCysteineMod.ToString(CultureInfo.InvariantCulture));
configFile.WriteLine("add_L_leucine = 0.0000 # added to L - avg. 113.1576, mono. 113.08406");
configFile.WriteLine("add_I_isoleucine = 0.0000 # added to I - avg. 113.1576, mono. 113.08406");
configFile.WriteLine("add_N_asparagine = 0.0000 # added to N - avg. 114.1026, mono. 114.04293");
configFile.WriteLine("add_D_aspartic_acid = 0.0000 # added to D - avg. 115.0874, mono. 115.02694");
configFile.WriteLine("add_Q_glutamine = 0.0000 # added to Q - avg. 128.1292, mono. 128.05858");
configFile.WriteLine("add_K_lysine = 0.0000 # added to K - avg. 128.1723, mono. 128.09496");
configFile.WriteLine("add_E_glutamic_acid = 0.0000 # added to E - avg. 129.1140, mono. 129.04259");
configFile.WriteLine("add_M_methionine = 0.0000 # added to M - avg. 131.1961, mono. 131.04048");
configFile.WriteLine("add_O_ornithine = 0.0000 # added to O - avg. 132.1610, mono 132.08988");
configFile.WriteLine("add_H_histidine = 0.0000 # added to H - avg. 137.1393, mono. 137.05891");
configFile.WriteLine("add_F_phenylalanine = 0.0000 # added to F - avg. 147.1739, mono. 147.06841");
configFile.WriteLine("add_R_arginine = 0.0000 # added to R - avg. 156.1857, mono. 156.10111");
configFile.WriteLine("add_Y_tyrosine = 0.0000 # added to Y - avg. 163.0633, mono. 163.06333");
configFile.WriteLine("add_W_tryptophan = 0.0000 # added to W - avg. 186.0793, mono. 186.07931");
configFile.WriteLine("add_B_user_amino_acid = 0.0000 # added to B - avg. 0.0000, mono. 0.00000");
configFile.WriteLine("add_J_user_amino_acid = 0.0000 # added to J - avg. 0.0000, mono. 0.00000");
configFile.WriteLine("add_U_user_amino_acid = 0.0000 # added to U - avg. 0.0000, mono. 0.00000");
configFile.WriteLine("add_X_user_amino_acid = 0.0000 # added to X - avg. 0.0000, mono. 0.00000");
configFile.WriteLine("add_Z_user_amino_acid = 0.0000 # added to Z - avg. 0.0000, mono. 0.00000");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# COMET_ENZYME_INFO _must_ be at the end of this parameters file");
configFile.WriteLine("#");
configFile.WriteLine("[COMET_ENZYME_INFO]");
configFile.WriteLine("0. No_enzyme 0 - -");
configFile.WriteLine("1. Trypsin 1 KR P");
configFile.WriteLine("2. Trypsin/P 1 KR -");
configFile.WriteLine("3. Lys_C 1 K P");
configFile.WriteLine("4. Lys_N 0 K -");
configFile.WriteLine("5. Arg_C 1 R P");
configFile.WriteLine("6. Asp_N 0 D -");
configFile.WriteLine("7. CNBr 1 M -");
configFile.WriteLine("8. Glu_C 1 DE P");
configFile.WriteLine("9. PepsinA 1 FL P");
configFile.WriteLine("10. Chymotrypsin 1 FWYL P");
configFile.WriteLine("");
return(configFile.ToString());
}
public static CometParams FileContentsToCometParams(string fileContents)
{
var config = CometParams.GetIonTrapParams();
var fileLines = fileContents.Split(Environment.NewLine.ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
var rx = new Regex(@"^([\w]+)\s*=\s*([\w\s\.]+)");
foreach (var nextLine in fileLines)
{
if (!rx.IsMatch(nextLine))
{
continue;
}
var match = rx.Match(nextLine);
if (match.Groups.Count < 3)
{
continue;
}
double nextNumber;
var validNumber = double.TryParse(match.Groups[2].Value, out nextNumber);
switch (match.Groups[1].Value)
{
case "peptide_mass_tolerance":
if (!validNumber)
{
break;
}
config.PrecursorTolerance = nextNumber;
break;
case "peptide_mass_units":
if (!validNumber)
{
break;
}
config.PrecursorUnit = (int)nextNumber;
break;
case "search_enzyme_number":
if (!validNumber)
{
break;
}
config.CleavageAgent = (int)nextNumber;
break;
case "num_enzyme_termini":
if (!validNumber)
{
break;
}
config.Specificity = (int)nextNumber;
break;
case "allowed_missed_cleavage":
if (!validNumber)
{
break;
}
config.MaxMissedCleavages = (int)nextNumber;
break;
case "max_variable_mods_in_peptide":
if (!validNumber)
{
break;
}
config.MaxMods = (int)nextNumber;
break;
case "fragment_bin_tol":
if (!validNumber)
{
break;
}
config.FragmentBinTolerance = nextNumber;
break;
case "fragment_bin_offset":
if (!validNumber)
{
break;
}
config.FragmentBinOffset = nextNumber;
break;
case "add_C_cysteine":
if (!validNumber)
{
break;
}
config.StaticCysteineMod = nextNumber;
break;
}
if (match.Groups[1].Value.StartsWith("variable_mod"))
{
var splitValue = match.Groups[2].Value.Split(" ".ToCharArray(),
StringSplitOptions.RemoveEmptyEntries);
if (splitValue.Length < 4)
{
continue;
}
double massShift;
if (!double.TryParse(splitValue[0], out massShift))
{
continue;
}
config.DynamicModifications.Add(new CometParams.Modification(splitValue[1], massShift));
}
}
return(config);
}
public static string CometParamsToFileContents(CometParams options)
{
var configFile = new StringWriter();
configFile.WriteLine("# comet_version 2013.02 rev. 1");
configFile.WriteLine("# Comet MS/MS search engine parameters file.");
configFile.WriteLine("# Everything following the '#' symbol is treated as a comment.");
configFile.WriteLine("");
configFile.WriteLine("decoy_search = 1 # 0=no (default), 1=concatenated search, 2=separate search");
configFile.WriteLine("");
configFile.WriteLine("num_threads = 0 # 0=poll CPU to set num threads; else specify num threads directly (max 64)");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# masses");
configFile.WriteLine("#");
configFile.WriteLine("peptide_mass_tolerance = {0}",options.PrecursorTolerance.ToString(CultureInfo.InvariantCulture));
configFile.WriteLine("peptide_mass_units = {0} # 0=amu, 1=mmu, 2=ppm",options.PrecursorUnit);
configFile.WriteLine("mass_type_parent = 1 # 0=average masses, 1=monoisotopic masses");
configFile.WriteLine("mass_type_fragment = 1 # 0=average masses, 1=monoisotopic masses");
configFile.WriteLine("precursor_tolerance_type = 1 # 0=MH+ (default), 1=precursor m/z");
configFile.WriteLine("isotope_error = 1 # 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling)");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# search enzyme");
configFile.WriteLine("#");
configFile.WriteLine("search_enzyme_number = {0} # choose from list at end of this params file", options.CleavageAgent);
configFile.WriteLine("num_enzyme_termini = {0} # valid values are 1 (semi-digested), 2 (fully digested, default), 8 N-term, 9 C-term",options.Specificity);
configFile.WriteLine("allowed_missed_cleavage = {0} # maximum value is 5; for enzyme search",options.MaxMissedCleavages);
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# Up to 6 variable modifications are supported");
configFile.WriteLine("# format: <mass> <residues> <0=variable/1=binary> <max mods per a peptide>");
configFile.WriteLine("# e.g. 79.966331 STY 0 3");
configFile.WriteLine("#");
for (var x = 1; x <= 6; x++)
if (options.DynamicModifications.Count >= x)
configFile.WriteLine("variable_mod{0} = {1} {2} 0 3", x, options.DynamicModifications[x - 1].MassChange.ToString(CultureInfo.InvariantCulture),
options.DynamicModifications[x-1].Residue);
else
configFile.WriteLine("variable_mod{0} = 0.0 X 0 3", x);
configFile.WriteLine("max_variable_mods_in_peptide = {0}",options.MaxMods);
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# fragment ions");
configFile.WriteLine("#");
configFile.WriteLine("# ion trap ms/ms: 1.0005 tolerance, 0.4 offset (mono masses), theoretical_fragment_ions = 1");
configFile.WriteLine("# high res ms/ms: 0.02 tolerance, 0.0 offset (mono masses), theoretical_fragment_ions = 0");
configFile.WriteLine("#");
configFile.WriteLine("fragment_bin_tol = {0} # binning to use on fragment ions", options.FragmentBinTolerance.ToString(CultureInfo.InvariantCulture));
configFile.WriteLine("fragment_bin_offset = {0} # offset position to start the binning (0.0 to 1.0)", options.FragmentBinOffset.ToString(CultureInfo.InvariantCulture));
configFile.WriteLine("theoretical_fragment_ions = 0 # 0=default peak shape, 1=M peak only");
configFile.WriteLine("use_A_ions = 0");
configFile.WriteLine("use_B_ions = 1");
configFile.WriteLine("use_C_ions = 0");
configFile.WriteLine("use_X_ions = 0");
configFile.WriteLine("use_Y_ions = 1");
configFile.WriteLine("use_Z_ions = 0");
configFile.WriteLine("use_NL_ions = 1 # 0=no, 1=yes to consider NH3/H2O neutral loss peaks");
configFile.WriteLine("use_sparse_matrix = 1");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# output");
configFile.WriteLine("#");
configFile.WriteLine("output_sqtstream = 0 # 0=no, 1=yes write sqt to standard output");
configFile.WriteLine("output_sqtfile = 0 # 0=no, 1=yes write sqt file");
configFile.WriteLine("output_txtfile = 0 # 0=no, 1=yes write tab-delimited txt file");
configFile.WriteLine("output_pepxmlfile = 1 # 0=no, 1=yes write pep.xml file");
configFile.WriteLine("output_pinxmlfile = 0 # 0=no, 1=yes write pin.xml file");
configFile.WriteLine("output_outfiles = 0 # 0=no, 1=yes write .out files");
configFile.WriteLine("print_expect_score = 1 # 0=no, 1=yes to replace Sp with expect in out & sqt");
configFile.WriteLine("num_output_lines = 5 # num peptide results to show");
configFile.WriteLine("show_fragment_ions = 0 # 0=no, 1=yes for out files only");
configFile.WriteLine("output_suffix = {0}", options.OutputSuffix);
configFile.WriteLine("");
configFile.WriteLine("sample_enzyme_number = 1 # Sample enzyme which is possibly different than the one applied to the search.");
configFile.WriteLine(" # Used to calculate NTT & NMC in pepXML output (default=1 for trypsin).");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# mzXML parameters");
configFile.WriteLine("#");
configFile.WriteLine("scan_range = 0 0 # start and scan scan range to search; 0 as 1st entry ignores parameter");
configFile.WriteLine("precursor_charge = 0 0 # precursor charge range to analyze; does not override mzXML charge; 0 as 1st entry ignores parameter");
configFile.WriteLine("ms_level = 2 # MS level to analyze, valid are levels 2 (default) or 3");
configFile.WriteLine("activation_method = ALL # activation method; used if activation method set; allowed ALL, CID, ECD, ETD, PQD, HCD, IRMPD");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# misc parameters");
configFile.WriteLine("#");
configFile.WriteLine("digest_mass_range = 600.0 5000.0 # MH+ peptide mass range to analyze");
configFile.WriteLine("num_results = 5 # number of search hits to store internally");
configFile.WriteLine("skip_researching = 1 # for '.out' file output only, 0=search everything again (default), 1=don't search if .out exists");
configFile.WriteLine("max_fragment_charge = 3 # set maximum fragment charge state to analyze (allowed max 5)");
configFile.WriteLine("max_precursor_charge = 6 # set maximum precursor charge state to analyze (allowed max 9)");
configFile.WriteLine("nucleotide_reading_frame = 0 # 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six");
configFile.WriteLine("clip_nterm_methionine = 0 # 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine");
configFile.WriteLine("spectrum_batch_size = 8000 # max. # of spectra to search at a time; 0 to search the entire scan range in one loop");
configFile.WriteLine("decoy_prefix = XXX_ # decoy entries are denoted by this string which is pre-pended to each protein accession");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# spectral processing");
configFile.WriteLine("#");
configFile.WriteLine("minimum_peaks = 10 # required minimum number of peaks in spectrum to search");
configFile.WriteLine("minimum_intensity = 0 # minimum intensity value to read in");
configFile.WriteLine("remove_precursor_peak = 0 # 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD)");
configFile.WriteLine("remove_precursor_tolerance = 1.5 # +- Da tolerance for precursor removal");
configFile.WriteLine("clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# additional modifications");
configFile.WriteLine("#");
configFile.WriteLine("");
configFile.WriteLine("variable_C_terminus = 0.0");
configFile.WriteLine("variable_N_terminus = 0.0");
configFile.WriteLine("variable_C_terminus_distance = -1 # -1=all peptides, 0=protein terminus, 1-N = maximum offset from C-terminus");
configFile.WriteLine("variable_N_terminus_distance = -1 # -1=all peptides, 0=protein terminus, 1-N = maximum offset from N-terminus");
configFile.WriteLine("");
configFile.WriteLine("add_Cterm_peptide = 0.0");
configFile.WriteLine("add_Nterm_peptide = 0.0");
configFile.WriteLine("add_Cterm_protein = 0.0");
configFile.WriteLine("add_Nterm_protein = 0.0");
configFile.WriteLine("");
configFile.WriteLine("add_G_glycine = 0.0000 # added to G - avg. 57.0513, mono. 57.02146");
configFile.WriteLine("add_A_alanine = 0.0000 # added to A - avg. 71.0779, mono. 71.03711");
configFile.WriteLine("add_S_serine = 0.0000 # added to S - avg. 87.0773, mono. 87.03203");
configFile.WriteLine("add_P_proline = 0.0000 # added to P - avg. 97.1152, mono. 97.05276");
configFile.WriteLine("add_V_valine = 0.0000 # added to V - avg. 99.1311, mono. 99.06841");
configFile.WriteLine("add_T_threonine = 0.0000 # added to T - avg. 101.1038, mono. 101.04768");
configFile.WriteLine("add_C_cysteine = {0} # added to C - avg. 103.1429, mono. 103.00918", options.StaticCysteineMod.ToString(CultureInfo.InvariantCulture));
configFile.WriteLine("add_L_leucine = 0.0000 # added to L - avg. 113.1576, mono. 113.08406");
configFile.WriteLine("add_I_isoleucine = 0.0000 # added to I - avg. 113.1576, mono. 113.08406");
configFile.WriteLine("add_N_asparagine = 0.0000 # added to N - avg. 114.1026, mono. 114.04293");
configFile.WriteLine("add_D_aspartic_acid = 0.0000 # added to D - avg. 115.0874, mono. 115.02694");
configFile.WriteLine("add_Q_glutamine = 0.0000 # added to Q - avg. 128.1292, mono. 128.05858");
configFile.WriteLine("add_K_lysine = 0.0000 # added to K - avg. 128.1723, mono. 128.09496");
configFile.WriteLine("add_E_glutamic_acid = 0.0000 # added to E - avg. 129.1140, mono. 129.04259");
configFile.WriteLine("add_M_methionine = 0.0000 # added to M - avg. 131.1961, mono. 131.04048");
configFile.WriteLine("add_O_ornithine = 0.0000 # added to O - avg. 132.1610, mono 132.08988");
configFile.WriteLine("add_H_histidine = 0.0000 # added to H - avg. 137.1393, mono. 137.05891");
configFile.WriteLine("add_F_phenylalanine = 0.0000 # added to F - avg. 147.1739, mono. 147.06841");
configFile.WriteLine("add_R_arginine = 0.0000 # added to R - avg. 156.1857, mono. 156.10111");
configFile.WriteLine("add_Y_tyrosine = 0.0000 # added to Y - avg. 163.0633, mono. 163.06333");
configFile.WriteLine("add_W_tryptophan = 0.0000 # added to W - avg. 186.0793, mono. 186.07931");
configFile.WriteLine("add_B_user_amino_acid = 0.0000 # added to B - avg. 0.0000, mono. 0.00000");
configFile.WriteLine("add_J_user_amino_acid = 0.0000 # added to J - avg. 0.0000, mono. 0.00000");
configFile.WriteLine("add_U_user_amino_acid = 0.0000 # added to U - avg. 0.0000, mono. 0.00000");
configFile.WriteLine("add_X_user_amino_acid = 0.0000 # added to X - avg. 0.0000, mono. 0.00000");
configFile.WriteLine("add_Z_user_amino_acid = 0.0000 # added to Z - avg. 0.0000, mono. 0.00000");
configFile.WriteLine("");
configFile.WriteLine("#");
configFile.WriteLine("# COMET_ENZYME_INFO _must_ be at the end of this parameters file");
configFile.WriteLine("#");
configFile.WriteLine("[COMET_ENZYME_INFO]");
configFile.WriteLine("0. No_enzyme 0 - -");
configFile.WriteLine("1. Trypsin 1 KR P");
configFile.WriteLine("2. Trypsin/P 1 KR -");
configFile.WriteLine("3. Lys_C 1 K P");
configFile.WriteLine("4. Lys_N 0 K -");
configFile.WriteLine("5. Arg_C 1 R P");
configFile.WriteLine("6. Asp_N 0 D -");
configFile.WriteLine("7. CNBr 1 M -");
configFile.WriteLine("8. Glu_C 1 DE P");
configFile.WriteLine("9. PepsinA 1 FL P");
configFile.WriteLine("10. Chymotrypsin 1 FWYL P");
configFile.WriteLine("");
return configFile.ToString();
}