/// returns false on failure
void translateModifications(StringList& static_mod_list, StringList& variable_mod_list)
{
// translating UNIMOD notation to MyriMatch notation of PTMs.
ModificationDefinitionsSet mod_set(getStringList_("fixed_modifications"), getStringList_("variable_modifications"));
if (!getStringList_("fixed_modifications").empty())
{
set<String> mod_names = mod_set.getFixedModificationNames();
for (set<String>::const_iterator it = mod_names.begin(); it != mod_names.end(); ++it)
{
ResidueModification mod = ModificationsDB::getInstance()->getModification(*it);
String origin = String(mod.getOrigin());
String mass_diff = String(mod.getDiffMonoMass());
if (origin == "N-term")
{
origin = "(";
}
else if (origin == "C-term")
{
origin = ")";
}
else if (mod.getTermSpecificityName(mod.getTermSpecificity()) == "N-term")
{
origin = "(" + origin;
}
else if (mod.getTermSpecificityName(mod.getTermSpecificity()) == "C-term")
{
origin = ")" + origin;
}
static_mod_list.push_back(origin + " " + mod.getDiffMonoMass());
}
}
if (!getStringList_("variable_modifications").empty())
{
set<String> mod_names = mod_set.getVariableModificationNames();
for (set<String>::const_iterator it = mod_names.begin(); it != mod_names.end(); ++it)
{
ResidueModification mod = ModificationsDB::getInstance()->getModification(*it);
String origin = String(mod.getOrigin());
String mass_diff = String(mod.getDiffMonoMass());
if (origin == "N-term")
{
origin = "(";
}
else if (origin == "C-term")
{
origin = ")";
}
else if (mod.getTermSpecificityName(mod.getTermSpecificity()) == "N-term")
{
origin = "(" + origin;
}
else if (mod.getTermSpecificityName(mod.getTermSpecificity()) == "C-term")
{
origin = ")" + origin;
}
variable_mod_list.push_back(origin + " * " + mass_diff); // use * for all mods (no unique-per-mod symbol should be required)
}
}
}
void createParamFile_(ostream& os)
{
os << "# comet_version " << getStringOption_("comet_version") << "\n"; //required as first line in the param file
os << "# Comet MS/MS search engine parameters file.\n";
os << "# Everything following the '#' symbol is treated as a comment.\n";
os << "database_name = " << getStringOption_("database") << "\n";
os << "decoy_search = " << 0 << "\n"; // 0=no (default), 1=concatenated search, 2=separate search
os << "num_threads = " << getIntOption_("threads") << "\n"; // 0=poll CPU to set num threads; else specify num threads directly (max 64)
// masses
map<String,int> precursor_error_units;
precursor_error_units["amu"] = 0;
precursor_error_units["mmu"] = 1;
precursor_error_units["ppm"] = 2;
map<string,int> isotope_error;
isotope_error["off"] = 0;
isotope_error["-1/0/1/2/3"] = 1;
isotope_error["-8/-4/0/4/8"] = 2;
os << "peptide_mass_tolerance = " << getDoubleOption_("precursor_mass_tolerance") << "\n";
os << "peptide_mass_units = " << precursor_error_units[getStringOption_("precursor_error_units")] << "\n"; // 0=amu, 1=mmu, 2=ppm
os << "mass_type_parent = " << 1 << "\n"; // 0=average masses, 1=monoisotopic masses
os << "mass_type_fragment = " << 1 << "\n"; // 0=average masses, 1=monoisotopic masses
os << "precursor_tolerance_type = " << 0 << "\n"; // 0=MH+ (default), 1=precursor m/z; only valid for amu/mmu tolerances
os << "isotope_error = " << isotope_error[getStringOption_("isotope_error")] << "\n"; // 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling)
// search enzyme
String enzyme_name = getStringOption_("enzyme");
String enzyme_number = String(ProteaseDB::getInstance()->getEnzyme(enzyme_name)->getCometID());
map<string,int> num_enzyme_termini;
num_enzyme_termini["semi"] = 1;
num_enzyme_termini["fully"] = 2;
num_enzyme_termini["C-term unspecific"] = 8;
num_enzyme_termini["N-term unspecific"] = 9;
os << "search_enzyme_number = " << enzyme_number << "\n"; // choose from list at end of this params file
os << "num_enzyme_termini = " << num_enzyme_termini[getStringOption_("num_enzyme_termini")] << "\n"; // 1 (semi-digested), 2 (fully digested, default), 8 C-term unspecific , 9 N-term unspecific
os << "allowed_missed_cleavage = " << getIntOption_("allowed_missed_cleavages") << "\n"; // maximum value is 5; for enzyme search
// Up to 9 variable modifications are supported
// format: <mass> <residues> <0=variable/else binary> <max_mods_per_peptide> <term_distance> <n/c-term> <required>
// e.g. 79.966331 STY 0 3 -1 0 0
vector<String> variable_modifications_names = getStringList_("variable_modifications");
vector<ResidueModification> variable_modifications = getModifications_(variable_modifications_names);
if (variable_modifications.size() > 9)
{
throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Error: Comet only supports 9 variable modifications. " + String(variable_modifications.size()) + " provided.");
}
int max_variable_mods_in_peptide = getIntOption_("max_variable_mods_in_peptide");
Size var_mod_index = 0;
// write out user specified modifications
for (; var_mod_index < variable_modifications.size(); ++var_mod_index)
{
const ResidueModification mod = variable_modifications[var_mod_index];
double mass = mod.getDiffMonoMass();
String residues = mod.getOrigin();
//TODO support binary groups, e.g. for SILAC
int binary_group = 0;
//TODO support mod-specific limit (default for now is the overall max per peptide)
int max_current_mod_per_peptide = max_variable_mods_in_peptide;
//TODO support term-distances?
int term_distance = -1;
int nc_term = 0;
//TODO support agglomeration of Modifications to same AA. Watch out for nc_term value then.
if (mod.getTermSpecificity() == ResidueModification::C_TERM)
{
residues = "c";
term_distance = 0;
// Since users need to specify mods that apply to multiple residues/terms separately
// 3 and -1 should be equal for now.
nc_term = 3;
}
else if (mod.getTermSpecificity() == ResidueModification::N_TERM)
{
residues = "n";
term_distance = 0;
// Since users need to specify mods that apply to multiple residues/terms separately
// 2 and -1 should be equal for now.
nc_term = 2;
}
else if (mod.getTermSpecificity() == ResidueModification::PROTEIN_N_TERM) // not yet available
{
term_distance = 0;
nc_term = 0;
}
else if (mod.getTermSpecificity() == ResidueModification::PROTEIN_C_TERM) // not yet available
{
term_distance = 0;
nc_term = 1;
}
//TODO support required variable mods
bool required = false;
os << "variable_mod0" << var_mod_index+1 << " = " << mass << " " << residues << " " << binary_group << " " << max_current_mod_per_peptide << " " << term_distance << " " << nc_term << " " << required << "\n";
}
// fill remaining modification slots (if any) in Comet with "no modification"
for (; var_mod_index < 9; ++var_mod_index)
{
os << "variable_mod0" << var_mod_index+1 << " = " << "0.0 X 0 3 -1 0 0" << "\n";
}
os << "max_variable_mods_in_peptide = " << getIntOption_("max_variable_mods_in_peptide") << "\n";
os << "require_variable_mod = " << (int) (getStringOption_("require_variable_mod") == "true") << "\n";
// fragment ion defaults
// ion trap ms/ms: 1.0005 tolerance, 0.4 offset (mono masses), theoretical_fragment_ions = 1
// high res ms/ms: 0.02 tolerance, 0.0 offset (mono masses), theoretical_fragment_ions = 0
String instrument = getStringOption_("instrument");
double bin_tol = getDoubleOption_("fragment_bin_tolerance");
double bin_offset = getDoubleOption_("fragment_bin_offset");
if (instrument == "low_res" && (bin_tol < 0.9 || bin_offset <= 0.2))
{
LOG_WARN << "Fragment bin size or tolerance is quite low for low res instruments." << "\n";
}
else if (instrument == "high_res" && (bin_tol > 0.2 || bin_offset > 0.1))
{
LOG_WARN << "Fragment bin size or tolerance is quite high for high res instruments." << "\n";
};
os << "fragment_bin_tol = " << bin_tol << "\n"; // binning to use on fragment ions
os << "fragment_bin_offset = " << bin_offset << "\n"; // offset position to start the binning (0.0 to 1.0)
os << "theoretical_fragment_ions = " << (int)(instrument == "low_res") << "\n"; // 0=use flanking bin, 1=use M bin only
os << "use_A_ions = " << (int)(getStringOption_("use_A_ions")=="true") << "\n";
os << "use_B_ions = " << (int)(getStringOption_("use_B_ions")=="true") << "\n";
os << "use_C_ions = " << (int)(getStringOption_("use_C_ions")=="true") << "\n";
os << "use_X_ions = " << (int)(getStringOption_("use_X_ions")=="true") << "\n";
os << "use_Y_ions = " << (int)(getStringOption_("use_Y_ions")=="true") << "\n";
os << "use_Z_ions = " << (int)(getStringOption_("use_Z_ions")=="true") << "\n";
os << "use_NL_ions = " << (int)(getStringOption_("use_NL_ions")=="true") << "\n"; // 0=no, 1=yes to consider NH3/H2O neutral loss peaks
// output
os << "output_sqtstream = " << 0 << "\n"; // 0=no, 1=yes write sqt to standard output
os << "output_sqtfile = " << 0 << "\n"; // 0=no, 1=yes write sqt file
os << "output_txtfile = " << 0 << "\n"; // 0=no, 1=yes write tab-delimited txt file
os << "output_pepxmlfile = " << 1 << "\n"; // 0=no, 1=yes write pep.xml file
os << "output_percolatorfile = " << !getStringOption_("pin_out").empty() << "\n"; // 0=no, 1=yes write Percolator tab-delimited input file
os << "output_outfiles = " << 0 << "\n"; // 0=no, 1=yes write .out files
os << "print_expect_score = " << 1 << "\n"; // 0=no, 1=yes to replace Sp with expect in out & sqt
os << "num_output_lines = " << getIntOption_("num_hits") << "\n"; // num peptide results to show
os << "show_fragment_ions = " << 0 << "\n"; // 0=no, 1=yes for out files only
os << "sample_enzyme_number = " << enzyme_number << "\n"; // Sample enzyme which is possibly different than the one applied to the search.
// mzXML parameters
map<string,int> override_charge;
override_charge["keep any known"] = 0;
override_charge["ignore known"] = 1;
override_charge["ignore outside range"] = 2;
override_charge["keep known search unknown"] = 3;
int precursor_charge_min(0), precursor_charge_max(0);
if (!parseRange_(getStringOption_("precursor_charge"), precursor_charge_min, precursor_charge_max))
{
LOG_INFO << "precursor_charge range not set. Defaulting to 0:0 (disable charge filtering)." << endl;
}
os << "scan_range = " << "0 0" << "\n"; // start and scan scan range to search; 0 as 1st entry ignores parameter
os << "precursor_charge = " << precursor_charge_min << " " << precursor_charge_max << "\n"; // precursor charge range to analyze; does not override any existing charge; 0 as 1st entry ignores parameter
os << "override_charge = " << override_charge[getStringOption_("override_charge")] << "\n"; // 0=no, 1=override precursor charge states, 2=ignore precursor charges outside precursor_charge range, 3=see online
os << "ms_level = " << getIntOption_("ms_level") << "\n"; // MS level to analyze, valid are levels 2 (default) or 3
os << "activation_method = " << getStringOption_("activation_method") << "\n"; // activation method; used if activation method set; allowed ALL, CID, ECD, ETD, PQD, HCD, IRMPD
// misc parameters
double digest_mass_range_min(600.0), digest_mass_range_max(5000.0);
if (!parseRange_(getStringOption_("digest_mass_range"), digest_mass_range_min, digest_mass_range_max))
{
LOG_INFO << "digest_mass_range not set. Defaulting to 600.0 5000.0." << endl;
}
os << "digest_mass_range = " << digest_mass_range_min << " " << digest_mass_range_max << "\n"; // MH+ peptide mass range to analyze
os << "num_results = " << 100 << "\n"; // number of search hits to store internally
os << "skip_researching = " << 1 << "\n"; // for '.out' file output only, 0=search everything again (default), 1=don't search if .out exists
os << "max_fragment_charge = " << getIntOption_("max_fragment_charge") << "\n"; // set maximum fragment charge state to analyze (allowed max 5)
os << "max_precursor_charge = " << getIntOption_("max_precursor_charge") << "\n"; // set maximum precursor charge state to analyze (allowed max 9)
os << "nucleotide_reading_frame = " << 0 << "\n"; // 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six
os << "clip_nterm_methionine = " << (int)(getStringOption_("clip_nterm_methionine")=="true") << "\n"; // 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine
os << "spectrum_batch_size = " << getIntOption_("spectrum_batch_size") << "\n"; // max. // of spectra to search at a time; 0 to search the entire scan range in one loop
os << "decoy_prefix = " << "--decoysearch-not-used--" << "\n"; // decoy entries are denoted by this string which is pre-pended to each protein accession
os << "output_suffix = " << "" << "\n"; // add a suffix to output base names i.e. suffix "-C" generates base-C.pep.xml from base.mzXML input
os << "mass_offsets = " << ListUtils::concatenate(getDoubleList_("mass_offsets"), " ") << "\n"; // one or more mass offsets to search (values subtracted from deconvoluted precursor mass)
// spectral processing
map<string,int> remove_precursor_peak;
remove_precursor_peak["no"] = 0;
remove_precursor_peak["yes"] = 1;
remove_precursor_peak["charge_reduced"] = 2;
remove_precursor_peak["phosphate_loss"] = 3;
double clear_mz_range_min(0.0), clear_mz_range_max(0.0);
if (!parseRange_(getStringOption_("clear_mz_range"), clear_mz_range_min, clear_mz_range_max))
{
LOG_INFO << "clear_mz_range not set. Defaulting to 0:0 (disable m/z filter)." << endl;
}
os << "minimum_peaks = " << getIntOption_("minimum_peaks") << "\n"; // required minimum number of peaks in spectrum to search (default 10)
os << "minimum_intensity = " << getDoubleOption_("minimum_intensity") << "\n"; // minimum intensity value to read in
os << "remove_precursor_peak = " << remove_precursor_peak[getStringOption_("remove_precursor_peak")] << "\n"; // 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD)
os << "remove_precursor_tolerance = " << getDoubleOption_("remove_precursor_tolerance") << "\n"; // +- Da tolerance for precursor removal
os << "clear_mz_range = " << clear_mz_range_min << " " << clear_mz_range_max << "\n"; // for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range
// write fixed modifications - if not specified residue parameter is zero
// Aminoacid:
// add_AA.OneletterCode_AA.ThreeLetterCode = xxx
// Terminus:
// add_N/Cterm_peptide = xxx protein not available yet
vector<String> fixed_modifications_names = getStringList_("fixed_modifications");
vector<ResidueModification> fixed_modifications = getModifications_(fixed_modifications_names);
// Comet sets Carbamidometyl (C) as modification as default even if not specified
// Therefor there is the need to set it to 0 if not set as flag
if (fixed_modifications.empty())
{
os << "add_C_cysteine = 0.0000" << endl;
}
else
{
for (vector<ResidueModification>::const_iterator it = fixed_modifications.begin(); it != fixed_modifications.end(); ++it)
{
String AA = it->getOrigin();
if ((AA!="N-term") && (AA!="C-term"))
{
const Residue* r = ResidueDB::getInstance()->getResidue(AA);
String name = r->getName();
os << "add_" << r->getOneLetterCode() << "_" << name.toLower() << " = " << it->getDiffMonoMass() << endl;
}
else
{
os << "add_" << AA.erase(1,1) << "_peptide = " << it->getDiffMonoMass() << endl;
}
}
}
//TODO register cut_before and cut_after in Enzymes.xml plus datastructures to add all our Enzymes with our names instead.
// COMET_ENZYME_INFO _must_ be at the end of this parameters file
os << "[COMET_ENZYME_INFO]" << "\n";
os << "0. No_enzyme 0 - -" << "\n";
os << "1. Trypsin 1 KR P" << "\n";
os << "2. Trypsin/P 1 KR -" << "\n";
os << "3. Lys_C 1 K P" << "\n";
os << "4. Lys_N 0 K -" << "\n";
os << "5. Arg_C 1 R P" << "\n";
os << "6. Asp_N 0 D -" << "\n";
os << "7. CNBr 1 M -" << "\n";
os << "8. Glu_C 1 DE P" << "\n";
os << "9. PepsinA 1 FL P" << "\n";
os << "10. Chymotrypsin 1 FWYL P" << "\n";
}