Method search

src/openms/source/ANALYSIS/ID/SimpleSearchEngineAlgorithm.cpp:400–648

  }

  SimpleSearchEngineAlgorithm::ExitCodes SimpleSearchEngineAlgorithm::search(const String& in_mzML, const String& in_db, vector<ProteinIdentification>& protein_ids, vector<PeptideIdentification>& peptide_ids) const
  {
    boost::regex peptide_motif_regex(peptide_motif_);

    bool precursor_mass_tolerance_unit_ppm = (precursor_mass_tolerance_unit_ == "ppm");
    bool fragment_mass_tolerance_unit_ppm = (fragment_mass_tolerance_unit_ == "ppm");

    ModifiedPeptideGenerator::MapToResidueType fixed_modifications = ModifiedPeptideGenerator::getModifications(modifications_fixed_);
    ModifiedPeptideGenerator::MapToResidueType variable_modifications = ModifiedPeptideGenerator::getModifications(modifications_variable_);

    // load MS2 map
    PeakMap spectra;
    MzMLFile f;
    //f.setLogType(log_type_);

    PeakFileOptions options;
    options.clearMSLevels();
    options.addMSLevel(2);
    f.getOptions() = options;
    f.load(in_mzML, spectra);
    spectra.sortSpectra(true);

    startProgress(0, 1, "Filtering spectra...");
    preprocessSpectra_(spectra, fragment_mass_tolerance_, fragment_mass_tolerance_unit_ppm);
    endProgress();

    // build multimap of precursor mass to scan index
    multimap<double, Size> multimap_mass_2_scan_index;
    for (PeakMap::ConstIterator s_it = spectra.begin(); s_it != spectra.end(); ++s_it)
    {
      int scan_index = s_it - spectra.begin();
      vector<Precursor> precursor = s_it->getPrecursors();

      // there should only one precursor and MS2 should contain at least a few peaks to be considered (e.g. at least for every AA in the peptide)
      if (precursor.size() == 1 && s_it->size() >= peptide_min_size_)
      {
        Size precursor_charge = precursor[0].getCharge();

        if (precursor_charge < precursor_min_charge_ 
         || precursor_charge > precursor_max_charge_)
        {
          continue;
        }

        double precursor_mz = precursor[0].getMZ();

        // calculate precursor mass (optionally corrected for misassignment) and map it to MS scan index
        for (int isotope_number : precursor_isotopes_)
        {
          double precursor_mass = (double) precursor_charge * precursor_mz - (double) precursor_charge * Constants::PROTON_MASS_U;

          // correct for monoisotopic misassignments of the precursor annotation
          if (isotope_number != 0) { precursor_mass -= isotope_number * Constants::C13C12_MASSDIFF_U; }

          multimap_mass_2_scan_index.insert(make_pair(precursor_mass, scan_index));
        }
      }
    }