void CompNovoIonScoring::scoreSpectra(Map<double, IonScore> & ion_scores, PeakSpectrum & CID_spec, PeakSpectrum & ETD_spec, double precursor_weight, Size charge) { // adds single charged variants of putative single charged ions //addSingleChargedIons_(ion_scores, CID_spec); for (PeakSpectrum::ConstIterator it = CID_spec.begin(); it != CID_spec.end(); ++it) { double it_pos(it->getPosition()[0]); IonScore ion_score; ion_scores[it_pos] = ion_score; } for (PeakSpectrum::ConstIterator it = CID_spec.begin(); it != CID_spec.end(); ++it) { ion_scores[it->getPosition()[0]].s_isotope_pattern_1 = scoreIsotopes_(CID_spec, it, ion_scores, 1); if (it->getPosition()[0] < precursor_weight / 2.0) { ion_scores[it->getPosition()[0]].s_isotope_pattern_2 = scoreIsotopes_(CID_spec, it, ion_scores, 2); } else { ion_scores[it->getPosition()[0]].s_isotope_pattern_2 = -1; } } // find possible supporting ions from ETD spec to CID spec scoreETDFeatures_(charge, precursor_weight, ion_scores, CID_spec, ETD_spec); // combine the features and give b-ion scores scoreWitnessSet_(charge, precursor_weight, ion_scores, CID_spec); for (Map<double, IonScore>::iterator it = ion_scores.begin(); it != ion_scores.end(); ++it) { it->second.score = it->second.s_witness; } MassDecompositionAlgorithm decomp_algo; // check whether a PRMNode_ can be decomposed into amino acids // rescore the peaks that cannot be possible y-ion candidates double max_decomp_weight((double)param_.getValue("max_decomp_weight")); for (Map<double, IonScore>::iterator it = ion_scores.begin(); it != ion_scores.end(); ++it) { if (it->first > 19.0 && (it->first - 19.0) < max_decomp_weight) { vector<MassDecomposition> decomps; decomp_algo.getDecompositions(decomps, it->first - 19.0); #ifdef ION_SCORING_DEBUG cerr << "Decomps: " << it->first << " " << it->first - 19.0 << " " << decomps.size() << " " << it->second.score << endl; #endif if (decomps.empty()) { it->second.score = 0; } } if (it->first < precursor_weight && precursor_weight - it->first < max_decomp_weight) { vector<MassDecomposition> decomps; decomp_algo.getDecompositions(decomps, precursor_weight - it->first); #ifdef ION_SCORING_DEBUG cerr << "Decomps: " << it->first << " " << precursor_weight - it->first << " " << decomps.size() << " " << it->second.score << endl; #endif if (decomps.empty()) { it->second.score = 0; } } } ion_scores[CID_spec.begin()->getPosition()[0]].score = 1; ion_scores[(CID_spec.end() - 1)->getPosition()[0]].score = 1; }
void CompNovoIdentificationCID::getIdentification(PeptideIdentification & id, const PeakSpectrum & CID_spec) { //if (CID_spec.getPrecursors().begin()->getMZ() > 1000.0) //{ //cerr << "Weight of precursor has been estimated to exceed 2000.0 Da which is the current limit" << endl; //return; //} PeakSpectrum new_CID_spec(CID_spec); windowMower_(new_CID_spec, 0.3, 1); Param zhang_param; zhang_param = zhang_.getParameters(); zhang_param.setValue("tolerance", fragment_mass_tolerance_); zhang_param.setValue("use_gaussian_factor", "true"); zhang_param.setValue("use_linear_factor", "false"); zhang_.setParameters(zhang_param); Normalizer normalizer; Param n_param(normalizer.getParameters()); n_param.setValue("method", "to_one"); normalizer.setParameters(n_param); normalizer.filterSpectrum(new_CID_spec); Size charge(2); double precursor_weight(0); // [M+H]+ if (!CID_spec.getPrecursors().empty()) { // believe charge of spectrum? if (CID_spec.getPrecursors().begin()->getCharge() != 0) { charge = CID_spec.getPrecursors().begin()->getCharge(); } else { // TODO estimate charge state } precursor_weight = CID_spec.getPrecursors().begin()->getMZ() * charge - ((charge - 1) * Constants::PROTON_MASS_U); } //cerr << "charge=" << charge << ", [M+H]=" << precursor_weight << endl; // now delete all peaks that are right of the estimated precursor weight Size peak_counter(0); for (PeakSpectrum::ConstIterator it = new_CID_spec.begin(); it != new_CID_spec.end(); ++it, ++peak_counter) { if (it->getPosition()[0] > precursor_weight) { break; } } if (peak_counter < new_CID_spec.size()) { new_CID_spec.resize(peak_counter); } static double oxonium_mass = EmpiricalFormula("H2O+").getMonoWeight(); Peak1D p; p.setIntensity(1); p.setPosition(oxonium_mass); new_CID_spec.push_back(p); p.setPosition(precursor_weight); new_CID_spec.push_back(p); // add complement to spectrum /* for (PeakSpectrum::ConstIterator it1 = CID_spec.begin(); it1 != CID_spec.end(); ++it1) { // get m/z of complement double mz_comp = precursor_weight - it1->getPosition()[0] + Constants::PROTON_MASS_U; // search if peaks are available that have similar m/z values Size count(0); bool found(false); for (PeakSpectrum::ConstIterator it2 = CID_spec.begin(); it2 != CID_spec.end(); ++it2, ++count) { if (fabs(mz_comp - it2->getPosition()[0]) < fragment_mass_tolerance) { // add peak intensity to corresponding peak in new_CID_spec new_CID_spec[count].setIntensity(new_CID_spec[count].getIntensity()); } } if (!found) { // infer this peak Peak1D p; p.setIntensity(it1->getIntensity()); p.setPosition(mz_comp); new_CID_spec.push_back(p); } }*/ CompNovoIonScoringCID ion_scoring; Param ion_scoring_param(ion_scoring.getParameters()); ion_scoring_param.setValue("fragment_mass_tolerance", fragment_mass_tolerance_); ion_scoring_param.setValue("precursor_mass_tolerance", precursor_mass_tolerance_); ion_scoring_param.setValue("decomp_weights_precision", decomp_weights_precision_); ion_scoring_param.setValue("double_charged_iso_threshold", (double)param_.getValue("double_charged_iso_threshold")); ion_scoring_param.setValue("max_isotope_to_score", param_.getValue("max_isotope_to_score")); ion_scoring_param.setValue("max_isotope", max_isotope_); ion_scoring.setParameters(ion_scoring_param); Map<double, IonScore> ion_scores; ion_scoring.scoreSpectrum(ion_scores, new_CID_spec, precursor_weight, charge); new_CID_spec.sortByPosition(); /* cerr << "Size of ion_scores " << ion_scores.size() << endl; for (Map<double, IonScore>::const_iterator it = ion_scores.begin(); it != ion_scores.end(); ++it) { cerr << it->first << " " << it->second.score << endl; }*/ #ifdef WRITE_SCORED_SPEC PeakSpectrum filtered_spec(new_CID_spec); filtered_spec.clear(); for (Map<double, CompNovoIonScoringCID::IonScore>::const_iterator it = ion_scores.begin(); it != ion_scores.end(); ++it) { Peak1D p; p.setIntensity(it->second.score); p.setPosition(it->first); filtered_spec.push_back(p); } DTAFile().store("spec_scored.dta", filtered_spec); #endif set<String> sequences; getDecompositionsDAC_(sequences, 0, new_CID_spec.size() - 1, precursor_weight, new_CID_spec, ion_scores); #ifdef SPIKE_IN sequences.insert("AFCVDGEGR"); sequences.insert("APEFAAPWPDFVPR"); sequences.insert("AVKQFEESQGR"); sequences.insert("CCTESLVNR"); sequences.insert("DAFLGSFLYEYSR"); sequences.insert("DAIPENLPPLTADFAEDK"); sequences.insert("DDNKVEDIWSFLSK"); sequences.insert("DDPHACYSTVFDK"); sequences.insert("DEYELLCLDGSR"); sequences.insert("DGAESYKELSVLLPNR"); sequences.insert("DGASCWCVDADGR"); sequences.insert("DLFIPTCLETGEFAR"); sequences.insert("DTHKSEIAHR"); sequences.insert("DVCKNYQEAK"); sequences.insert("EACFAVEGPK"); sequences.insert("ECCHGDLLECADDR"); sequences.insert("EFLGDKFYTVISSLK"); sequences.insert("EFTPVLQADFQK"); sequences.insert("ELFLDSGIFQPMLQGR"); sequences.insert("ETYGDMADCCEK"); sequences.insert("EVGCPSSSVQEMVSCLR"); sequences.insert("EYEATLEECCAK"); sequences.insert("FADLIQSGTFQLHLDSK"); sequences.insert("FFSASCVPGATIEQK"); sequences.insert("FLANVSTVLTSK"); sequences.insert("FLSGSDYAIR"); sequences.insert("FTASCPPSIK"); sequences.insert("GAIEWEGIESGSVEQAVAK"); sequences.insert("GDVAFIQHSTVEENTGGK"); sequences.insert("GEPPSCAEDQSCPSER"); sequences.insert("GEYVPTSLTAR"); sequences.insert("GQEFTITGQKR"); sequences.insert("GTFAALSELHCDK"); sequences.insert("HLVDEPQNLIK"); sequences.insert("HQDCLVTTLQTQPGAVR"); sequences.insert("HTTVNENAPDQK"); sequences.insert("ILDCGSPDTEVR"); sequences.insert("KCPSPCQLQAER"); sequences.insert("KGTEFTVNDLQGK"); sequences.insert("KQTALVELLK"); sequences.insert("KVPQVSTPTLVEVSR"); sequences.insert("LALQFTTNAKR"); sequences.insert("LCVLHEKTPVSEK"); sequences.insert("LFTFHADICTLPDTEK"); sequences.insert("LGEYGFQNALIVR"); sequences.insert("LHVDPENFK"); sequences.insert("LKECCDKPLLEK"); sequences.insert("LKHLVDEPQNLIK"); sequences.insert("LKPDPNTLCDEFK"); sequences.insert("LLGNVLVVVLAR"); sequences.insert("LLVVYPWTQR"); sequences.insert("LRVDPVNFK"); sequences.insert("LTDEELAFPPLSPSR"); sequences.insert("LVNELTEFAK"); sequences.insert("MFLSFPTTK"); sequences.insert("MPCTEDYLSLILNR"); sequences.insert("NAPYSGYSGAFHCLK"); sequences.insert("NECFLSHKDDSPDLPK"); sequences.insert("NEPNKVPACPGSCEEVK"); sequences.insert("NLQMDDFELLCTDGR"); sequences.insert("QAGVQAEPSPK"); sequences.insert("RAPEFAAPWPDFVPR"); sequences.insert("RHPEYAVSVLLR"); sequences.insert("RPCFSALTPDETYVPK"); sequences.insert("RSLLLAPEEGPVSQR"); sequences.insert("SAFPPEPLLCSVQR"); sequences.insert("SAGWNIPIGTLLHR"); sequences.insert("SCWCVDEAGQK"); sequences.insert("SGNPNYPHEFSR"); sequences.insert("SHCIAEVEK"); sequences.insert("SISSGFFECER"); sequences.insert("SKYLASASTMDHAR"); sequences.insert("SLHTLFGDELCK"); sequences.insert("SLLLAPEEGPVSQR"); sequences.insert("SPPQCSPDGAFRPVQCK"); sequences.insert("SREGDPLAVYLK"); sequences.insert("SRQIPQCPTSCER"); sequences.insert("TAGTPVSIPVCDDSSVK"); sequences.insert("TCVADESHAGCEK"); sequences.insert("TQFGCLEGFGR"); sequences.insert("TVMENFVAFVDK"); sequences.insert("TYFPHFDLSHGSAQVK"); sequences.insert("TYMLAFDVNDEK"); sequences.insert("VDEVGGEALGR"); sequences.insert("VDLLIGSSQDDGLINR"); sequences.insert("VEDIWSFLSK"); sequences.insert("VGGHAAEYGAEALER"); sequences.insert("VGTRCCTKPESER"); sequences.insert("VKVDEVGGEALGR"); sequences.insert("VKVDLLIGSSQDDGLINR"); sequences.insert("VLDSFSNGMK"); sequences.insert("VLSAADKGNVK"); sequences.insert("VPQVSTPTLVEVSR"); sequences.insert("VTKCCTESLVNR"); sequences.insert("VVAASDASQDALGCVK"); sequences.insert("VVAGVANALAHR"); sequences.insert("YICDNQDTISSK"); sequences.insert("YLASASTMDHAR"); sequences.insert("YNGVFQECCQAEDK"); #endif SpectrumAlignmentScore spectra_zhang; spectra_zhang.setParameters(zhang_param); vector<PeptideHit> hits; Size missed_cleavages = param_.getValue("missed_cleavages"); for (set<String>::const_iterator it = sequences.begin(); it != sequences.end(); ++it) { Size num_missed = countMissedCleavagesTryptic_(*it); if (missed_cleavages < num_missed) { //cerr << "Two many missed cleavages: " << *it << ", found " << num_missed << ", allowed " << missed_cleavages << endl; continue; } PeakSpectrum CID_sim_spec; getCIDSpectrum_(CID_sim_spec, *it, charge); //normalizer.filterSpectrum(CID_sim_spec); double cid_score = zhang_(CID_sim_spec, CID_spec); PeptideHit hit; hit.setScore(cid_score); hit.setSequence(getModifiedAASequence_(*it)); hit.setCharge((Int)charge); //TODO unify charge interface: int or size? hits.push_back(hit); //cerr << getModifiedAASequence_(*it) << " " << cid_score << " " << endl; } // rescore the top hits id.setHits(hits); id.assignRanks(); hits = id.getHits(); SpectrumAlignmentScore alignment_score; Param align_param(alignment_score.getParameters()); align_param.setValue("tolerance", fragment_mass_tolerance_); align_param.setValue("use_linear_factor", "true"); alignment_score.setParameters(align_param); for (vector<PeptideHit>::iterator it = hits.begin(); it != hits.end(); ++it) { //cerr << "Pre: " << it->getRank() << " " << it->getSequence() << " " << it->getScore() << " " << endl; } Size number_of_prescoring_hits = param_.getValue("number_of_prescoring_hits"); if (hits.size() > number_of_prescoring_hits) { hits.resize(number_of_prescoring_hits); } for (vector<PeptideHit>::iterator it = hits.begin(); it != hits.end(); ++it) { PeakSpectrum CID_sim_spec; getCIDSpectrum_(CID_sim_spec, getModifiedStringFromAASequence_(it->getSequence()), charge); normalizer.filterSpectrum(CID_sim_spec); //DTAFile().store("sim_specs/" + it->getSequence().toUnmodifiedString() + "_sim_CID.dta", CID_sim_spec); //double cid_score = spectra_zhang(CID_sim_spec, CID_spec); double cid_score = alignment_score(CID_sim_spec, CID_spec); //cerr << "Final: " << it->getSequence() << " " << cid_score << endl; it->setScore(cid_score); } id.setHits(hits); id.assignRanks(); hits = id.getHits(); for (vector<PeptideHit>::iterator it = hits.begin(); it != hits.end(); ++it) { //cerr << "Fin: " << it->getRank() << " " << it->getSequence() << " " << it->getScore() << " " << endl; } Size number_of_hits = param_.getValue("number_of_hits"); if (id.getHits().size() > number_of_hits) { hits.resize(number_of_hits); } id.setHits(hits); id.assignRanks(); return; }