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;
}