void CompNovoIdentificationBase::getCIDSpectrumLight_(PeakSpectrum & spec, const String & sequence, DoubleReal prefix, DoubleReal suffix)
{
static DoubleReal h2o_mass = EmpiricalFormula("H2O").getMonoWeight();
Peak1D p;
DoubleReal b_pos(0.0 + prefix);
DoubleReal y_pos(h2o_mass + suffix);
for (Size i = 0; i != sequence.size() - 1; ++i)
{
char aa(sequence[i]);
b_pos += aa_to_weight_[aa];
char aa2(sequence[sequence.size() - i - 1]);
y_pos += aa_to_weight_[aa2];
if (b_pos > min_mz_ && b_pos < max_mz_)
{
p.setPosition(b_pos + Constants::PROTON_MASS_U);
p.setIntensity(1.0f);
spec.push_back(p);
}
if (y_pos > min_mz_ && y_pos < max_mz_)
{
p.setPosition(y_pos + Constants::PROTON_MASS_U);
p.setIntensity(1.0f);
spec.push_back(p);
}
}
spec.sortByPosition();
return;
}
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;
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
StringList in_spec = getStringList_("in");
StringList out = getStringList_("out");
String in_lib = getStringOption_("lib");
String compare_function = getStringOption_("compare_function");
Int precursor_mass_multiplier = getIntOption_("round_precursor_to_integer");
float precursor_mass_tolerance = getDoubleOption_("precursor_mass_tolerance");
//Int min_precursor_charge = getIntOption_("min_precursor_charge");
//Int max_precursor_charge = getIntOption_("max_precursor_charge");
float remove_peaks_below_threshold = getDoubleOption_("filter:remove_peaks_below_threshold");
UInt min_peaks = getIntOption_("filter:min_peaks");
UInt max_peaks = getIntOption_("filter:max_peaks");
Int cut_peaks_below = getIntOption_("filter:cut_peaks_below");
StringList fixed_modifications = getStringList_("fixed_modifications");
StringList variable_modifications = getStringList_("variable_modifications");
Int top_hits = getIntOption_("top_hits");
if (top_hits < -1)
{
writeLog_("top_hits (should be >= -1 )");
return ILLEGAL_PARAMETERS;
}
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
if (out.size() != in_spec.size())
{
writeLog_("out (should be as many as input files)");
return ILLEGAL_PARAMETERS;
}
time_t prog_time = time(NULL);
MSPFile spectral_library;
RichPeakMap query, library;
//spectrum which will be identified
MzMLFile spectra;
spectra.setLogType(log_type_);
time_t start_build_time = time(NULL);
//-------------------------------------------------------------
//building map for faster search
//-------------------------------------------------------------
//library containing already identified peptide spectra
vector<PeptideIdentification> ids;
spectral_library.load(in_lib, ids, library);
map<Size, vector<PeakSpectrum> > MSLibrary;
{
RichPeakMap::iterator s;
vector<PeptideIdentification>::iterator i;
ModificationsDB* mdb = ModificationsDB::getInstance();
for (s = library.begin(), i = ids.begin(); s < library.end(); ++s, ++i)
{
double precursor_MZ = (*s).getPrecursors()[0].getMZ();
Size MZ_multi = (Size)precursor_MZ * precursor_mass_multiplier;
map<Size, vector<PeakSpectrum> >::iterator found;
found = MSLibrary.find(MZ_multi);
PeakSpectrum librar;
bool variable_modifications_ok = true;
bool fixed_modifications_ok = true;
const AASequence& aaseq = i->getHits()[0].getSequence();
//variable fixed modifications
if (!fixed_modifications.empty())
{
for (Size i = 0; i < aaseq.size(); ++i)
{
const Residue& mod = aaseq.getResidue(i);
for (Size s = 0; s < fixed_modifications.size(); ++s)
{
if (mod.getOneLetterCode() == mdb->getModification(fixed_modifications[s]).getOrigin() && fixed_modifications[s] != mod.getModification())
{
fixed_modifications_ok = false;
break;
}
}
}
}
//variable modifications
if (aaseq.isModified() && (!variable_modifications.empty()))
{
for (Size i = 0; i < aaseq.size(); ++i)
{
if (aaseq.isModified(i))
{
const Residue& mod = aaseq.getResidue(i);
for (Size s = 0; s < variable_modifications.size(); ++s)
{
if (mod.getOneLetterCode() == mdb->getModification(variable_modifications[s]).getOrigin() && variable_modifications[s] != mod.getModification())
{
variable_modifications_ok = false;
break;
}
}
}
}
}
if (variable_modifications_ok && fixed_modifications_ok)
{
PeptideIdentification& translocate_pid = *i;
librar.getPeptideIdentifications().push_back(translocate_pid);
librar.setPrecursors(s->getPrecursors());
//library entry transformation
for (UInt l = 0; l < s->size(); ++l)
{
Peak1D peak;
if ((*s)[l].getIntensity() > remove_peaks_below_threshold)
{
const String& info = (*s)[l].getMetaValue("MSPPeakInfo");
if (info[0] == '?')
{
peak.setIntensity(sqrt(0.2 * (*s)[l].getIntensity()));
}
else
{
peak.setIntensity(sqrt((*s)[l].getIntensity()));
}
peak.setMZ((*s)[l].getMZ());
peak.setPosition((*s)[l].getPosition());
librar.push_back(peak);
}
}
if (found != MSLibrary.end())
{
found->second.push_back(librar);
}
else
{
vector<PeakSpectrum> tmp;
tmp.push_back(librar);
MSLibrary.insert(make_pair(MZ_multi, tmp));
}
}
}
}
time_t end_build_time = time(NULL);
cout << "Time needed for preprocessing data: " << (end_build_time - start_build_time) << "\n";
//compare function
PeakSpectrumCompareFunctor* comparor = Factory<PeakSpectrumCompareFunctor>::create(compare_function);
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
double score;
StringList::iterator in, out_file;
for (in = in_spec.begin(), out_file = out.begin(); in < in_spec.end(); ++in, ++out_file)
{
time_t start_time = time(NULL);
spectra.load(*in, query);
//Will hold valuable hits
vector<PeptideIdentification> peptide_ids;
vector<ProteinIdentification> protein_ids;
// Write parameters to ProteinIdentifcation
ProteinIdentification prot_id;
//Parameters of identificaion
prot_id.setIdentifier("test");
prot_id.setSearchEngineVersion("SpecLibSearcher");
prot_id.setDateTime(DateTime::now());
prot_id.setScoreType(compare_function);
ProteinIdentification::SearchParameters searchparam;
searchparam.precursor_tolerance = precursor_mass_tolerance;
prot_id.setSearchParameters(searchparam);
/***********SEARCH**********/
for (UInt j = 0; j < query.size(); ++j)
{
//Set identifier for each identifications
PeptideIdentification pid;
pid.setIdentifier("test");
pid.setScoreType(compare_function);
ProteinHit pr_hit;
pr_hit.setAccession(j);
prot_id.insertHit(pr_hit);
//RichPeak1D to Peak1D transformation for the compare function query
PeakSpectrum quer;
bool peak_ok = true;
query[j].sortByIntensity(true);
double min_high_intensity = 0;
if (query[j].empty() || query[j].getMSLevel() != 2)
{
continue;
}
if (query[j].getPrecursors().empty())
{
writeLog_("Warning MS2 spectrum without precursor information");
continue;
}
min_high_intensity = (1 / cut_peaks_below) * query[j][0].getIntensity();
query[j].sortByPosition();
for (UInt k = 0; k < query[j].size() && k < max_peaks; ++k)
{
if (query[j][k].getIntensity() > remove_peaks_below_threshold && query[j][k].getIntensity() >= min_high_intensity)
{
Peak1D peak;
peak.setIntensity(sqrt(query[j][k].getIntensity()));
peak.setMZ(query[j][k].getMZ());
peak.setPosition(query[j][k].getPosition());
quer.push_back(peak);
}
}
if (quer.size() >= min_peaks)
{
peak_ok = true;
}
else
{
peak_ok = false;
}
double query_MZ = query[j].getPrecursors()[0].getMZ();
if (peak_ok)
{
bool charge_one = false;
Int percent = (Int) Math::round((query[j].size() / 100.0) * 3.0);
Int margin = (Int) Math::round((query[j].size() / 100.0) * 1.0);
for (vector<RichPeak1D>::iterator peak = query[j].end() - 1; percent >= 0; --peak, --percent)
{
if (peak->getMZ() < query_MZ)
{
break;
}
}
if (percent > margin)
{
charge_one = true;
}
float min_MZ = (query_MZ - precursor_mass_tolerance) * precursor_mass_multiplier;
float max_MZ = (query_MZ + precursor_mass_tolerance) * precursor_mass_multiplier;
for (Size mz = (Size)min_MZ; mz <= ((Size)max_MZ) + 1; ++mz)
{
map<Size, vector<PeakSpectrum> >::iterator found;
found = MSLibrary.find(mz);
if (found != MSLibrary.end())
{
vector<PeakSpectrum>& library = found->second;
for (Size i = 0; i < library.size(); ++i)
{
float this_MZ = library[i].getPrecursors()[0].getMZ() * precursor_mass_multiplier;
if (this_MZ >= min_MZ && max_MZ >= this_MZ && ((charge_one == true && library[i].getPeptideIdentifications()[0].getHits()[0].getCharge() == 1) || charge_one == false))
{
PeptideHit hit = library[i].getPeptideIdentifications()[0].getHits()[0];
PeakSpectrum& librar = library[i];
//Special treatment for SpectraST score as it computes a score based on the whole library
if (compare_function == "SpectraSTSimilarityScore")
{
SpectraSTSimilarityScore* sp = static_cast<SpectraSTSimilarityScore*>(comparor);
BinnedSpectrum quer_bin = sp->transform(quer);
BinnedSpectrum librar_bin = sp->transform(librar);
score = (*sp)(quer, librar); //(*sp)(quer_bin,librar_bin);
double dot_bias = sp->dot_bias(quer_bin, librar_bin, score);
hit.setMetaValue("DOTBIAS", dot_bias);
}
else
{
score = (*comparor)(quer, librar);
}
DataValue RT(library[i].getRT());
DataValue MZ(library[i].getPrecursors()[0].getMZ());
hit.setMetaValue("RT", RT);
hit.setMetaValue("MZ", MZ);
hit.setScore(score);
PeptideEvidence pe;
pe.setProteinAccession(pr_hit.getAccession());
hit.addPeptideEvidence(pe);
pid.insertHit(hit);
}
}
}
}
}
pid.setHigherScoreBetter(true);
pid.sort();
if (compare_function == "SpectraSTSimilarityScore")
{
if (!pid.empty() && !pid.getHits().empty())
{
vector<PeptideHit> final_hits;
final_hits.resize(pid.getHits().size());
SpectraSTSimilarityScore* sp = static_cast<SpectraSTSimilarityScore*>(comparor);
Size runner_up = 1;
for (; runner_up < pid.getHits().size(); ++runner_up)
{
if (pid.getHits()[0].getSequence().toUnmodifiedString() != pid.getHits()[runner_up].getSequence().toUnmodifiedString() || runner_up > 5)
{
break;
}
}
double delta_D = sp->delta_D(pid.getHits()[0].getScore(), pid.getHits()[runner_up].getScore());
for (Size s = 0; s < pid.getHits().size(); ++s)
{
final_hits[s] = pid.getHits()[s];
final_hits[s].setMetaValue("delta D", delta_D);
final_hits[s].setMetaValue("dot product", pid.getHits()[s].getScore());
final_hits[s].setScore(sp->compute_F(pid.getHits()[s].getScore(), delta_D, pid.getHits()[s].getMetaValue("DOTBIAS")));
//final_hits[s].removeMetaValue("DOTBIAS");
}
pid.setHits(final_hits);
pid.sort();
pid.setMZ(query[j].getPrecursors()[0].getMZ());
pid.setRT(query_MZ);
}
}
if (top_hits != -1 && (UInt)top_hits < pid.getHits().size())
{
vector<PeptideHit> hits;
hits.resize(top_hits);
for (Size i = 0; i < (UInt)top_hits; ++i)
{
hits[i] = pid.getHits()[i];
}
pid.setHits(hits);
}
peptide_ids.push_back(pid);
}
protein_ids.push_back(prot_id);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
IdXMLFile id_xml_file;
id_xml_file.store(*out_file, protein_ids, peptide_ids);
time_t end_time = time(NULL);
cout << "Search time: " << difftime(end_time, start_time) << " seconds for " << *in << "\n";
}
time_t end_time = time(NULL);
cout << "Total time: " << difftime(end_time, prog_time) << " secconds\n";
return EXECUTION_OK;
}
bool ShiftModel1D::finish()
{
if (!isValid())
{
return false;
}
if (!system_)
{
Log.info() << "No valid system found!" << std::endl;
return false;
}
// compute the shift model if necessary
if (compute_shifts_)
{
BALL::ShiftModel sm(parameters_.getFilename());
system_->apply(sm);
}
String element = "";
// Peter Bayer proposed as peak width
// for H 15Hz
// for N 10hz
// for C 5Hz
// peakwidth is meassured in ppm, since
// experiments were done in Hz, we convert the values
// according to the formular
//
// offset [Hz] = offset[ppm] * basic frequency
//
// for our prediction we assume a basic frequency of 700 MHz
float peakwidth = 0.0;
switch(type_)
{
case H:
case H_ON_BACKBONE:
element = "H";
//peakwidth = 0.02142; // Peter Bayers estimation
peakwidth = 0.0032; // this is the former BALL estimation
break;
case N:
case N_BACKBONE:
element = "N";
peakwidth = 0.01428;
break;
case C:
case C_BACKBONE:
element = "C";
peakwidth = 0.00714;
break;
}
int counter = 0;
if (element == "" )
return true;
for (BALL::ResidueIterator r_it = system_->beginResidue(); +r_it; ++r_it)
{
Atom* atom = NULL;
for (BALL::AtomIterator at_it = r_it->beginAtom(); +at_it; ++at_it)
{
if (hasType_(&(*at_it), type_))
{
counter++;
atom = &(*at_it);
// we have, get the shift
float shift = atom->getProperty(BALL::ShiftModule::PROPERTY__SHIFT).getFloat();
Peak1D peak;
float pos = shift;
peak.setPosition(pos);
peak.setWidth(peakwidth);
peak.setIntensity(peak.getIntensity()+1);
//setAtom();
peaks_.push_back(peak);
}
}
}
std::cout << "Number of considered atoms: "<< counter << std::endl;
return true;
}
void CompNovoIdentificationBase::getCIDSpectrum_(PeakSpectrum & spec, const String & sequence, Size charge, DoubleReal prefix, DoubleReal suffix)
{
static DoubleReal h2o_mass = EmpiricalFormula("H2O").getMonoWeight();
static DoubleReal nh3_mass = EmpiricalFormula("NH3").getMonoWeight();
static DoubleReal co_mass = EmpiricalFormula("CO").getMonoWeight();
Peak1D p;
DoubleReal b_pos(0 + prefix);
DoubleReal y_pos(h2o_mass + suffix);
bool b_H2O_loss(false), b_NH3_loss(false), y_NH3_loss(false);
for (Size i = 0; i != sequence.size() - 1; ++i)
{
char aa(sequence[i]);
b_pos += aa_to_weight_[aa];
char aa2(sequence[sequence.size() - i - 1]);
y_pos += aa_to_weight_[aa2];
for (Size z = 1; z <= charge && z < 3; ++z)
{
// b-ions
if (b_pos >= min_mz_ && b_pos <= max_mz_)
{
for (Size j = 0; j != max_isotope_; ++j)
{
if (z == 1 /*|| b_pos > MIN_DOUBLE_MZ*/)
{
p.setPosition((b_pos + (DoubleReal)z * Constants::PROTON_MASS_U + (DoubleReal)j + Constants::NEUTRON_MASS_U) / (DoubleReal)z);
p.setIntensity(isotope_distributions_[(Size)b_pos][j] * 0.8 / (z * z));
spec.push_back(p);
}
}
}
// b-ion losses
if (b_pos - h2o_mass > min_mz_ && b_pos - h2o_mass < max_mz_)
{
if (b_H2O_loss || aa == 'S' || aa == 'T' || aa == 'E' || aa == 'D')
{
b_H2O_loss = true;
p.setPosition((b_pos + z * Constants::PROTON_MASS_U - h2o_mass) / z);
p.setIntensity(0.02 / (DoubleReal)(z * z));
if (z == 1 /* || b_pos > MIN_DOUBLE_MZ*/)
{
spec.push_back(p);
}
}
if (b_NH3_loss || aa == 'Q' || aa == 'N' || aa == 'R' || aa == 'K')
{
b_NH3_loss = true;
p.setPosition((b_pos + z * Constants::PROTON_MASS_U - nh3_mass) / z);
p.setIntensity(0.02 / (DoubleReal)(z * z));
if (z == 1 /* || b_pos > MIN_DOUBLE_MZ*/)
{
spec.push_back(p);
}
}
}
// a-ions only for charge 1
if (z == 1)
{
if (b_pos - co_mass > min_mz_ && b_pos - co_mass < max_mz_)
{
// a-ions
p.setPosition((b_pos + z * Constants::PROTON_MASS_U - co_mass) / (DoubleReal)z);
p.setIntensity(0.1f);
spec.push_back(p);
}
}
if (y_pos > min_mz_ && y_pos < max_mz_)
{
// y-ions
for (Size j = 0; j != max_isotope_; ++j)
{
if (z == 1 /* || y_pos > MIN_DOUBLE_MZ*/)
{
p.setPosition((y_pos + (DoubleReal)z * Constants::PROTON_MASS_U + (DoubleReal)j * Constants::NEUTRON_MASS_U) / (DoubleReal)z);
p.setIntensity(isotope_distributions_[(Size)y_pos][j] / (DoubleReal) (z * z));
spec.push_back(p);
}
}
// H2O loss
p.setPosition((y_pos + z * Constants::PROTON_MASS_U - h2o_mass) / (DoubleReal)z);
p.setIntensity(0.1 / (DoubleReal)(z * z));
if (aa2 == 'Q') // pyroglutamic acid formation
{
p.setIntensity(0.5f);
}
if (z == 1 /* || y_pos > MIN_DOUBLE_MZ*/)
{
spec.push_back(p);
}
// NH3 loss
if (y_NH3_loss || aa2 == 'Q' || aa2 == 'N' || aa2 == 'R' || aa2 == 'K')
{
y_NH3_loss = true;
p.setPosition((y_pos + z * Constants::PROTON_MASS_U - nh3_mass) / (DoubleReal)z);
p.setIntensity(0.1 / (DoubleReal)(z * z));
if (z == 1 /*|| y_pos > MIN_DOUBLE_MZ*/)
{
spec.push_back(p);
}
}
}
}
}
// if Q1 abundant loss of water -> pyroglutamic acid formation
if (sequence[0] == 'Q' && prefix == 0 && suffix == 0)
{
/*
for (PeakSpectrum::Iterator it = spec.begin(); it != spec.end(); ++it)
{
it->setIntensity(it->getIntensity() * 0.5);
}*/
/*
for (Size j = 0; j != max_isotope; ++j)
{
p.setPosition((precursor_weight + charge - 1 + j)/(DoubleReal)charge);
p.setIntensity(isotope_distributions_[(Int)p.getPosition()[0]][j] * 0.1);
spec.push_back(p);
}
*/
}
spec.sortByPosition();
return;
}