public double ProbabilityScore(Peptide peptide)
{
double score = 0;
foreach (Precursor precursor in precursors)
{
score += /*(1 - score) * */ precursor.ProbabilityScore(peptide, true);
}
return(score);
}
public PeptideMatches Search(List <Cluster> clusters, List <Precursor> precursors, bool DiffByMod = true)
{
options.ConSole.WriteLine("Creating the list of peptide found...");
Dictionary <string, PeptideMatch> peptideMatches = new Dictionary <string, PeptideMatch>();
foreach (Precursor prec in precursors)
{
foreach (PeptideSpectrumMatch psm in prec.OptimizedBestPsms())
{
Peptide pep = psm.Peptide;
string seq = (DiffByMod ? pep.Sequence : pep.BaseSequence);
if (!peptideMatches.ContainsKey(seq))
{
peptideMatches.Add(seq, new PeptideMatch(pep));
}
else if (pep.Target)
{
peptideMatches[seq].peptide = pep;
}
}
}
int nbClusterNewSeq = 0;
foreach (Cluster cl in clusters)
{
foreach (clCondition condition in cl.conditions)
{
if (condition != null)
{
foreach (clReplicate replicate in condition.replicates)
{
foreach (Precursor precursor in replicate.precursors)
{
foreach (PeptideSpectrumMatch psm in precursor.OptimizedBestPsms())
{
string seq = (DiffByMod ? psm.Peptide.Sequence : psm.Peptide.BaseSequence);
if (peptideMatches.ContainsKey(seq))
{
peptideMatches[seq].AddOnlyOnce(cl);
}
}
}
}
}
}
}
PeptideMatches TotalList = new PeptideMatches(peptideMatches.Values);
options.ConSole.WriteLine(TotalList.Count + " distinct peptides (based on sequence" + (DiffByMod ? " and modifications)" : ")") + " [" + nbClusterNewSeq + " added from clusters]");
return(TotalList);
}
public double ProbabilityScore(Peptide peptide)
{
double score = 0;
foreach (clReplicate replicate in replicates)
{
if (replicate != null)
{
score += /*(1 - score) * */ replicate.ProbabilityScore(peptide);
}
}
return(score);
}
public double OptimizedBestPsmScore(Peptide peptide = null, bool checkMods = false)
{
PeptideSpectrumMatch psm = OptimizedBestPsm(peptide, checkMods);
if (psm != null)
{
return(psm.ProbabilityScore());
}
else
{
return(0);
}
}
//public ConcurrentDictionary<string, List<Protein>> DicOfProteins = new ConcurrentDictionary<string, List<Protein>>();
private void ComputePSMs(Query query, Peptide modified_peptide)
{
PeptideSpectrumMatch psm = new PeptideSpectrumMatch(query, modified_peptide, options);
if (psm.MatchingProducts > options.fragments.Count)
{
//DicOfProteins.GetOrAdd(psm.Peptide.BaseSequence, new List<Protein>()).Add(psm.Peptide.Parent);
// if (!DicOfProteins.ContainsKey(psm.Peptide.BaseSequence))
// DicOfProteins.AddOrUpdate(psm.Peptide.BaseSequence, new List<Protein>());
// DicOfProteins[psm.Peptide.BaseSequence].Add(psm.Peptide.Parent);
//List<PeptideSpectrumMatch> psmsOfQuery = query.psms;
if (query.psms.Count < options.NbPSMToKeep)
{
query.psms.Add(psm);
}
else if (query.psms[options.NbPSMToKeep - 1].ProbabilityScore() < psm.ProbabilityScore())
{
for (int i = 0; i < query.psms.Count; i++)
{
if (query.psms[i].ProbabilityScore() <= psm.ProbabilityScore())
{
query.psms.Insert(i, psm);
break;
}
}
if (query.psms.Count > options.NbPSMToKeep)
{
query.psms.RemoveAt(options.NbPSMToKeep - 1);
}
}//*/
//TODO check optimal number of PSM to store
/*
* //TODO Reactivate this to save on memory space
* if (psmsOfPrecursor.Count == 0 || psmsOfPrecursor[0].MaxQuantScore() == psm.MaxQuantScore())
* psmsOfPrecursor.Add(psm);
* else
* if (psm.MaxQuantScore() > psmsOfPrecursor[0].MaxQuantScore())
* {
* psmsOfPrecursor.Clear();
* psmsOfPrecursor.Add(psm);
* }
* //*/
}
}
/*
* public static int TargetDecoyComparison(Protein left, Protein right)
* {
* if (left.Target)
* if (right.Target)
* return 0;
* else
* return -1;
* else
* if (right.Target)
* return 1;
* else
* return 0;
* }//*/
public IEnumerable <Peptide> Digest(Protease protease, int maximumMissedCleavages, InitiatorMethionineBehavior initiatorMethionineBehavior,
int?minimumPeptideLength, int?maximumPeptideLength, bool onTheFlyDecoy)
{
List <int> indices = protease.GetDigestionSiteIndices(this);
indices.Insert(0, -1);
indices.Add(Length - 1);
for (int missed_cleavages = 0; missed_cleavages <= maximumMissedCleavages; missed_cleavages++)
{
for (int i = 0; i < indices.Count - missed_cleavages - 1; i++)
{
if (initiatorMethionineBehavior != InitiatorMethionineBehavior.Cleave || indices[i] + 1 != 0 || this[0] != 'M')
{
Peptide peptide = new Peptide(this, indices[i] + 1, indices[i + missed_cleavages + 1], missed_cleavages);
if ((!minimumPeptideLength.HasValue || peptide.Length >= minimumPeptideLength.Value) &&
(!maximumPeptideLength.HasValue || peptide.Length <= maximumPeptideLength.Value))
{
yield return(peptide);
if (onTheFlyDecoy)
{
yield return(new Peptide(this, indices[i + missed_cleavages + 1], indices[i] + 1, missed_cleavages));
}
}
}
if (initiatorMethionineBehavior != InitiatorMethionineBehavior.Retain && indices[i] + 1 == 0 && this[0] == 'M')
{
Peptide peptide_without_initiator_methionine = new Peptide(this, indices[i] + 1 + 1, indices[i + missed_cleavages + 1], missed_cleavages);
if ((!minimumPeptideLength.HasValue || peptide_without_initiator_methionine.Length >= minimumPeptideLength.Value) &&
(!maximumPeptideLength.HasValue || peptide_without_initiator_methionine.Length <= maximumPeptideLength.Value))
{
yield return(peptide_without_initiator_methionine);
if (onTheFlyDecoy)
{
yield return(new Peptide(this, indices[i + missed_cleavages + 1], indices[i] + 1 + 1, missed_cleavages));
}
}
}
}
}
}
public PeptideSpectrumMatch OptimizedBestPsm(Peptide peptide = null, bool checkMods = false)
{
if (psms.Count > 0)
{
if (peptide == null)
{
double bestScore = psms[0].ProbabilityScore();
int bestProteinIndex = 0;
double tmpScore;
for (int i = 1; i < psms.Count; i++)
{
tmpScore = psms[i].ProbabilityScore();
if (tmpScore > bestScore || (tmpScore == bestScore && psms[i].Target))//.ProteinScore >= proteinScore))
{
bestProteinIndex = i;
bestScore = tmpScore;
}
}
return(psms[bestProteinIndex]);
}
else
{
double bestScore = 0;
int bestProteinIndex = 0;
double proteinScore = 0;
for (int i = 0; i < psms.Count; i++)
{
if (peptide.IsSamePeptide(psms[i].Peptide, checkMods) && (psms[i].ProbabilityScore() > bestScore || (psms[i].ProbabilityScore() == bestScore && psms[i].Target)))//.ProteinScore > proteinScore)))
{
bestProteinIndex = i;
bestScore = psms[i].ProbabilityScore();
proteinScore = psms[i].ProteinScore;
}
}
if (bestScore > 0)
{
return(psms[bestProteinIndex]);
}
}
}
return(null);
}
public double ProbabilityScore(Peptide peptide = null, bool checkMods = false)
{/*
* double score = 0;
* foreach(PeptideSpectrumMatch psm in psms)
* if(
* foreach (PeptideSpectrumMatch psm in OptimizedBestPsms(peptide))
* score += (1 - score) * psm.OptimizedScore();
* return score;
* //*/
if (peptide != null)
{
double score = 0;
foreach (PeptideSpectrumMatch psm in psms)
{
if (peptide.IsSamePeptide(psm.Peptide, checkMods))
{
score += psm.ProbabilityScore();
}
}
return(score);
}
else
{
return(OptimizedBestPsmScore(peptide, checkMods));//TODO Reactivate Optimized Precursor Score
}
//PeptideSpectrumMatch psmLeft = OptimizedBestPsm(peptide, checkMods);
//if (psmLeft != null)
// return psmLeft.OptimizedScore();
/* (dIntensity * psmLeft.MatchingIntensityFraction +
* dProduct * psmLeft.ProductScore +
* dPrecursor * psmLeft.PrecursorScore +
* dMatching * psmLeft.MatchingProductsFraction +
* dProtein * psmLeft.ProteinScore +
* dScore * psmLeft.MaxQuantScore() +
* (Isotopes.Count > 0 ? dIsotope : 0) +
* (Track.Invented ? dInvented : 0) +
* dPeptideScore * psmLeft.PeptideScore);//*/
//else
// return 0;//*/
}
}//*/
public double GetPrecursorMassError(Peptide peptide)
{
//Reproducibility is average number of replicates for conditions where seen
double cumul = 0;
int nbSeen = 0;
foreach (clCondition condition in conditions)
{
if (condition != null)
{
foreach (clReplicate replicate in condition.replicates)
{
foreach (Precursor precursor in replicate.precursors)
{
cumul += peptide.MonoisotopicMass - precursor.Mass;
nbSeen++;
}
}
}
}
return(cumul / (double)nbSeen);
}//*/
public IEnumerable <Peptide> GetSNPsdPeptides()
{
string strCumul = "";
for (int i = 0; i < BaseSequence.Length; i++)
{
foreach (char letter in AminoAcidMasses.AMINO_ACIDS)
{
if (BaseSequence[i] != letter)
{
Peptide newPeptide = new Peptide(this);
if (i + 1 < BaseSequence.Length)
{
newPeptide.BaseSequence = strCumul + letter + BaseSequence.Substring(i + 1);
}
else
{
newPeptide.BaseSequence = strCumul + letter;
}
yield return(newPeptide);
}
}
}
}
public bool IsSamePeptide(Peptide peptide, bool checkMods)
{
if (BaseSequence.Equals(peptide.BaseSequence))
{
if (checkMods)
{
if (VariableModifications != null && peptide.VariableModifications != null)
{
foreach (int key in VariableModifications.Keys)
{
if (!peptide.VariableModifications.ContainsKey(key) || VariableModifications[key] != peptide.VariableModifications[key])
{
return(false);
}
}
}
}
return(true);
}
else
{
return(false);
}
}
public Peptide ComputeBestPeptide()
{
Dictionary <Peptide, double> peptides = new Dictionary <Peptide, double>();
foreach (clCondition condition in conditions)
{
if (condition != null)
{
foreach (clReplicate replicate in condition.replicates)
{
foreach (Precursor precursor in replicate.precursors)
{
foreach (PeptideSpectrumMatch psm in precursor.OptimizedBestPsms())
{
if (!peptides.ContainsKey(psm.Peptide))
{
peptides.Add(psm.Peptide, ProbabilityScore(psm.Peptide));
}
}
}
}
}
}
double best = -1;
Peptide bestPeptide = null;
foreach (Peptide key in peptides.Keys)
{
if (peptides[key] > best || (peptides[key] == best && bestPeptide.Decoy))
{
best = peptides[key];
bestPeptide = key;
}
}
return(bestPeptide);
}
private Peptide(Peptide peptide) : this(peptide.Parent, peptide.StartResidueNumber - 1, peptide.EndResidueNumber - 1, peptide.MissedCleavages)
{
}
public void ExportFragmentIntensitiesForAllPSM(List <PeptideSpectrumMatch> psms, Peptide peptide, int psmCharge, string fileName)
{
vsCSVWriter writer = new vsCSVWriter(fileName);
string title = "Retention Time";
for (int i = 1; i <= peptide.Length; i++)
{
for (int charge = 1; charge <= psmCharge; charge++)
{
foreach (FragmentClass fragment in dbOptions.fragments)
{
title += "," + i + fragment.Name + " ^" + charge;
}
}
}
writer.AddLine(title);
foreach (PeptideSpectrumMatch psm in psms)
{
string line = psm.Query.spectrum.RetentionTimeInMin.ToString();
for (int i = 1; i <= peptide.Length; i++)
{
for (int charge = 1; charge <= psmCharge; charge++)
{
foreach (FragmentClass fragment in dbOptions.fragments)
{
double cumul = 0.0;
foreach (ProductMatch match in psm.AllProductMatches)
{
if (fragment == match.Fragment && match.fragmentPos == i && match.charge == charge)
{
cumul += match.obsIntensity;
}
}
line += "," + cumul;
}
}
}
writer.AddLine(line);
}
writer.WriteToFile();
}
public void ExportFragmentIntensities(List <PeptideSpectrumMatch> psms, Peptide peptide, int psmCharge, string fileName)
{
vsCSVWriter writer = new vsCSVWriter(fileName);
List <FragmentClass> fragments = new List <FragmentClass>();
foreach (FragmentClass fragment in dbOptions.fragments)
//foreach (string fragment in FragmentDictionary.Fragments.Keys)
{
bool found = false;
foreach (ProductMatch match in dbOptions.fragments.ComputeFragments(peptide, psmCharge, dbOptions))
{
if (fragment == match.Fragment)
{
found = true;
break;
}
}
if (found)
{
fragments.Add(fragment);
}
}
string title = "Cumulated Product Intensities";
for (int charge = 1; charge <= psmCharge; charge++)
{
foreach (FragmentClass fragment in dbOptions.fragments)
{
title += "," + fragment.Name + " ^" + charge;
}
}
for (int charge = 1; charge <= psmCharge; charge++)
{
foreach (FragmentClass fragment in fragments)
{
title += "," + fragment.Name + " ^" + charge;
}
}
writer.AddLine(title);
for (int i = 1; i <= peptide.Length; i++)
{
string line = i.ToString();
for (int charge = 1; charge <= psmCharge; charge++)
{
foreach (FragmentClass fragment in dbOptions.fragments)
{
double cumul = 0.0;
foreach (PeptideSpectrumMatch psm in psms)
{
foreach (ProductMatch match in psm.AllProductMatches)
{
if (fragment == match.Fragment && match.fragmentPos == i && match.charge == charge)
{
cumul += match.obsIntensity;
}
}
}
line += "," + cumul;
}
}
for (int charge = 1; charge <= psmCharge; charge++)
{
foreach (FragmentClass fragment in fragments)
{
double cumul = 0.0;
foreach (PeptideSpectrumMatch psm in psms)
{
foreach (ProductMatch match in psm.AllProductMatches)
{
if (fragment == match.Fragment && match.fragmentPos == i && match.charge == charge)
{
cumul += match.obsIntensity;
}
}
}
line += "," + cumul;
}
}
writer.AddLine(line);
}
writer.WriteToFile();
}
public IEnumerable <ProductMatch> ComputeFragments(Peptide peptide, int precursorKnownCharge, DBOptions dbOptions)
{
int maxCharge;
if (precursorKnownCharge > 1)
{
maxCharge = precursorKnownCharge - 1;
}
else
{
maxCharge = precursorKnownCharge;
}
string sequence = peptide.BaseSequence;
ProductMatch match = new ProductMatch();
double cumulativeNTerminalMass = 0; // 1.007276 + 15.9949;//TODO Add NTerminal modifications here
double cumulativeCTerminalMass = 0; // 1.007276;//TODO Add CTerminal modifications here
string cumulSeq = "";
string cumulRevSeq = "";
for (int r = 1; r <= sequence.Length; r++)
{
match.fragmentPos = r;
//Peptide mods, computed during digestion
//TODO Only search for modifications that were seen in the spectrum
double tmp = 0;
cumulSeq += sequence[r - 1];
if (peptide.FixedModifications != null && peptide.FixedModifications.ContainsKey(r + 1))
{
foreach (Modification mod in peptide.FixedModifications[r + 1])
{
tmp += mod.MonoisotopicMassShift;
}
}
if (peptide.VariableModifications != null && peptide.VariableModifications.ContainsKey(r + 1))
{
tmp += peptide.VariableModifications[r + 1].MonoisotopicMassShift;
}
cumulativeNTerminalMass += AminoAcidMasses.GetMonoisotopicMass(sequence[r - 1]) + tmp;
tmp = 0;
cumulRevSeq += sequence[sequence.Length - r];
if (peptide.FixedModifications != null && peptide.FixedModifications.ContainsKey(sequence.Length + 2 - r))
{
foreach (Modification mod in peptide.FixedModifications[sequence.Length + 2 - r])
{
tmp += mod.MonoisotopicMassShift;
}
}
if (peptide.VariableModifications != null && peptide.VariableModifications.ContainsKey(sequence.Length + 2 - r))
{
tmp += peptide.VariableModifications[sequence.Length + 2 - r].MonoisotopicMassShift;
}
cumulativeCTerminalMass += AminoAcidMasses.GetMonoisotopicMass(sequence[sequence.Length - r]) + tmp;
for (int c = maxCharge; c > 0; c--)
{
match.charge = c;
foreach (FragmentClass fragment in this)
{
if (fragment.IsReverse)
{
match.fragmentPos = 1 + sequence.Length - r;
}
else
{
match.fragmentPos = r;
}
match.Fragment = fragment;
foreach (double product_mass in fragment.ComputeFragment(cumulativeCTerminalMass, cumulativeNTerminalMass))
{
match.weight = fragment.Distribution;//TODO Adjust this value by computing overall impact (times 10?)
//ModLess
match.theoMz = Numerics.MZFromMass(product_mass, c);
yield return(match);
//Added mods
if (dbOptions.addFragmentMods)
{
foreach (Modification mod in FragmentDictionary.Fragments.Values)
{
if ((fragment.IsReverse ? cumulRevSeq : cumulSeq).Contains(mod.AminoAcid))
{
//!!!!match.Fragment = mod;
match.weight = fragment.Distribution * mod.Probability;
match.theoMz = Numerics.MZFromMass(product_mass + mod.MonoisotopicMassShift, c);
yield return(match);
}
}
}
}
}
}
}
if (dbOptions.addFragmentLoss)
{
match.charge = 1;
match.Fragment = FragLossObject;
foreach (Modification mod in FragmentDictionary.AAFragments.Values)
{
if (peptide.BaseSequence.Contains(mod.AminoAcid))
{
match.fragmentPos = peptide.BaseSequence.IndexOf(mod.AminoAcid);
match.theoMz = mod.MonoisotopicMassShift;// Numerics.MZFromMass(mod.MonoisotopicMassShift, 1);
match.weight = mod.Probability;
yield return(match);
}
}
}
}
}//*/
/*
* private static IEnumerable<double> fragmentsTypesCTerm(double cTermCumul)
* {
* yield return cTermCumul + Constants.OXYGEN_MASS * 2 + Constants.HYDROGEN_MASS + Constants.CARBON_MASS;//X
* yield return cTermCumul + Constants.OXYGEN_MASS + Constants.HYDROGEN_MASS * 3;//Y
* yield return cTermCumul + Constants.OXYGEN_MASS + Constants.HYDROGEN_MASS - Constants.NITROGEN_MASS - Constants.HYDROGEN_MASS;//Z
* } //*/
public static IEnumerable <ProductMatch> ComputeAllFragments(Peptide peptide, int precursorKnownCharge, DBOptions dbOptions)
{
int maxCharge;
if (precursorKnownCharge > 1)
{
maxCharge = precursorKnownCharge - 1;
}
else
{
maxCharge = 1;
}
FragmentA fragNTerm = new FragmentA();
FragmentX fragCTerm = new FragmentX();
double[] masses = peptide.GetMasses();
ProductMatch match = new ProductMatch();
match.weight = 1;
double cumulN = 0.0; // Constants.WATER_MONOISOTOPIC_MASS;
double cumulC = 0.0; // Constants.WATER_MONOISOTOPIC_MASS;
for (int r = 0; r < masses.Length; r++)
{
cumulN += masses[r];
cumulC += masses[masses.Length - r - 1];
foreach (double product_mass in fragmentsTypesCTerm(cumulC))
{
match.fragmentPos = masses.Length - r;
match.Fragment = fragCTerm;
for (int c = maxCharge; c > 0; c--)
{
match.theoMz = Numerics.MZFromMass(product_mass, c);
match.charge = c;
yield return(match);
//match.theoMz = Numerics.MZFromMass(product_mass - Constants.WATER_MONOISOTOPIC_MASS, c);
//yield return match;
}
}
foreach (double product_mass in fragmentsTypesNTerm(cumulN))
{
match.fragmentPos = r + 1;
match.Fragment = fragNTerm;
for (int c = maxCharge; c > 0; c--)
{
match.theoMz = Numerics.MZFromMass(product_mass, c);
match.charge = c;
yield return(match);
match.theoMz = Numerics.MZFromMass(product_mass - Constants.WATER_MONOISOTOPIC_MASS, c);
yield return(match);
match.theoMz = Numerics.MZFromMass(product_mass - Constants.AMONIA_MASS, c);
yield return(match);
}
}
}
//Single charge immonium ions
//Water Loss
//Amonia Loss
//Internal fragments
//Fragment types
}
public IEnumerable <Peptide> GetVariablyModifiedPeptides(IEnumerable <Modification> variableModifications, int maximumVariableModificationIsoforms)
{
Dictionary <int, List <Modification> > possible_modifications = new Dictionary <int, List <Modification> >(Length + 4);
foreach (Modification variable_modification in variableModifications)
{
if (variable_modification.Type == ModificationType.ProteinNTerminus && (StartResidueNumber == 1 || (StartResidueNumber == 2 && Parent[0] == 'M')))
{
List <Modification> prot_n_term_variable_mods;
if (!possible_modifications.TryGetValue(0, out prot_n_term_variable_mods))
{
prot_n_term_variable_mods = new List <Modification>();
prot_n_term_variable_mods.Add(variable_modification);
possible_modifications.Add(0, prot_n_term_variable_mods);
}
else
{
prot_n_term_variable_mods.Add(variable_modification);
}
}
if (variable_modification.Type == ModificationType.PeptideNTerminus)
{
List <Modification> pep_n_term_variable_mods;
if (!possible_modifications.TryGetValue(1, out pep_n_term_variable_mods))
{
pep_n_term_variable_mods = new List <Modification>();
pep_n_term_variable_mods.Add(variable_modification);
possible_modifications.Add(1, pep_n_term_variable_mods);
}
else
{
pep_n_term_variable_mods.Add(variable_modification);
}
}
for (int r = 0; r < Length; r++)
{
if (variable_modification.Type == ModificationType.AminoAcidResidue && this[r] == variable_modification.AminoAcid)
{
List <Modification> residue_variable_mods;
if (!possible_modifications.TryGetValue(r + 2, out residue_variable_mods))
{
residue_variable_mods = new List <Modification>();
residue_variable_mods.Add(variable_modification);
possible_modifications.Add(r + 2, residue_variable_mods);
}
else
{
residue_variable_mods.Add(variable_modification);
}
}
}
if (variable_modification.Type == ModificationType.PeptideCTerminus)
{
List <Modification> pep_c_term_variable_mods;
if (!possible_modifications.TryGetValue(Length + 2, out pep_c_term_variable_mods))
{
pep_c_term_variable_mods = new List <Modification>();
pep_c_term_variable_mods.Add(variable_modification);
possible_modifications.Add(Length + 2, pep_c_term_variable_mods);
}
else
{
pep_c_term_variable_mods.Add(variable_modification);
}
}
if (variable_modification.Type == ModificationType.ProteinCTerminus && (EndResidueNumber == Parent.Length - 1))
{
List <Modification> prot_c_term_variable_mods;
if (!possible_modifications.TryGetValue(Length + 3, out prot_c_term_variable_mods))
{
prot_c_term_variable_mods = new List <Modification>();
prot_c_term_variable_mods.Add(variable_modification);
possible_modifications.Add(Length + 3, prot_c_term_variable_mods);
}
else
{
prot_c_term_variable_mods.Add(variable_modification);
}
}
}
int variable_modification_isoforms = 0;
foreach (Dictionary <int, Modification> kvp in GetVariableModificationPatterns(possible_modifications))
{
Peptide peptide = new Peptide(this);
peptide.SetFixedModifications(FixedModifications);
peptide.SetVariableModifications(kvp);
yield return(peptide);
variable_modification_isoforms++;
if (variable_modification_isoforms >= maximumVariableModificationIsoforms)
{
yield break;
}
}
}
public PeptideMatch(Peptide peptide)
{
this.peptide = peptide;
clusters = new GraphML_List <Cluster>();
}
public double ScoreFct(Peptide peptide = null)
{
return(precursor.ProbabilityScore(peptide));
}
}//*/
public IEnumerable <ProductMatch> GetProductMZs(DBOptions options, GraphML_List <MsMsPeak> peaks)//, List<double> theoretical_product_mzs = null)
{
// speed optimizations
//double[] experimental_masses = Query.spectrum.Masses;
//GraphML_List<MSPeak> peaks = Query.spectrum.Peaks;
int num_experimental_peaks = peaks.Count;
TotalTheoreticalProducts = 0;
TotalWeightedProducts = 0;
//New version that should include charged ions
//foreach (ProductMatch matchTheo in AllFragmentSearch.ComputeAllFragments(Peptide, Query.precursor.Charge, options))
foreach (ProductMatch matchTheo in options.fragments.ComputeFragmentsFast(Peptide.GetMasses(), Query.precursor.Charge, options))
//foreach (ProductMatch matchTheo in options.fragments.ComputeFragments(Peptide, Query.precursor.Charge, options))
{
TotalTheoreticalProducts++;
TotalWeightedProducts += matchTheo.weight;//++;
//TODO test what is most common between charged ions, and uncharged ions
//for (int charge = 1; charge <= Query.precursor.Charge; charge++)
//for (int charge = Query.precursor.Charge; charge >= 1; charge--)
//{
double massDiff = options.productMassTolerance.Value;
double bestMz = -1;
double bestInt = 0;
foreach (int index in Query.spectrum.GetIndexOfMZInRange(matchTheo.theoMz, options.productMassTolerance))
{
if (peaks[index].Charge <= 0 || peaks[index].Charge == matchTheo.charge)
{
double diff = Numerics.CalculateMassError(peaks[index].MZ, matchTheo.theoMz, options.productMassTolerance.Units);
//double diff = matchTheo.theoMz - peaks[index].MZ;// experimental_masses[index];//TODO DALTON ONLY : add product mass tolerance unit test
if (Math.Abs(diff) < options.productMassTolerance.Value)
{
if (Math.Abs(diff) < Math.Abs(massDiff))//TODO Priority to intensity, or precision?
{
massDiff = diff;
bestMz = peaks[index].MZ;
}
//if (peaks[index].Intensity > bestInt)
bestInt += peaks[index].Intensity;
}
}
}
if (bestMz >= 0)
{
ProductMatch pMatch = new ProductMatch();
pMatch.weight = matchTheo.weight;
pMatch.theoMz = matchTheo.theoMz; // Utilities.MZFromMzSingleCharge(theoMass, charge);
pMatch.obsMz = bestMz; // experimental_masses[bestIndex];
pMatch.mass_diff = massDiff;
pMatch.obsIntensity = bestInt; // Intensities[bestIndex];
pMatch.charge = matchTheo.charge; // peaks[bestIndex].Charge;
pMatch.Fragment = matchTheo.Fragment;
pMatch.fragmentPos = matchTheo.fragmentPos;
pMatch.normalizedIntensity = pMatch.obsIntensity / (Query.spectrum.InjectionTime * Query.spectrum.PrecursorIntensityPerMilliSecond);
yield return(pMatch);
//break;
}
}
}
public AnnotatedSpectrum(Sample sample, ProductSpectrum spectrum, Peptide peptide)
{
sequence = peptide.BaseSequence;
peaks = new double[spectrum.Peaks.Count][];
for (int i = 0; i < peaks.Length; i++)
{
peaks[i] = new double[2];
peaks[i][0] = spectrum.Peaks[i].MZ;
peaks[i][1] = spectrum.Peaks[i].Intensity;
}
scanNum = spectrum.ScanNumber;
charge = spectrum.PrecursorCharge;
precursorMz = spectrum.PrecursorMZ;
fileName = sample.sSDF;
//Fixed modifications
List <AnnotatedSpectrumModification> fixedMods = new List <AnnotatedSpectrumModification>();
if (peptide.FixedModifications != null)
{
foreach (int position in peptide.FixedModifications.Keys)
{
if (position == 1)
{
foreach (Modification mod in peptide.FixedModifications[position])
{
ntermMod += mod.MonoisotopicMassShift;
}
}
else
if (position == sequence.Length + 2)
{
foreach (Modification mod in peptide.FixedModifications[position])
{
ctermMod += mod.MonoisotopicMassShift;
}
}
else
{
foreach (Modification mod in peptide.FixedModifications[position])
{
fixedMods.Add(new AnnotatedSpectrumModification(mod.AminoAcid, mod.MonoisotopicMassShift, position - 1));
}
}
}
}
staticMods = fixedMods.ToArray();
//Variable modifications
List <AnnotatedSpectrumModification> varMods = new List <AnnotatedSpectrumModification>();
if (peptide.VariableModifications != null)
{
foreach (int position in peptide.VariableModifications.Keys)
{
if (position == 1)
{
ntermMod += peptide.VariableModifications[position].MonoisotopicMassShift;
}
else
if (position == sequence.Length + 2)
{
ctermMod += peptide.VariableModifications[position].MonoisotopicMassShift;
}
else
{
varMods.Add(new AnnotatedSpectrumModification(peptide.VariableModifications[position].AminoAcid, peptide.VariableModifications[position].MonoisotopicMassShift, position - 1));
}
}
}
variableMods = varMods.ToArray();
/*
* var sequence = "FDSFGDLSSASAIMGNPK";
* var varMods = [];
* // modification index = 14; modification mass = 16.0; modified residue = 'M'
* varMods[0] = { index: 14, modMass: 16.0, aminoAcid: 'M' };
* // mass to be added to the N-terminus
* var ntermMod = 164.07;//*/
}