private MoleculeMasses GetCrosslinkMasses(SrmSettings settings)
{
var predictDocNode = MakeTransitionGroupWithAllPossibleChildren(settings, TargetInfoObj.TransitionGroupDocNode.LabelType);
TransitionGroupDocNode matchDocNode;
if (Equals(TargetInfoObj.TransitionGroupDocNode.LabelType, TargetInfoObj.SpectrumLabelType))
{
matchDocNode = predictDocNode;
}
else
{
matchDocNode = MakeTransitionGroupWithAllPossibleChildren(settings, TargetInfoObj.SpectrumLabelType);
}
var matchTransitions = matchDocNode.Transitions.ToDictionary(child => child.Key(matchDocNode));
var predictFragments = new List <MatchedFragmentIon>();
var matchFragments = new List <MatchedFragmentIon>();
foreach (var predictedTransition in predictDocNode.Transitions)
{
var key = predictedTransition.Key(null);
TransitionDocNode matchTransition;
if (!matchTransitions.TryGetValue(key, out matchTransition))
{
continue;
}
var complexFragmentIonName = predictedTransition.ComplexFragmentIon.GetName();
var ionType = DecideIonType(complexFragmentIonName);
string fragmentName = predictedTransition.ComplexFragmentIon.GetFragmentIonName();
var predictedIon = new MatchedFragmentIon(ionType, predictFragments.Count + 1,
predictedTransition.Transition.Adduct, fragmentName, predictedTransition.Losses,
predictedTransition.Mz)
.ChangeComplexFragmentIonName(complexFragmentIonName);
predictFragments.Add(predictedIon);
matchFragments.Add(predictedIon.ChangePredictedMz(matchTransition.Mz));
}
var matchMasses = new IonMasses(
SequenceMassCalc.GetMH(matchDocNode.PrecursorMz, matchDocNode.PrecursorAdduct,
MassType.MonoisotopicMassH), IonTable <TypedMass> .EMPTY)
.ChangeKnownFragments(matchFragments);
var predictMasses = new IonMasses(
SequenceMassCalc.GetMH(predictDocNode.PrecursorMz, predictDocNode.PrecursorAdduct,
MassType.MonoisotopicMassH), IonTable <TypedMass> .EMPTY)
.ChangeKnownFragments(predictFragments);
return(new MoleculeMasses(predictDocNode.PrecursorMz, matchMasses).ChangePredictIonMasses(predictMasses));
}
public MoleculeMasses ChangePredictIonMasses(IonMasses predictIonMasses)
{
return(ChangeProp(ImClone(this), im => im.PredictIonMasses = predictIonMasses));
}
public MoleculeMasses(double precursorMz, IonMasses ionMasses)
{
this.precursorMz = precursorMz;
PredictIonMasses = MatchIonMasses = ionMasses;
}
public SpectrumRanker(TargetInfo targetInfo, SrmSettings settings,
FragmentFilter fragmentFilter)
{
TargetInfoObj = targetInfo;
FragmentFilterObj = fragmentFilter;
var groupDocNode = TargetInfoObj.TransitionGroupDocNode;
TransitionGroup group = groupDocNode.TransitionGroup;
bool isProteomic = group.IsProteomic;
bool limitRanks =
groupDocNode.IsCustomIon && // For small molecules, cap the number of ranked ions displayed if we don't have any peak metadata
groupDocNode.Transitions.Any(t => string.IsNullOrEmpty(t.FragmentIonName));
RankLimit = limitRanks ? settings.TransitionSettings.Libraries.IonCount : (int?)null;
// Get necessary mass calculators and masses
var labelType = targetInfo.SpectrumLabelType;
var lookupMods = targetInfo.LookupMods;
var calcMatchPre = settings.GetPrecursorCalc(labelType, lookupMods);
var calcMatch = isProteomic ? settings.GetFragmentCalc(labelType, lookupMods) : settings.GetDefaultFragmentCalc();
var calcPredict = isProteomic ? settings.GetFragmentCalc(group.LabelType, lookupMods) : calcMatch;
MoleculeMasses moleculeMasses;
if (null != lookupMods && lookupMods.HasCrosslinks)
{
moleculeMasses = GetCrosslinkMasses(settings);
}
else
{
if (isProteomic && Sequence.IsProteomic)
{
moleculeMasses = new MoleculeMasses(
SequenceMassCalc.GetMZ(calcMatchPre.GetPrecursorMass(Sequence), PrecursorAdduct),
new IonMasses(calcMatch.GetPrecursorFragmentMass(Sequence),
calcMatch.GetFragmentIonMasses(Sequence)));
}
else if (!isProteomic && !Sequence.IsProteomic)
{
string isotopicFormula;
var knownFragments = new List <MatchedFragmentIon>();
foreach (var tran in groupDocNode.Transitions)
{
if (tran.Transition.IsNonPrecursorNonReporterCustomIon())
{
knownFragments.Add(new MatchedFragmentIon(IonType.custom, knownFragments.Count + 1,
tran.Transition.Adduct,
tran.GetFragmentIonName(CultureInfo.CurrentCulture,
settings.TransitionSettings.Libraries.IonMatchTolerance),
null,
tran.Mz));
}
}
var ionMasses =
new IonMasses(calcMatch.GetPrecursorFragmentMass(Sequence), IonTable <TypedMass> .EMPTY)
.ChangeKnownFragments(knownFragments);
moleculeMasses =
new MoleculeMasses(
SequenceMassCalc.GetMZ(
calcMatchPre.GetPrecursorMass(Sequence.Molecule, null, PrecursorAdduct,
out isotopicFormula), PrecursorAdduct), ionMasses);
}
else
{
moleculeMasses = new MoleculeMasses(0.0,
new IonMasses(TypedMass.ZERO_MONO_MASSH, IonTable <TypedMass> .EMPTY));
}
if (!ReferenceEquals(calcPredict, calcMatch))
{
var ionTable = moleculeMasses.MatchIonMasses.FragmentMasses;
if (Sequence.IsProteomic
) // CONSIDER - eventually we may be able to predict fragments for small molecules?
{
ionTable = calcPredict.GetFragmentIonMasses(Sequence);
}
moleculeMasses =
moleculeMasses.ChangePredictIonMasses(new IonMasses(
calcPredict.GetPrecursorFragmentMass(Sequence),
ionTable));
}
}
MoleculeMassesObj = moleculeMasses;
// Get values of interest from the settings.
TransitionSettings = settings.TransitionSettings;
// Get potential losses to all fragments in this peptide
PotentialLosses = TransitionGroup.CalcPotentialLosses(Sequence, settings.PeptideSettings.Modifications,
lookupMods, MassType);
}