// Returns molecule mass (or massH, for peptides)
public TypedMass GetMoleculeMass()
{
Assume.IsTrue(Transition.IsCustom() || MzMassType.IsMassH());
return(Transition.IsCustom()
? Transition.Adduct.MassFromMz(Mz, MzMassType)
: new TypedMass(SequenceMassCalc.GetMH(Mz, Transition.Charge), MzMassType));
}
public double GetMassI(int massIndex, int?decoyMassShift = null)
{
// Return the original monoisotopic mass + H, if requested to maintain an exact match.
if (massIndex == 0 && !decoyMassShift.HasValue)
{
return(_monoisotopicMass);
}
// Otherwize use the charge to convert from the peak center m/z values
double shift = SequenceMassCalc.GetPeptideInterval(decoyMassShift); // Correct for shift applied to the distribution
return(_isMassH ? SequenceMassCalc.GetMH(ExpectedPeaks[MassIndexToPeakIndex(massIndex)].Mz - shift, _charge) : BioMassCalc.CalculateIonMassFromMz(ExpectedPeaks[MassIndexToPeakIndex(massIndex)].Mz - shift, _charge));
}
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 TypedMass GetMassI(int massIndex, int?decoyMassShift = null)
{
// Return the original monoisotopic mass + H, if requested to maintain an exact match.
if (massIndex == 0 && !decoyMassShift.HasValue)
{
return(_monoisotopicMass);
}
// Otherwize use the charge to convert from the peak center m/z values
double shift = SequenceMassCalc.GetPeptideInterval(decoyMassShift); // Correct for shift applied to the distribution
// ReSharper disable ImpureMethodCallOnReadonlyValueField
return(_monoisotopicMass.IsMassH() ?
new TypedMass(SequenceMassCalc.GetMH(ExpectedPeaks[MassIndexToPeakIndex(massIndex)].Mz - shift, _adduct.AdductCharge), _monoisotopicMass.MassType) :
_adduct.MassFromMz(ExpectedPeaks[MassIndexToPeakIndex(massIndex)].Mz - shift, _monoisotopicMass.MassType));
// ReSharper restore ImpureMethodCallOnReadonlyValueField
}
public double GetIonMass()
{
return(Transition.IsCustom()
? BioMassCalc.CalculateIonMassFromMz(Mz, Transition.Charge)
: SequenceMassCalc.GetMH(Mz, Transition.Charge));
}
public static Adduct CalcProductCharge(TypedMass productPrecursorMass,
int?productZ,
Adduct precursorCharge,
IList <IonType> acceptedIonTypes,
IonTable <TypedMass> productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double?minDelta = null;
double?minFragmentMass = null, maxFragmentMass = null, maxLoss = null;
if (massShiftType == MassShiftType.none)
{
if (!productZ.HasValue)
{
minFragmentMass = productMz - tolerance;
}
else
{
minFragmentMass = SequenceMassCalc.GetMH(productMz - tolerance, productZ.Value);
maxFragmentMass = SequenceMassCalc.GetMH(productMz + tolerance, productZ.Value);
}
}
var bestCharge = Adduct.EMPTY;
IonType? bestIonType = null;
int? bestOrdinal = null;
TransitionLosses bestLosses = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
var productMass = productPrecursorMass;
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
maxLoss = Math.Max(maxLoss ?? 0, lossesTrial.Mass);
}
int potentialMassShift;
int nearestCharge;
var charge = CalcProductCharge(productMass, productZ, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (Equals(charge, precursorCharge))
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
if (maxLoss.HasValue)
{
maxFragmentMass += maxLoss.Value;
}
var categoryLast = -1;
foreach (var typeAccepted in GetIonTypes(acceptedIonTypes))
{
var type = typeAccepted.IonType;
var category = typeAccepted.IonCategory;
// Types have priorities. If changing type category, and there is already a
// suitable answer stop looking.
if (category != categoryLast && minDelta.HasValue && MatchMz(minDelta.Value, tolerance))
{
break;
}
categoryLast = category;
// The peptide length is 1 longer than the mass array
for (int ord = len; ord > 0; ord--)
{
int offset = Transition.OrdinalToOffset(type, ord, len + 1);
var productMassBase = productMasses[type, offset];
// Until below the maximum fragment mass no possible matches
if (maxFragmentMass.HasValue && productMassBase > maxFragmentMass.Value)
{
continue;
}
// Once below the minimum fragment mass no more possible matches, so stop
if (minFragmentMass.HasValue && productMassBase < minFragmentMass.Value)
{
break;
}
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
var productMass = productMassBase;
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
var chargeFound = CalcProductCharge(productMass, productZ, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (!chargeFound.IsEmpty)
{
var charge = chargeFound;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = type;
bestOrdinal = ord;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}