public TransitionQuantInfo(TransitionIsotopeDistInfo isotopeDistInfo, TransitionLibInfo libInfo,
bool quantitative) : this()
{
IsotopeDistInfo = isotopeDistInfo;
LibInfo = libInfo;
Quantititative = quantitative;
}
public TransitionDocNode(Transition id,
Annotations annotations,
TransitionLosses losses,
double massH,
TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLibInfo libInfo,
Results <TransitionChromInfo> results)
: base(id, annotations)
{
Losses = losses;
if (losses != null)
{
massH -= losses.Mass;
}
if (id.IsCustom())
{
Mz = new SignedMz(BioMassCalc.CalculateIonMz(massH, id.Charge), id.IsNegative());
}
else
{
Mz = new SignedMz(SequenceMassCalc.GetMZ(massH, id.Charge) + SequenceMassCalc.GetPeptideInterval(id.DecoyMassShift), id.IsNegative());
}
IsotopeDistInfo = isotopeDistInfo;
LibInfo = libInfo;
Results = results;
}
public TransitionDocNode(Transition id,
TransitionLosses losses,
double massH,
TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLibInfo libInfo)
: this(id, Annotations.EMPTY, losses, massH, isotopeDistInfo, libInfo, null)
{
}
public TransitionQuantInfo ChangeIsotopeDistInfo(TransitionIsotopeDistInfo transitionIsotopeDistInfo)
{
var quantInfo = this;
quantInfo.IsotopeDistInfo = transitionIsotopeDistInfo;
if (transitionIsotopeDistInfo != null)
{
quantInfo.LibInfo = null;
}
return(quantInfo);
}
private TransitionDocNode CreateTransitionNode(int massIndex, double precursorMassH, TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, CustomIon customIon = null)
{
Transition transition = new Transition(this, massIndex, customIon);
var info = isotopeDistInfo == null?TransitionDocNode.GetLibInfo(transition, Transition.CalcMass(precursorMassH, losses), transitionRanks) : null;
return(new TransitionDocNode(transition, losses, precursorMassH, isotopeDistInfo, info));
}
public IEnumerable <TransitionDocNode> GetPrecursorTransitions(SrmSettings settings,
ExplicitMods mods,
IPrecursorMassCalc calcFilterPre,
IFragmentMassCalc calcPredict,
double precursorMz,
IsotopeDistInfo isotopeDist,
IList <IList <ExplicitLoss> > potentialLosses,
IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks,
bool libraryFilter,
bool useFilter)
{
var tranSettings = settings.TransitionSettings;
var fullScan = tranSettings.FullScan;
MassType massType = tranSettings.Prediction.FragmentMassType;
int minMz = tranSettings.Instrument.GetMinMz(precursorMz);
int maxMz = tranSettings.Instrument.MaxMz;
bool precursorMS1 = fullScan.IsEnabledMs;
if (IsCustomIon)
{
var ionMz =
BioMassCalc.CalculateIonMz(
CustomIon.GetMass(settings.TransitionSettings.Prediction.PrecursorMassType),
PrecursorCharge);
if (!useFilter ||
!libraryFilter ||
IsMatched(transitionRanks,
ionMz, IonType.precursor,
PrecursorCharge, null))
{
if (precursorMS1 && isotopeDist != null)
{
foreach (int i in fullScan.SelectMassIndices(isotopeDist, useFilter))
{
double precursorMS1Mass = isotopeDist.GetMassI(i);
ionMz = BioMassCalc.CalculateIonMz(precursorMS1Mass, PrecursorCharge);
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
var isotopeDistInfo = new TransitionIsotopeDistInfo(isotopeDist.GetRankI(i), isotopeDist.GetProportionI(i));
yield return(CreateTransitionNode(i, precursorMS1Mass, isotopeDistInfo, null, transitionRanks, CustomIon));
}
}
else
{
var transition = new Transition(this, PrecursorCharge, null, CustomIon, IonType.precursor);
double massH = CustomIon.GetMass(settings.TransitionSettings.Prediction.PrecursorMassType);
yield return(new TransitionDocNode(transition, null, massH, null, null));
}
}
yield break;
}
string sequence = Peptide.Sequence;
bool precursorNoProducts = precursorMS1 && !fullScan.IsEnabledMsMs &&
tranSettings.Filter.IonTypes.Count == 1 && tranSettings.Filter.IonTypes[0] == IonType.precursor;
double precursorMassPredict = calcPredict.GetPrecursorFragmentMass(sequence);
foreach (var losses in CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
double ionMz = SequenceMassCalc.GetMZ(Transition.CalcMass(precursorMassPredict, losses), PrecursorCharge);
if (losses == null)
{
if (precursorMS1 && isotopeDist != null)
{
foreach (int i in fullScan.SelectMassIndices(isotopeDist, useFilter))
{
double precursorMS1Mass = isotopeDist.GetMassI(i, DecoyMassShift);
ionMz = SequenceMassCalc.GetMZ(precursorMS1Mass, PrecursorCharge);
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
var isotopeDistInfo = new TransitionIsotopeDistInfo(
isotopeDist.GetRankI(i), isotopeDist.GetProportionI(i));
yield return(CreateTransitionNode(i, precursorMS1Mass, isotopeDistInfo, null, transitionRanks));
}
continue;
}
}
// If there was loss, it is possible (though not likely) that the ion m/z value
// will now fall below the minimum measurable value for the instrument
else if (minMz > ionMz)
{
continue;
}
// If filtering precursors from MS1 scans, then ranking in MS/MS does not apply
bool precursorIsProduct = !precursorMS1 || losses != null;
// Skip product ion precursors, if the should not be included
if (useFilter && precursorIsProduct && precursorNoProducts)
{
continue;
}
if (!useFilter || !precursorIsProduct ||
!libraryFilter || IsMatched(transitionRanks, ionMz, IonType.precursor,
PrecursorCharge, losses))
{
yield return(CreateTransitionNode(0, precursorMassPredict, null, losses,
precursorIsProduct ? transitionRanks : null));
}
}
}
private TransitionDocNode CreateTransitionNode(int massIndex, TypedMass precursorMassH, TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, CustomMolecule customMolecule = null)
{
Transition transition = new Transition(this, massIndex, customMolecule);
var quantInfo = TransitionDocNode.TransitionQuantInfo.GetLibTransitionQuantInfo(transition, losses,
Transition.CalcMass(precursorMassH, losses), transitionRanks).ChangeIsotopeDistInfo(isotopeDistInfo);
return(new TransitionDocNode(transition, losses, precursorMassH, quantInfo));
}
private TransitionDocNode CreateTransitionNode(int massIndex, TypedMass precursorMassH, TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, Adduct productAdduct, CustomMolecule customMolecule = null)
{
Transition transition = new Transition(this, massIndex, productAdduct, customMolecule);
var quantInfo = TransitionDocNode.TransitionQuantInfo.GetLibTransitionQuantInfo(transition, losses,
Transition.CalcMass(precursorMassH, losses), transitionRanks).ChangeIsotopeDistInfo(isotopeDistInfo);
var transitionDocNode = new TransitionDocNode(transition, losses, precursorMassH, quantInfo, ExplicitTransitionValues.EMPTY);
if (massIndex < 0)
{
transitionDocNode = transitionDocNode.ChangeQuantitative(false);
}
return(transitionDocNode);
}
public IEnumerable <TransitionDocNode> GetPrecursorTransitions(SrmSettings settings,
ExplicitMods mods,
IPrecursorMassCalc calcPredictPre,
IFragmentMassCalc calcPredict,
double precursorMz,
IsotopeDistInfo isotopeDist,
IList <IList <ExplicitLoss> > potentialLosses,
IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks,
bool libraryFilter,
bool useFilter,
bool ensureMassesAreMeasurable)
{
var tranSettings = settings.TransitionSettings;
var fullScan = tranSettings.FullScan;
int minMz = tranSettings.Instrument.GetMinMz(precursorMz);
int maxMz = tranSettings.Instrument.MaxMz;
bool precursorMS1 = fullScan.IsEnabledMs;
MassType massType = tranSettings.Prediction.FragmentMassType;
MassType massTypeIon = precursorMS1 ? tranSettings.Prediction.PrecursorMassType : massType;
var sequence = Peptide.Target;
var ionTypes = IsProteomic ? tranSettings.Filter.PeptideIonTypes : tranSettings.Filter.SmallMoleculeIonTypes;
bool precursorNoProducts = precursorMS1 && !fullScan.IsEnabledMsMs &&
ionTypes.Count == 1 && ionTypes[0] == IonType.precursor;
var precursorMassPredict = precursorMS1
? calcPredictPre.GetPrecursorMass(sequence)
: calcPredict.GetPrecursorFragmentMass(sequence);
foreach (var losses in CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
Adduct productAdduct;
if (losses == null)
{
productAdduct = PrecursorAdduct;
}
else
{
productAdduct = losses.GetProductAdduct(PrecursorAdduct);
if (productAdduct == null)
{
continue;
}
}
double ionMz = IsProteomic ?
SequenceMassCalc.GetMZ(Transition.CalcMass(precursorMassPredict, losses), PrecursorAdduct) :
PrecursorAdduct.MzFromNeutralMass(CustomMolecule.GetMass(massTypeIon), massTypeIon);
if (losses == null)
{
if (precursorMS1 && isotopeDist != null && ensureMassesAreMeasurable)
{
foreach (int i in fullScan.SelectMassIndices(isotopeDist, useFilter))
{
var precursorMS1Mass = isotopeDist.GetMassI(i, DecoyMassShift);
ionMz = SequenceMassCalc.GetMZ(precursorMS1Mass, PrecursorAdduct);
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
var isotopeDistInfo = new TransitionIsotopeDistInfo(
isotopeDist.GetRankI(i), isotopeDist.GetProportionI(i));
yield return(CreateTransitionNode(i, precursorMS1Mass, isotopeDistInfo, null, transitionRanks, productAdduct));
}
continue;
}
}
// If there was loss, it is possible (though not likely) that the ion m/z value
// will now fall below the minimum measurable value for the instrument
else if (ensureMassesAreMeasurable && minMz > ionMz)
{
continue;
}
// If filtering precursors from MS1 scans, then ranking in MS/MS does not apply
bool precursorIsProduct = !precursorMS1 || losses != null;
// Skip product ion precursors, if the should not be included
if (useFilter && precursorIsProduct && precursorNoProducts)
{
continue;
}
if (!useFilter || !precursorIsProduct ||
!libraryFilter || IsMatched(transitionRanks, ionMz, IonType.precursor,
PrecursorAdduct, losses))
{
yield return(CreateTransitionNode(0, precursorMassPredict, null, losses,
precursorIsProduct ? transitionRanks : null, productAdduct));
}
}
}
