public TransitionLossKey(TransitionGroupDocNode parent, TransitionDocNode transition, TransitionLosses losses)
{
Transition = transition.Transition;
Losses = losses;
if (Transition.IsCustom())
{
if (!string.IsNullOrEmpty(transition.PrimaryCustomIonEquivalenceKey))
{
CustomIonEquivalenceTestValue = transition.PrimaryCustomIonEquivalenceKey;
}
else if (!string.IsNullOrEmpty(transition.SecondaryCustomIonEquivalenceKey))
{
CustomIonEquivalenceTestValue = transition.SecondaryCustomIonEquivalenceKey;
}
else if (Transition.IsNonReporterCustomIon())
{
CustomIonEquivalenceTestValue = "_mzSortIndex_" + parent.Children.IndexOf(transition); // Not L10N
}
else
{
CustomIonEquivalenceTestValue = null;
}
}
else
{
CustomIonEquivalenceTestValue = null;
}
}
public DocNode EnsureChildren(TransitionGroupDocNode parent, SrmSettings settings)
{
// Make sure node points to correct parent.
if (ReferenceEquals(parent.TransitionGroup, Transition.Group))
{
return(this);
}
var transition = Transition.IsCustom()
? new Transition(parent.TransitionGroup,
Transition.Adduct,
Transition.MassIndex,
Transition.CustomIon,
Transition.IonType)
: new Transition(parent.TransitionGroup,
Transition.IonType,
Transition.CleavageOffset,
Transition.MassIndex,
Transition.Adduct);
return(new TransitionDocNode(transition,
Annotations,
Losses,
TypedMass.ZERO_MONO_MASSH,
QuantInfo,
ExplicitValues,
null)
{
Mz = Mz, MzMassType = MzMassType
});
}
// 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 TransitionDocNode(Transition id,
Annotations annotations,
TransitionLosses losses,
TypedMass mass,
TransitionQuantInfo transitionQuantInfo,
Results <TransitionChromInfo> results)
: base(id, annotations)
{
Losses = losses;
if (losses != null)
{
mass -= losses.Mass;
}
Mz = id.IsCustom() ?
new SignedMz(id.Adduct.MzFromNeutralMass(mass), id.IsNegative()) :
new SignedMz(SequenceMassCalc.GetMZ(mass, id.Adduct) + SequenceMassCalc.GetPeptideInterval(id.DecoyMassShift), id.IsNegative());
MzMassType = mass.MassType;
IsotopeDistInfo = transitionQuantInfo.IsotopeDistInfo;
LibInfo = transitionQuantInfo.LibInfo;
Results = results;
Quantitative = transitionQuantInfo.Quantititative;
}
public double GetIonMass()
{
return(Transition.IsCustom()
? BioMassCalc.CalculateIonMassFromMz(Mz, Transition.Charge)
: SequenceMassCalc.GetMH(Mz, Transition.Charge));
}
/// <summary>
/// Return product's neutral mass rounded for XML I/O
/// </summary>
public double GetIonPersistentNeutralMass()
{
double ionMass = GetIonMass();
return(Transition.IsCustom() ? Math.Round(ionMass, SequenceMassCalc.MassPrecision) : SequenceMassCalc.PersistentNeutral(ionMass));
}
public double GetFragmentMass(Transition transition, IsotopeDistInfo isotopeDist, ExplicitSequenceMods mods)
{
if (transition.IsCustom())
{
var type = transition.IonType;
var massIndex = transition.MassIndex;
if (Transition.IsPrecursor(type) && (isotopeDist != null))
{
var i = isotopeDist.MassIndexToPeakIndex(massIndex);
if (0 > i || i >= isotopeDist.CountPeaks)
{
throw new IndexOutOfRangeException(
string.Format(Resources.SequenceMassCalc_GetFragmentMass_Precursor_isotope__0__is_outside_the_isotope_distribution__1__to__2__,
GetMassIDescripion(massIndex), isotopeDist.PeakIndexToMassIndex(0),
isotopeDist.PeakIndexToMassIndex(isotopeDist.CountPeaks - 1)));
}
return isotopeDist.GetMassI(massIndex);
}
return (MassType == MassType.Average)
? transition.CustomIon.AverageMass
: transition.CustomIon.MonoisotopicMass;
}
return GetFragmentMass(transition.Group.Peptide.Sequence,
transition.IonType,
transition.Ordinal,
transition.DecoyMassShift,
transition.MassIndex,
isotopeDist,
mods);
}
public static TransitionDocNode FromTransitionProto(AnnotationScrubber scrubber, SrmSettings settings,
TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues,
SkylineDocumentProto.Types.Transition transitionProto)
{
var stringPool = scrubber.StringPool;
IonType ionType = DataValues.FromIonType(transitionProto.FragmentType);
MeasuredIon measuredIon = null;
if (transitionProto.MeasuredIonName != null)
{
measuredIon = settings.TransitionSettings.Filter.MeasuredIons.SingleOrDefault(
i => i.Name.Equals(transitionProto.MeasuredIonName.Value));
if (measuredIon == null)
{
throw new InvalidDataException(string.Format(Resources.TransitionInfo_ReadXmlAttributes_The_reporter_ion__0__was_not_found_in_the_transition_filter_settings_, transitionProto.MeasuredIonName));
}
ionType = IonType.custom;
}
bool isCustom = Transition.IsCustom(ionType, group);
bool isPrecursor = Transition.IsPrecursor(ionType);
CustomMolecule customIon = null;
if (isCustom)
{
if (measuredIon != null)
{
customIon = measuredIon.SettingsCustomIon;
}
else if (isPrecursor)
{
customIon = group.CustomMolecule;
}
else
{
var formula = DataValues.FromOptional(transitionProto.Formula);
var moleculeID = MoleculeAccessionNumbers.FromString(DataValues.FromOptional(transitionProto.MoleculeId)); // Tab separated list of InChiKey, CAS etc
var monoMassH = DataValues.FromOptional(transitionProto.MonoMassH);
var averageMassH = DataValues.FromOptional(transitionProto.AverageMassH);
var monoMass = DataValues.FromOptional(transitionProto.MonoMass) ?? monoMassH;
var averageMass = DataValues.FromOptional(transitionProto.AverageMass) ?? averageMassH;
customIon = new CustomMolecule(formula,
new TypedMass(monoMass.Value, monoMassH.HasValue ? MassType.MonoisotopicMassH : MassType.Monoisotopic),
new TypedMass(averageMass.Value, averageMassH.HasValue ? MassType.AverageMassH : MassType.Average),
DataValues.FromOptional(transitionProto.CustomIonName), moleculeID);
}
}
Transition transition;
var adductString = DataValues.FromOptional(transitionProto.Adduct);
var adduct = string.IsNullOrEmpty(adductString)
? Adduct.FromChargeProtonated(transitionProto.Charge)
: Adduct.FromStringAssumeChargeOnly(adductString);
if (isCustom)
{
transition = new Transition(group, isPrecursor ? group.PrecursorAdduct :adduct, transitionProto.MassIndex, customIon, ionType);
}
else if (isPrecursor)
{
transition = new Transition(group, ionType, group.Peptide.Length - 1, transitionProto.MassIndex,
group.PrecursorAdduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
else
{
int offset = Transition.OrdinalToOffset(ionType, transitionProto.FragmentOrdinal,
group.Peptide.Length);
transition = new Transition(group, ionType, offset, transitionProto.MassIndex, adduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
var losses = TransitionLosses.FromLossProtos(settings, transitionProto.Losses);
var mass = settings.GetFragmentMass(group, mods, transition, isotopeDist);
var isotopeDistInfo = GetIsotopeDistInfo(transition, losses, isotopeDist);
if (group.DecoyMassShift.HasValue && transitionProto.DecoyMassShift == null)
{
throw new InvalidDataException(Resources.SrmDocument_ReadTransitionXml_All_transitions_of_decoy_precursors_must_have_a_decoy_mass_shift);
}
TransitionLibInfo libInfo = null;
if (transitionProto.LibInfo != null)
{
libInfo = new TransitionLibInfo(transitionProto.LibInfo.Rank, transitionProto.LibInfo.Intensity);
}
var annotations = scrubber.ScrubAnnotations(Annotations.FromProtoAnnotations(transitionProto.Annotations), AnnotationDef.AnnotationTarget.transition);
var results = TransitionChromInfo.FromProtoTransitionResults(scrubber, settings, transitionProto.Results);
var explicitTransitionValues = pre422ExplicitTransitionValues ?? ExplicitTransitionValues.Create(
DataValues.FromOptional(transitionProto.ExplicitCollisionEnergy),
DataValues.FromOptional(transitionProto.ExplicitIonMobilityHighEnergyOffset),
DataValues.FromOptional(transitionProto.ExplicitSLens),
DataValues.FromOptional(transitionProto.ExplicitConeVoltage),
DataValues.FromOptional(transitionProto.ExplicitDeclusteringPotential));
return(new TransitionDocNode(transition, annotations, losses, mass, new TransitionQuantInfo(isotopeDistInfo, libInfo, !transitionProto.NotQuantitative), explicitTransitionValues, results));
}
public SkylineDocumentProto.Types.Transition ToTransitionProto(SrmSettings settings)
{
var transitionProto = new SkylineDocumentProto.Types.Transition
{
FragmentType = DataValues.ToIonType(Transition.IonType),
NotQuantitative = !ExplicitQuantitative
};
if (Transition.IsCustom() && !Transition.IsPrecursor())
{
SetCustomIonFragmentInfo(transitionProto);
}
transitionProto.DecoyMassShift = DataValues.ToOptional(Transition.DecoyMassShift);
transitionProto.MassIndex = Transition.MassIndex;
if (HasDistInfo)
{
transitionProto.IsotopeDistRank = DataValues.ToOptional(IsotopeDistInfo.Rank);
transitionProto.IsotopeDistProportion = DataValues.ToOptional(IsotopeDistInfo.Proportion);
}
if (!Transition.IsPrecursor())
{
if (!Transition.IsCustom())
{
transitionProto.FragmentOrdinal = Transition.Ordinal;
transitionProto.CalcNeutralMass = GetMoleculePersistentNeutralMass();
}
transitionProto.Charge = Transition.Charge;
if (!Transition.Adduct.IsProteomic)
{
transitionProto.Adduct = DataValues.ToOptional(Transition.Adduct.AsFormulaOrSignedInt());
}
if (!Transition.IsCustom())
{
transitionProto.CleavageAa = Transition.AA;
transitionProto.LostMass = LostMass;
}
}
if (Annotations != null)
{
transitionProto.Annotations = Annotations.ToProtoAnnotations();
}
transitionProto.ProductMz = Mz;
if (Losses != null)
{
foreach (var loss in Losses.Losses)
{
var neutralLoss = new SkylineDocumentProto.Types.TransitionLoss();
if (loss.PrecursorMod == null)
{
neutralLoss.Formula = loss.Loss.Formula;
neutralLoss.MonoisotopicMass = loss.Loss.MonoisotopicMass;
neutralLoss.AverageMass = loss.Loss.AverageMass;
neutralLoss.LossInclusion = DataValues.ToLossInclusion(loss.Loss.Inclusion);
neutralLoss.Charge = loss.Loss.Charge;
}
else
{
neutralLoss.ModificationName = loss.PrecursorMod.Name;
neutralLoss.LossIndex = loss.LossIndex;
}
transitionProto.Losses.Add(neutralLoss);
}
}
if (HasLibInfo)
{
transitionProto.LibInfo = new SkylineDocumentProto.Types.TransitionLibInfo
{
Intensity = LibInfo.Intensity,
Rank = LibInfo.Rank
};
}
if (Results != null)
{
transitionProto.Results = new SkylineDocumentProto.Types.TransitionResults();
transitionProto.Results.Peaks.AddRange(GetTransitionPeakProtos(settings.MeasuredResults));
}
if (!Equals(ExplicitValues, ExplicitTransitionValues.EMPTY))
{
transitionProto.ExplicitCollisionEnergy = DataValues.ToOptional(ExplicitValues.CollisionEnergy);
transitionProto.ExplicitConeVoltage = DataValues.ToOptional(ExplicitValues.ConeVoltage);
transitionProto.ExplicitDeclusteringPotential = DataValues.ToOptional(ExplicitValues.DeclusteringPotential);
transitionProto.ExplicitIonMobilityHighEnergyOffset = DataValues.ToOptional(ExplicitValues.IonMobilityHighEnergyOffset);
transitionProto.ExplicitSLens = DataValues.ToOptional(ExplicitValues.SLens);
}
return(transitionProto);
}
/// <summary>
/// Return product's neutral mass rounded for XML I/O
/// </summary>
public double GetMoleculePersistentNeutralMass()
{
var moleculeMass = GetMoleculeMass();
return(Transition.IsCustom() ? Math.Round(moleculeMass, SequenceMassCalc.MassPrecision) : SequenceMassCalc.PersistentNeutral(moleculeMass));
}