private void SetCustomIonFragmentInfo(SkylineDocumentProto.Types.Transition transitionProto)
{
if (Transition.IsNonReporterCustomIon())
{
transitionProto.Formula = DataValues.ToOptional(Transition.CustomIon.Formula);
if (Transition.CustomIon.AverageMass.IsMassH())
{
transitionProto.AverageMassH = DataValues.ToOptional(Transition.CustomIon.AverageMass);
}
else
{
transitionProto.AverageMass = DataValues.ToOptional(Transition.CustomIon.AverageMass);
}
if (Transition.CustomIon.MonoisotopicMass.IsMassH())
{
transitionProto.MonoMassH = DataValues.ToOptional(Transition.CustomIon.MonoisotopicMass);
}
else
{
transitionProto.MonoMass = DataValues.ToOptional(Transition.CustomIon.MonoisotopicMass);
}
transitionProto.CustomIonName = DataValues.ToOptional(Transition.CustomIon.Name);
transitionProto.MoleculeId = DataValues.ToOptional(Transition.CustomIon.AccessionNumbers.ToString());
}
else
{
transitionProto.MeasuredIonName = DataValues.ToOptional(Transition.CustomIon.Name);
}
}
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);
}
