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 IEnumerable <SkylineDocumentProto.Types.TransitionPeak> GetTransitionPeakProtos(MeasuredResults measuredResults)
{
if (Results == null)
{
yield break;
}
for (int replicateIndex = 0; replicateIndex < Results.Count; replicateIndex++)
{
var replicateResults = Results[replicateIndex];
if (replicateResults.IsEmpty)
{
continue;
}
foreach (var transitionChromInfo in replicateResults)
{
if (transitionChromInfo == null)
{
continue;
}
var transitionPeak = new SkylineDocumentProto.Types.TransitionPeak();
transitionPeak.OptimizationStep = transitionChromInfo.OptimizationStep;
if (null != transitionChromInfo.Annotations)
{
transitionPeak.Annotations = transitionChromInfo.Annotations.ToProtoAnnotations();
}
transitionPeak.ReplicateIndex = replicateIndex;
transitionPeak.FileIndexInReplicate = measuredResults.Chromatograms[replicateIndex].IndexOfId(transitionChromInfo.FileId);
transitionPeak.MassError = DataValues.ToOptional(transitionChromInfo.MassError);
transitionPeak.RetentionTime = transitionChromInfo.RetentionTime;
transitionPeak.StartRetentionTime = transitionChromInfo.StartRetentionTime;
transitionPeak.EndRetentionTime = transitionChromInfo.EndRetentionTime;
transitionPeak.IonMobility = DataValues.ToOptional(transitionChromInfo.IonMobility.IonMobility.Mobility);
transitionPeak.IonMobilityWindow = DataValues.ToOptional(transitionChromInfo.IonMobility.IonMobilityExtractionWindowWidth);
transitionPeak.Area = transitionChromInfo.Area;
transitionPeak.BackgroundArea = transitionChromInfo.BackgroundArea;
transitionPeak.Height = transitionChromInfo.Height;
transitionPeak.Fwhm = transitionChromInfo.Fwhm;
transitionPeak.IsFwhmDegenerate = transitionChromInfo.IsFwhmDegenerate;
transitionPeak.Truncated = DataValues.ToOptional(transitionChromInfo.IsTruncated);
transitionPeak.UserSet = DataValues.ToUserSet(transitionChromInfo.UserSet);
transitionPeak.ForcedIntegration = transitionChromInfo.IsForcedIntegration;
switch (transitionChromInfo.Identified)
{
case PeakIdentification.ALIGNED:
transitionPeak.Identified = SkylineDocumentProto.Types.PeakIdentification.Aligned;
break;
case PeakIdentification.FALSE:
transitionPeak.Identified = SkylineDocumentProto.Types.PeakIdentification.False;
break;
case PeakIdentification.TRUE:
transitionPeak.Identified = SkylineDocumentProto.Types.PeakIdentification.True;
break;
}
transitionPeak.Rank = transitionChromInfo.Rank;
transitionPeak.RankByLevel = transitionChromInfo.RankByLevel;
transitionPeak.PointsAcrossPeak = DataValues.ToOptional(transitionChromInfo.PointsAcrossPeak);
yield return(transitionPeak);
}
}
}
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);
}