public PrecursorQuantificationResult GetPrecursorQuantificationResult(int replicateIndex, TransitionGroupDocNode transitionGroupDocNode)
{
PrecursorQuantificationResult result = null;
if (IsotopologResponseCurve)
{
result = new PrecursorQuantificationResult();
var calibrationPoint = new CalibrationPoint(replicateIndex, transitionGroupDocNode.LabelType);
CalibrationCurve calibrationCurve = GetCalibrationCurve();
result = (PrecursorQuantificationResult)result.ChangeNormalizedArea(GetNormalizedPeakArea(calibrationPoint));
if (HasExternalStandards() || HasInternalStandardConcentration())
{
double?calculatedConcentration = GetCalculatedConcentration(calibrationCurve, calibrationPoint);
result = (PrecursorQuantificationResult)result.ChangeCalculatedConcentration(calculatedConcentration);
double?expectedConcentration = transitionGroupDocNode.PrecursorConcentration;
result = (PrecursorQuantificationResult)result.ChangeAccuracy(calculatedConcentration / expectedConcentration);
result = (PrecursorQuantificationResult)result.ChangeUnits(QuantificationSettings.Units);
}
}
var targetIonRatio = GetTargetIonRatio(transitionGroupDocNode);
var ionRatio = PeptideQuantifier.GetQualitativeIonRatio(SrmSettings, transitionGroupDocNode, replicateIndex);
if (targetIonRatio.HasValue || ionRatio.HasValue)
{
result = result ?? new PrecursorQuantificationResult();
var status = ValueStatus.GetStatus(ionRatio, GetTargetIonRatio(transitionGroupDocNode),
SrmSettings.PeptideSettings.Quantification.QualitativeIonRatioThreshold / 100);
result = result.ChangeIonRatio(targetIonRatio, ionRatio, status);
}
return(result);
}
public double?GetSpecifiedXValue(CalibrationPoint calibrationPoint)
{
var chromatogramSet = GetChromatogramSet(calibrationPoint.ReplicateIndex);
if (chromatogramSet == null)
{
return(null);
}
if (null != calibrationPoint.LabelType)
{
var transitionGroup = PeptideQuantifier.PeptideDocNode.TransitionGroups.FirstOrDefault(tg =>
Equals(tg.LabelType, calibrationPoint.LabelType) && tg.PrecursorConcentration.HasValue);
if (transitionGroup != null)
{
return(transitionGroup.PrecursorConcentration / chromatogramSet.SampleDilutionFactor);
}
return(null);
}
double?peptideConcentration = GetPeptideConcentration(chromatogramSet);
if (peptideConcentration.HasValue)
{
if (HasExternalStandards() && HasInternalStandardConcentration())
{
return(peptideConcentration / PeptideQuantifier.PeptideDocNode.InternalStandardConcentration);
}
return(peptideConcentration);
}
return(null);
}
public double?GetCalculatedConcentration(CalibrationCurve calibrationCurve, CalibrationPoint calibrationPoint)
{
if (!HasExternalStandards() && !HasInternalStandardConcentration())
{
return(null);
}
return(GetConcentrationFromXValue(GetCalculatedXValue(calibrationCurve, calibrationPoint) * GetDilutionFactor(calibrationPoint.ReplicateIndex)));
}
public SampleType GetSampleType(CalibrationPoint calibrationPoint)
{
if (null == calibrationPoint.LabelType)
{
ChromatogramSet chromatogramSet = SrmSettings.MeasuredResults.Chromatograms[calibrationPoint.ReplicateIndex];
return(chromatogramSet.SampleType);
}
return(GetSpecifiedXValue(calibrationPoint).HasValue ? SampleType.STANDARD : SampleType.UNKNOWN);
}
public QuantificationResult GetPrecursorQuantificationResult(int replicateIndex, TransitionGroupDocNode transitionGroupDocNode)
{
QuantificationResult result = new QuantificationResult();
var calibrationPoint = new CalibrationPoint(replicateIndex, transitionGroupDocNode.LabelType);
CalibrationCurve calibrationCurve = GetCalibrationCurve();
result = result.ChangeNormalizedArea(GetNormalizedPeakArea(calibrationPoint));
if (HasExternalStandards() || HasInternalStandardConcentration())
{
double?calculatedConcentration = GetCalculatedConcentration(calibrationCurve, calibrationPoint);
result = result.ChangeCalculatedConcentration(calculatedConcentration);
double?expectedConcentration = transitionGroupDocNode.PrecursorConcentration;
result = result.ChangeAccuracy(calculatedConcentration / expectedConcentration);
result = result.ChangeUnits(SrmSettings.PeptideSettings.Quantification.Units);
}
return(result);
}
public IDictionary <CalibrationPoint, double> GetStandardConcentrations()
{
Dictionary <CalibrationPoint, double> result = new Dictionary <CalibrationPoint, double>();
var measuredResults = SrmSettings.MeasuredResults;
if (null == measuredResults)
{
return(result);
}
if (IsotopologResponseCurve)
{
foreach (var precursor in PeptideQuantifier.PeptideDocNode.TransitionGroups)
{
if (precursor.PrecursorConcentration.HasValue)
{
foreach (var replicateIndex in EnumerateReplicates())
{
var standardIdentifier = new CalibrationPoint(replicateIndex, precursor.LabelType);
result[standardIdentifier] = precursor.PrecursorConcentration.Value / measuredResults.Chromatograms[replicateIndex].SampleDilutionFactor;
}
}
}
}
else
{
foreach (int replicateIndex in EnumerateReplicates())
{
var chromatogramSet = measuredResults.Chromatograms[replicateIndex];
if (!SampleType.STANDARD.Equals(chromatogramSet.SampleType))
{
continue;
}
if (PeptideQuantifier.PeptideDocNode.IsExcludeFromCalibration(replicateIndex))
{
continue;
}
double?concentration = GetPeptideConcentration(chromatogramSet);
if (concentration.HasValue)
{
result.Add(new CalibrationPoint(replicateIndex, null), concentration.Value);
}
}
}
return(result);
}
public double?GetPeptideConcentration(CalibrationPoint calibrationPoint)
{
var chromatogramSet = GetChromatogramSet(calibrationPoint.ReplicateIndex);
if (chromatogramSet == null)
{
return(null);
}
if (calibrationPoint.LabelType != null)
{
var transitionGroup = PeptideQuantifier.PeptideDocNode.TransitionGroups.FirstOrDefault(tg =>
Equals(tg.LabelType, calibrationPoint.LabelType) && tg.PrecursorConcentration.HasValue);
if (transitionGroup == null)
{
return(null);
}
return(transitionGroup.PrecursorConcentration / chromatogramSet.SampleDilutionFactor);
}
return(GetPeptideConcentration(chromatogramSet));
}
public double?GetNormalizedPeakArea(CalibrationPoint calibrationPoint)
{
var allTransitionQuantities = GetTransitionQuantities(calibrationPoint);
ICollection <PeptideQuantifier.Quantity> quantitiesToSum;
if (!IsAllowMissingTransitions())
{
var completeTransitionSet = GetTransitionsToQuantifyOn();
quantitiesToSum = allTransitionQuantities
.Where(entry => completeTransitionSet.Contains(entry.Key))
.Select(entry => entry.Value)
.ToArray();
if (quantitiesToSum.Count != completeTransitionSet.Count)
{
return(null);
}
}
else
{
quantitiesToSum = allTransitionQuantities.Values;
}
return(PeptideQuantifier.SumQuantities(quantitiesToSum, PeptideQuantifier.NormalizationMethod));
}
public IDictionary <IdentityPath, PeptideQuantifier.Quantity> GetTransitionQuantities(CalibrationPoint calibrationPoint)
{
IDictionary <IdentityPath, PeptideQuantifier.Quantity> result;
if (!_replicateQuantities.TryGetValue(calibrationPoint, out result))
{
if (calibrationPoint.LabelType == null)
{
result = PeptideQuantifier.GetTransitionIntensities(SrmSettings, calibrationPoint.ReplicateIndex, false);
}
else
{
result = new Dictionary <IdentityPath, PeptideQuantifier.Quantity>
{
{
IdentityPath.ROOT,
new PeptideQuantifier.Quantity(PeptideQuantifier.GetIsotopologArea(SrmSettings, calibrationPoint.ReplicateIndex,
calibrationPoint.LabelType), 1)
}
};
}
_replicateQuantities.Add(calibrationPoint, result);
}
return(result);
}
public double?GetYValue(CalibrationPoint calibrationPoint)
{
return(GetNormalizedPeakArea(calibrationPoint));
}
public double?GetCalculatedXValue(CalibrationCurve calibrationCurve, CalibrationPoint calibrationPoint)
{
return(calibrationCurve.GetX(GetYValue(calibrationPoint)));
}
