public void TestDilutionFactor()
{
var baseDocument = LoadTestDocument();
baseDocument = ChangeQuantificationSettings(baseDocument,
QuantificationSettings.DEFAULT
.ChangeNormalizationMethod(NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy))
.ChangeRegressionFit(RegressionFit.LINEAR)
.ChangeUnits("ng/mL"));
var baseCurveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(baseDocument.Settings,
baseDocument.MoleculeGroups.First(), baseDocument.Molecules.First());
var baseCurve = baseCurveFitter.GetCalibrationCurve();
// Set the dilution factor of each external standard to 2.0, and each unknown to 3.0
var docWithDilutionFactor = baseDocument.ChangeMeasuredResults(
baseDocument.MeasuredResults.ChangeChromatograms(baseDocument.MeasuredResults.Chromatograms.Select(
chrom => Equals(chrom.SampleType, SampleType.STANDARD) ? chrom.ChangeDilutionFactor(2.0) :
chrom.ChangeDilutionFactor(3.0)).ToArray()));
var dilutionFactorCurveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(
docWithDilutionFactor.Settings, docWithDilutionFactor.MoleculeGroups.First(),
docWithDilutionFactor.Molecules.First());
var dilutionFactorCurve = dilutionFactorCurveFitter.GetCalibrationCurve();
Assert.AreEqual(2.0 * baseCurve.Slope, dilutionFactorCurve.Slope);
Assert.AreEqual(baseCurve.Intercept, dilutionFactorCurve.Intercept);
for (int replicateIndex = 0; replicateIndex < baseDocument.MeasuredResults.Chromatograms.Count; replicateIndex++)
{
var sampleType = baseDocument.MeasuredResults.Chromatograms[replicateIndex].SampleType;
var baseConcentration = baseCurveFitter.GetCalculatedConcentration(baseCurve, replicateIndex);
Assert.IsNotNull(baseConcentration);
var dilutionFactorConcentration =
dilutionFactorCurveFitter.GetCalculatedConcentration(dilutionFactorCurve, replicateIndex);
Assert.IsNotNull(dilutionFactorConcentration);
if (Equals(sampleType, SampleType.STANDARD))
{
Assert.AreEqual(baseConcentration.Value, dilutionFactorConcentration.Value, epsilon);
}
else
{
Assert.AreEqual(1.5 * baseConcentration.Value, dilutionFactorConcentration.Value, epsilon);
}
}
AssertEx.ValidatesAgainstSchema(docWithDilutionFactor);
}
public void TestMultipointExternalCalibrationWithoutNormalization()
{
var srmDocument = LoadTestDocument();
srmDocument = ChangeQuantificationSettings(srmDocument,
QuantificationSettings.DEFAULT
.ChangeNormalizationMethod(NormalizationMethod.NONE)
.ChangeRegressionFit(RegressionFit.LINEAR)
.ChangeUnits("ng/mL"));
PeptideGroupDocNode protein = srmDocument.MoleculeGroups.First();
PeptideDocNode peptide = srmDocument.Peptides.First();
peptide = peptide.ChangeInternalStandardConcentration(null);
CalibrationCurveFitter curveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(srmDocument.Settings, protein, peptide);
string expectedXAxis = CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, "ng/mL");
Assert.AreEqual(expectedXAxis, curveFitter.GetXAxisTitle());
string expectedYAxis = QuantificationStrings.CalibrationCurveFitter_GetYAxisTitle_Peak_Area;
Assert.AreEqual(expectedYAxis, curveFitter.GetYAxisTitle());
var chromatograms = srmDocument.Settings.MeasuredResults.Chromatograms;
var lightPrecursor = peptide.TransitionGroups
.First(tg => IsotopeLabelType.light.Equals(tg.TransitionGroup.LabelType));
for (int iReplicate = 0; iReplicate < chromatograms.Count; iReplicate++)
{
string msg = string.Format("Replicate {0}", iReplicate);
var expectedY = lightPrecursor.Results[iReplicate].First().Area.Value;
Assert.AreEqual(expectedY, curveFitter.GetYValue(iReplicate).Value, .01, msg);
var calibrationCurve = curveFitter.GetCalibrationCurve();
Assert.IsNotNull(calibrationCurve.Slope);
Assert.IsNotNull(calibrationCurve.RSquared);
double expectedConcentration = calibrationCurve.GetX(expectedY).Value;
Assert.AreEqual(expectedConcentration,
curveFitter.GetCalculatedXValue(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
Assert.AreEqual(expectedConcentration,
curveFitter.GetCalculatedConcentration(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
}
}
public void TestInternalCalibration()
{
const double internalStandardConcentration = 80.0;
var srmDocument = LoadTestDocument();
AssertEx.IsDocumentState(srmDocument, null, 1, 1, 2, 10);
srmDocument = ChangeStandardConcentrationCount(srmDocument, 0);
srmDocument = ChangeQuantificationSettings(srmDocument,
QuantificationSettings.DEFAULT
.ChangeRegressionFit(RegressionFit.NONE)
.ChangeNormalizationMethod(NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy))
.ChangeUnits("ng/mL"));
PeptideGroupDocNode protein = srmDocument.MoleculeGroups.First();
PeptideDocNode peptide = protein.Peptides.First();
peptide = peptide.ChangeInternalStandardConcentration(internalStandardConcentration);
CalibrationCurveFitter curveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(srmDocument.Settings, protein, peptide);
string expectedXAxis = CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, "ng/mL");
Assert.AreEqual(expectedXAxis, curveFitter.GetXAxisTitle());
string expectedYAxis = CalibrationCurveFitter.PeakAreaRatioText(IsotopeLabelType.light, IsotopeLabelType.heavy);
Assert.AreEqual(expectedYAxis, curveFitter.GetYAxisTitle());
var chromatograms = srmDocument.Settings.MeasuredResults.Chromatograms;
for (int iReplicate = 0; iReplicate < chromatograms.Count; iReplicate++)
{
string msg = string.Format("Replicate {0}", iReplicate);
var expectedY = peptide.Results[iReplicate].First().LabelRatios.First().Ratio.Ratio;
Assert.AreEqual(expectedY, curveFitter.GetYValue(iReplicate).Value, epsilon, msg);
var calibrationCurve = curveFitter.GetCalibrationCurve();
Assert.AreEqual(1 / internalStandardConcentration, calibrationCurve.Slope);
Assert.IsNull(calibrationCurve.RSquared);
Assert.AreEqual(expectedY * internalStandardConcentration,
curveFitter.GetCalculatedXValue(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
Assert.AreEqual(expectedY * internalStandardConcentration,
curveFitter.GetCalculatedConcentration(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
}
}