public void MQuestReferenceDetailScoreTest()
{
var peakData1 = new MockTranPeakData <IDetailedPeakData>(INTENS1, IonType.a, IsotopeLabelType.light);
var peakData2 = new MockTranPeakData <IDetailedPeakData>(INTENS2, IonType.a, IsotopeLabelType.heavy);
var peakData3 = new MockTranPeakData <IDetailedPeakData>(INTENS3, IonType.precursor, IsotopeLabelType.light);
var peakData4 = new MockTranPeakData <IDetailedPeakData>(INTENS3, IonType.precursor, IsotopeLabelType.heavy);
var tranGroupData1 = new MockTranGroupPeakData <IDetailedPeakData>(new[] { peakData1 });
var tranGroupData2 = new MockTranGroupPeakData <IDetailedPeakData>(new[] { peakData2 }, true);
var tranGroupData3 = new MockTranGroupPeakData <IDetailedPeakData>(new[] { peakData1, peakData3 });
var tranGroupData4 = new MockTranGroupPeakData <IDetailedPeakData>(new[] { peakData2, peakData4 }, true);
var peptidePeakData = new MockPeptidePeakData <IDetailedPeakData>(new[] { tranGroupData1, tranGroupData2 });
var peptidePeakDataMs1 = new MockPeptidePeakData <IDetailedPeakData>(new[] { tranGroupData3, tranGroupData4 });
var peptidePeakDatas = new List <MockPeptidePeakData <IDetailedPeakData> > {
peptidePeakData, peptidePeakDataMs1
};
var calcShape = new MQuestReferenceShapeCalc();
var calcCoelution = new MQuestReferenceCoElutionCalc();
var calcWeightedShape = new MQuestWeightedReferenceShapeCalc();
var calcWeightedCoelution = new MQuestWeightedReferenceCoElutionCalc();
// These scores are the same with or without an extra MS1 transition
foreach (var peptideData in peptidePeakDatas)
{
MQuestScoreEquals(calcShape, 0.3969832, peptideData);
MQuestScoreEquals(calcCoelution, 3.0, peptideData);
MQuestScoreEquals(calcWeightedShape, 0.3969832, peptideData);
MQuestScoreEquals(calcWeightedCoelution, 3.0, peptideData);
}
// TODO: Figure out OpenSWATH weights
// var calcWeighted = new MQuestWeightedShapeCalc();
// AreCloseEnough(calcWeighted.Calculate(new PeakScoringContext(), peptidePeakData), 0.6984916);
}
public void MQuestSummaryScoreTest()
{
var peakData1 = new MockTranPeakData <ISummaryPeakData>(INTENS1, IonType.a, null, 2, 0.5, 20);
var peakData2 = new MockTranPeakData <ISummaryPeakData>(INTENS2, IonType.a, null, 2, -1.0, 300);
var peakData3 = new MockTranPeakData <ISummaryPeakData>(INTENS3, IonType.precursor, null, 2, 5.0, 1000000, 0.8);
var peakData4 = new MockTranPeakData <ISummaryPeakData>(INTENS3, IonType.precursor, null, 2, 5.0, 1000000, 0.2);
var peptidePeakData = new MockPeptidePeakData <ISummaryPeakData>(new[] { peakData1, peakData2 });
var peptidePeakDataMs1 = new MockPeptidePeakData <ISummaryPeakData>(new[] { peakData1, peakData2, peakData3, peakData4 });
var calcPrecursorMassError = new NextGenPrecursorMassErrorCalc();
var calcProductMassError = new NextGenProductMassErrorCalc();
var calcIntensity = new MQuestIntensityCalc();
var calcCrossCorr = new MQuestIntensityCorrelationCalc();
var calcIdotp = new NextGenIsotopeDotProductCalc();
var peptidePeakDatas = new List <MockPeptidePeakData <ISummaryPeakData> > {
peptidePeakData, peptidePeakDataMs1
};
// These scores are the same with or without an extra MS1 transition
foreach (var peptideData in peptidePeakDatas)
{
MQuestScoreEquals(calcProductMassError, 0.99112, peptideData);
MQuestScoreEquals(calcIntensity, 2.84732, peptideData);
MQuestScoreEquals(calcCrossCorr, 0.924226, peptideData);
}
// The precursor mass error score differs when an MS1 transition is added
MQuestScoreEquals(calcPrecursorMassError, double.NaN, peptidePeakData);
MQuestScoreEquals(calcPrecursorMassError, 5.0, peptidePeakDataMs1);
MQuestScoreEquals(calcIdotp, double.NaN, peptidePeakData);
MQuestScoreEquals(calcIdotp, 0.795167, peptidePeakDataMs1);
// TODO: Figure out OpenSWATH weights
// var calcWeighted = new MQuestWeightedShapeCalc();
// AreCloseEnough(calcWeighted.Calculate(new PeakScoringContext(), peptidePeakData), 0.6984916);
}
public void MQuestDetailScoreTest()
{
var peakData1 = new MockTranPeakData <IDetailedPeakData>(INTENS1, IonType.a, null, 2, 0.5);
var peakData2 = new MockTranPeakData <IDetailedPeakData>(INTENS2, IonType.a, null, 2, -1.0);
var peakData3 = new MockTranPeakData <IDetailedPeakData>(INTENS3, IonType.precursor, null, 2, 5.0);
var peptidePeakData = new MockPeptidePeakData <IDetailedPeakData>(new[] { peakData1, peakData2 });
var peptidePeakDataMs1 = new MockPeptidePeakData <IDetailedPeakData>(new[] { peakData1, peakData2, peakData3 });
var calcShape = new MQuestShapeCalc();
var calcCoelution = new MQuestCoElutionCalc();
var calcWeightedShape = new MQuestWeightedShapeCalc();
var calcWeightedCoelution = new MQuestWeightedCoElutionCalc();
var calcWeightedCrossShape = new NextGenCrossWeightedShapeCalc();
var calcSignalNoise = new NextGenSignalNoiseCalc();
var peptidePeakDatas = new List <MockPeptidePeakData <IDetailedPeakData> > {
peptidePeakData, peptidePeakDataMs1
};
// These scores are the same with or without an extra MS1 transition
foreach (var peptideData in peptidePeakDatas)
{
MQuestScoreEquals(calcShape, 0.3969832, peptideData);
MQuestScoreEquals(calcCoelution, 3.0, peptideData);
MQuestScoreEquals(calcWeightedShape, 0.3969832, peptideData);
MQuestScoreEquals(calcWeightedCoelution, 3.0, peptideData);
MQuestScoreEquals(calcSignalNoise, 1.3086293, peptideData);
}
// The MS1-MS2 cross score differs when an MS1 transition is added
MQuestScoreEquals(calcWeightedCrossShape, 0.94669, peptidePeakDataMs1);
// TODO: Figure out OpenSWATH weights
// var calcWeighted = new MQuestWeightedShapeCalc();
// AreCloseEnough(calcWeighted.Calculate(new PeakScoringContext(), peptidePeakData), 0.6984916);
}
public void MQuestCrossCorrelationTest()
{
var peakData1 = new MockTranPeakData <IDetailedPeakData>(INTENS1);
var peakData2 = new MockTranPeakData <IDetailedPeakData>(INTENS2);
var xcorrMatrix = new MQuestCrossCorrelation(peakData1, peakData2, true);
Assert.AreEqual(xcorrMatrix.XcorrDict.Count, 23);
var xcorrDict = xcorrMatrix.XcorrDict;
AreCloseEnough(xcorrDict[2], -0.31165141);
AreCloseEnough(xcorrDict[1], -0.35036919);
AreCloseEnough(xcorrDict[0], 0.03129565);
AreCloseEnough(xcorrDict[-1], 0.30204049);
AreCloseEnough(xcorrDict[-2], 0.13012441);
AreCloseEnough(xcorrDict[-3], 0.39698322);
AreCloseEnough(xcorrDict[-4], 0.16608774);
var xcorrMatrixAuto = new MQuestCrossCorrelation(peakData1, new MockTranPeakData <IDetailedPeakData>(INTENS1), true);
var xcorrDictAuto = xcorrMatrixAuto.XcorrDict;
AreCloseEnough(xcorrDictAuto[0], 1);
AreCloseEnough(xcorrDictAuto[1], -0.227352707759245);
AreCloseEnough(xcorrDictAuto[-1], -0.227352707759245);
AreCloseEnough(xcorrDictAuto[2], -0.07501116);
AreCloseEnough(xcorrDictAuto[-2], -0.07501116);
}
