public override void Execute(ResultCollection resultList)
{
var mt = resultList.Run.CurrentMassTag;
Check.Require(mt != null, "Current mass tag is not defined.");
var currentResult = resultList.CurrentTargetedResult;
Check.Require(currentResult != null, "Quantifier failed. Result doesn't exist for current mass tag.");
Check.Require(currentResult is N14N15_TResult, "Quantifier failed. Result is not of the N14N15 type.");
var n14n15Result = ((N14N15_TResult)currentResult);
var quant = new BasicN14N15Quantifier(this.MSToleranceInPPM, this.RatioType);
var iso1 = ((N14N15_TResult)currentResult).IsotopicProfile;
var iso2 = ((N14N15_TResult)currentResult).IsotopicProfileLabeled;
if (iso1 == null || iso2 == null)
{
n14n15Result.RatioN14N15 = -1;
}
else
{
quant.GetRatioBasedOnTopPeaks(iso1, iso2, mt.IsotopicProfile, _N15IsotopicProfileGenerator.GetN15IsotopicProfile(mt, 0.005),
currentResult.ScanSet.BackgroundIntensity, NumPeaksUsedInRatioCalc,
out var ratio, out var ratioContribIso1, out var ratioContribIso2);
n14n15Result.RatioN14N15 = ratio;
n14n15Result.RatioContributionN14 = ratioContribIso1;
n14n15Result.RatioContributionN15 = ratioContribIso2;
}
//((N14N15_TResult)currentResult).RatioN14N15 = quant.GetRatioBasedOnAreaUnderPeaks(resultColl.Run.XYData.Xvalues, resultColl.Run.XYData.Yvalues, iso1, iso2, currentResult.ScanSet.BackgroundIntensity);
}
public void test01_mt230140708_z3()
{
double featureFinderTol = 15;
var featureFinderRequiresMonoPeak = false;
var numPeaksUsedInQuant = 3;
var n14n15Util = new N14N15TestingUtilities();
//get MS
var massSpectrum = n14n15Util.GetSpectrumAMTTag23140708_Z3_Sum3(); //this is the diff b/w previous test and this one
var smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(3, 2);
massSpectrum = smoother.Smooth(massSpectrum);
//get target MT
var mt23140708 = n14n15Util.CreateMT23140708_Z3();
//get ms peaks
var peakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, false);
var msPeakList = peakDet.FindPeaks(massSpectrum, 0, 0);
//TestUtilities.DisplayPeaks(msPeakList);
var featureGen = new TomTheorFeatureGenerator();
featureGen.GenerateTheorFeature(mt23140708);
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
var featureGen2 = new JoshTheorFeatureGenerator();
featureGen2.GenerateTheorFeature(mt23140708);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
var gen = new N15IsotopeProfileGenerator();
var theorN15Profile = gen.GetN15IsotopicProfile(mt23140708, 0.005);
var bff = new BasicTFF(featureFinderTol, featureFinderRequiresMonoPeak);
var n14Profile = bff.FindMSFeature(msPeakList, mt23140708.IsotopicProfile);
var n15Profile = bff.FindMSFeature(msPeakList, theorN15Profile);
Console.WriteLine(mt23140708.GetEmpiricalFormulaFromTargetCode());
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(theorN15Profile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n14Profile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n15Profile);
var quant = new BasicN14N15Quantifier(featureFinderTol);
double ratioContribIso1;
double ratioContribIso2;
double ratio;
quant.GetRatioBasedOnTopPeaks(n14Profile, n15Profile, mt23140708.IsotopicProfile, theorN15Profile, peakDet.BackgroundIntensity,
numPeaksUsedInQuant, out ratio, out ratioContribIso1, out ratioContribIso2);
Console.WriteLine("--------------------------------");
Console.WriteLine("Background intensity = " + peakDet.BackgroundIntensity);
Console.WriteLine("--------------------------------");
Console.WriteLine("Ratio = " + ratio);
Console.WriteLine("Ratio contrib Iso1 = " + ratioContribIso1);
Console.WriteLine("Ratio contrib Iso2 = " + ratioContribIso2);
Console.WriteLine("--------------------------------");
Assert.AreEqual(1.458267m, (decimal)Math.Round(ratio, 6)); //see 'N14N15Quantification_manualValidation_of_algorithm.xls' for manual validation
}
