public void GetMixedN15_Test1()
{
var isoCreator = new LabeledIsotopicProfileUtilities();
var peptideSeq = "SAMPLERSAMPLER";
var elementLabelled = "N";
var lightIsotope = 14;
var heavyIsotope = 15;
double percentLabelled1 = 0; // first peptide population is unlabelled (0%)
double percentLabelled2 = 20; // second peptide polulation has 8% of its carbons labelled.
var fractionPopulationLabelled = 0.50; // fraction of peptides that have heavy label.
var iso = isoCreator.CreateIsotopicProfileFromSequence(peptideSeq, elementLabelled, lightIsotope, heavyIsotope, percentLabelled1);
var labelledIso = isoCreator.CreateIsotopicProfileFromSequence(peptideSeq, elementLabelled, lightIsotope, heavyIsotope, percentLabelled2);
isoCreator.AddIsotopicProfile(iso, 1 - fractionPopulationLabelled);
isoCreator.AddIsotopicProfile(labelledIso, fractionPopulationLabelled);
var mixedIso = isoCreator.GetMixedIsotopicProfile();
TestUtilities.DisplayIsotopicProfileData(mixedIso);
}
public void PartialLabelingQuantifierTest1()
{
// see https://jira.pnnl.gov/jira/browse/OMCS-743
var peptideSeq = "SAMPLERSAMPLER";
var isoCreator = new LabeledIsotopicProfileUtilities();
var elementLabelled = "C";
var lightIsotope = 12;
var heavyIsotope = 13;
var target = new PeptideTarget();
target.Code = peptideSeq;
target.EmpiricalFormula = target.GetEmpiricalFormulaFromTargetCode();
target.ChargeState = 2;
target.CalculateMassesForIsotopicProfile(target.ChargeState);
target.IsotopicProfile = isoCreator.CreateIsotopicProfileFromEmpiricalFormula(target.EmpiricalFormula, elementLabelled, 12, 13, 0, target.ChargeState);
double[] obsMZVals =
{
794.4027177, 794.9043951, 795.4060725, 795.9077499, 796.4094273, 796.9111047,
797.4127822, 797.9144596, 798.416137, 798.9178144, 799.4194918, 799.9211693,
800.4228467, 800.9245241, 801.4262015, 801.9278789, 802.4295564, 802.9312338,
803.4329112, 803.9345886, 804.436266, 804.9379435, 805.4396209, 805.9412983,
806.4429757, 806.9446531, 807.4463306, 807.948008, 808.4496854, 808.9513628,
809.4530402, 809.9547176, 810.4563951
};
double[] obsIntensities =
{
0.202610146, 0.169786958, 0.10004317, 0.048528412, 0.023649271, 0.01375091,
0.011401505, 0.010165125, 0, 0, 0, 0,0, 0.016295369, 0.02039971, 0.02628524
, 0.034368448, 0.042300575, 0.050392505, 0.057402354, 0.061016738,
0.061990991, 0.059175713, 0.053291295, 0.046892873, 0.037952256, 0.030884989
, 0.024965924, 0.019531111, 0.01613184, 0, 0, 0
};
var peakList = obsMZVals.Select((t, i) => new Peak(t, (float)obsIntensities[i], 0)).ToList();
var partialLabelingQuantifier = new PartialLabelingQuantifier("C", 12, 13);
var bestIso = partialLabelingQuantifier.FindBestLabeledProfile(target, peakList, null);
var counter = 0;
foreach (var currentFitScore in partialLabelingQuantifier.FitScoreData)
{
Console.WriteLine(currentFitScore.Key + "\t" + currentFitScore.Value);
counter++;
}
}
