public static List <PeptideTarget> CreateN14N15TestMassTagList()
{
var mtList = new List <PeptideTarget>();
var mt1 = new PeptideTarget();
mt1.ID = 23085473;
mt1.NormalizedElutionTime = 0.3807834F;
mt1.MonoIsotopicMass = 2538.33284203802;
mt1.ChargeState = 3;
mt1.MZ = mt1.MonoIsotopicMass / mt1.ChargeState + Globals.PROTON_MASS;
mt1.Code = "AIHQPAPTFAEQSTTSEILVTGIK";
mt1.EmpiricalFormula = mt1.GetEmpiricalFormulaFromTargetCode();
mtList.Add(mt1);
var mt2 = new PeptideTarget();
mt2.ID = 23085470;
mt2.NormalizedElutionTime = 0.6053093f;
mt2.MonoIsotopicMass = 2329.24291507994;
mt2.ChargeState = 3;
mt2.MZ = mt2.MonoIsotopicMass / mt2.ChargeState + Globals.PROTON_MASS;
mt2.Code = "TAIRDPNPVIFLENEILYGR";
mt1.EmpiricalFormula = mt1.GetEmpiricalFormulaFromTargetCode();
mtList.Add(mt2);
return(mtList);
}
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++;
}
}
public void initializeFromEmpiricalFormula()
{
var mt = new PeptideTarget();
mt.Code = "SAMPLER";
mt.EmpiricalFormula = mt.GetEmpiricalFormulaFromTargetCode();
Assert.AreEqual("C33H58N10O11S", mt.EmpiricalFormula);
Assert.AreEqual(33, mt.GetAtomCountForElement("C"));
}
public void test3()
{
TargetBase target = new PeptideTarget();
target.Code = "TTPSIIAYTDDETIVGQPAKRTTPSIIAYTDDETIVGQPAKRTTPSIIAYTDDETIVGQPAKR";
target.EmpiricalFormula = target.GetEmpiricalFormulaFromTargetCode();
var cluster = _tomIsotopicPatternGenerator.GetIsotopePattern(target.EmpiricalFormula, _tomIsotopicPatternGenerator.aafIsos);
TestUtilities.DisplayIsotopicProfileData(cluster);
}
public PeptideTarget CreateMT23140708_Z2()
{
var mt = new PeptideTarget();
mt.ChargeState = 2;
mt.Code = "IVKVNVDENPESPAMLGVR";
mt.EmpiricalFormula = mt.GetEmpiricalFormulaFromTargetCode();
mt.MonoIsotopicMass = 2066.08292;
mt.MZ = 1034.048737;
mt.NormalizedElutionTime = 0.329644f;
return(mt);
}
public PeptideTarget CreateMT23085904_Z2()
{
var mt = new PeptideTarget();
mt.ChargeState = 2;
mt.Code = "AMPIDLSNLALLDANGK";
mt.EmpiricalFormula = mt.GetEmpiricalFormulaFromTargetCode();
mt.MonoIsotopicMass = 1754.923582420;
mt.MZ = 878.4690677;
mt.NormalizedElutionTime = 0.4509717f;
return(mt);
}
public static List <PeptideTarget> CreateO16O18TestMassTagList1()
{
var mtList = new List <PeptideTarget>();
var mt = new PeptideTarget();
mt.ID = 1142;
mt.MonoIsotopicMass = 921.4807035;
mt.ChargeState = 2;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
mt.Code = "AEFVEVTK";
mt.EmpiricalFormula = mt.GetEmpiricalFormulaFromTargetCode();
mtList.Add(mt);
return(mtList);
}
public static List <PeptideTarget> CreateTestMassTagList()
{
var mtList = new List <PeptideTarget>();
var mt = new PeptideTarget();
mt.ID = 24769;
mt.MonoIsotopicMass = 2086.0595;
mt.ChargeState = 2;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
mt.Code = "DFNEALVHQVVVAYAANAR";
mt.EmpiricalFormula = mt.GetEmpiricalFormulaFromTargetCode();
mtList.Add(mt);
return(mtList);
}
public static PeptideTarget GetMassTagStandard(int standardNum)
{
var mt = new PeptideTarget();
mt.ID = 86963986;
mt.MonoIsotopicMass = 1516.791851;
mt.Code = "AAKEGISCEIIDLR";
mt.EmpiricalFormula = mt.GetEmpiricalFormulaFromTargetCode();
mt.NormalizedElutionTime = 0.2284955f;
mt.ChargeState = 2;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
return(mt);
}
public static List <PeptideTarget> CreateN14N15TestMassTagList()
{
var mtList = new List <PeptideTarget>();
var mt = new PeptideTarget();
mt.ID = 23085473;
mt.NormalizedElutionTime = 0.3807834F;
mt.MonoIsotopicMass = 2538.33284203802;
mt.ChargeState = 3;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
mt.Code = "AIHQPAPTFAEQSTTSEILVTGIK";
mt.EmpiricalFormula = mt.GetEmpiricalFormulaFromTargetCode();
mtList.Add(mt);
return(mtList);
}