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); }