private IsotopicProfile GetTheorIsotopicProfile(IsosResult saturatedFeature, double lowerIntensityCutoff = 0.0001)
{
var theorTarget = new PeptideTarget
{
ChargeState = (short)saturatedFeature.IsotopicProfile.ChargeState,
MonoIsotopicMass = saturatedFeature.IsotopicProfile.MonoIsotopicMass
};
theorTarget.MZ = (theorTarget.MonoIsotopicMass / theorTarget.ChargeState) + Globals.PROTON_MASS;
var averagineFormula =
_tomIsotopicPatternGenerator.GetClosestAvnFormula(saturatedFeature.IsotopicProfile.MonoIsotopicMass, false);
theorTarget.IsotopicProfile = _tomIsotopicPatternGenerator.GetIsotopePattern(averagineFormula,
_tomIsotopicPatternGenerator.aafIsos);
theorTarget.EmpiricalFormula = averagineFormula;
theorTarget.CalculateMassesForIsotopicProfile(saturatedFeature.IsotopicProfile.ChargeState);
//NOTE: This is critical to choosing the optimum peak of the observed isotopic profile
//A value of 0.001 will leave more peaks in the theor profile. This
//can be bad with co-eluting peptides, so that a peak of the interfering peptide
//is used to correct the intensity of our target peptide.
//A value of 0.01 helps prevent this (by trimming the peaks of the theor profile,
//and reducing the peaks to be considered for peak intensity extrapolation of the target peptide.
PeakUtilities.TrimIsotopicProfile(theorTarget.IsotopicProfile, lowerIntensityCutoff);
return(theorTarget.IsotopicProfile);
}
private IsotopicProfile GetUnlabelledIsotopicProfile(TargetBase mt)
{
var iso = new IsotopicProfile();
try
{
//empirical formula may contain non-integer values for
iso = _isotopicDistCalculator.GetIsotopePattern(mt.EmpiricalFormula);
}
catch (Exception ex)
{
throw new Exception("Theoretical feature generator failed. Details: " + ex.Message);
}
PeakUtilities.TrimIsotopicProfile(iso, LowPeakCutOff);
iso.ChargeState = mt.ChargeState;
if (iso.ChargeState != 0)
{
calculateMassesForIsotopicProfile(iso, mt.MonoIsotopicMass, mt.ChargeState);
}
return(iso);
}
public override void GenerateTheorFeature(TargetBase mt)
{
Check.Require(mt != null, "FeatureGenerator failed. Target must not be null.");
var iso = IsotopicDistCalculator.GetAveraginePattern(mt.MZ);
PeakUtilities.TrimIsotopicProfile(iso, LowPeakCutOff);
iso.ChargeState = mt.ChargeState;
mt.IsotopicProfile = iso;
}
public void getN15IsotopicProfileTest1()
{
var isIt = isotopicDistributionCalculator.IsSetToLabeled;
var utils = new PeptideUtils();
//string formula = utils.GetEmpiricalFormulaForPeptideSequence("SAMPLERPAMPLERSAMPLERPAMPLERSAMPLERPAMPLERSAMPLERPAMPLER");
var formula = utils.GetEmpiricalFormulaForPeptideSequence("SAMPLERPAMPLERSAMPLERPAMPLER");
var numNitrogens = utils.GetNumAtomsForElement("N", formula);
var iso1 = isotopicDistributionCalculator.GetIsotopePattern(formula);
PeakUtilities.TrimIsotopicProfile(iso1, 0.001);
TestUtilities.DisplayIsotopicProfileData(iso1);
isotopicDistributionCalculator.SetLabeling("N", 14, 0.02, 15, 0.98);
var iso2 = isotopicDistributionCalculator.GetIsotopePattern(formula);
//PeakUtilities.TrimIsotopicProfile(iso2, 0.001);
isotopicDistributionCalculator.ResetToUnlabeled();
var iso3 = isotopicDistributionCalculator.GetIsotopePattern(formula);
PeakUtilities.TrimIsotopicProfile(iso3, 0.001);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(iso2);
for (var i = 0; i < iso1.Peaklist.Count; i++)
{
Assert.AreEqual((decimal)Math.Round(iso1.Peaklist[i].Height, 4), (decimal)Math.Round(iso3.Peaklist[i].Height, 4));
}
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(iso3);
Console.WriteLine("Num nitrogens= " + numNitrogens);
}
public IsotopicProfile GetN15IsotopicProfile(TargetBase mt, double lowpeakCutoff)
{
Check.Require(mt != null, "Mass tag not defined");
Check.Require(mt.IsotopicProfile != null, "Mass tag's theor isotopic profile not defined");
Check.Require(mt.ChargeState != 0, "Can't have a charge state of '0'");
var numNitrogens = mt.GetAtomCountForElement("N");
var labeledTheorProfile = _TomIsotopicPatternGenerator.GetIsotopePattern(mt.EmpiricalFormula, _TomIsotopicPatternGenerator.aafN15Isos);
addMZInfoToTheorProfile(mt.IsotopicProfile, labeledTheorProfile, numNitrogens, mt.ChargeState);
PeakUtilities.TrimIsotopicProfile(labeledTheorProfile, lowpeakCutoff);
labeledTheorProfile.ChargeState = mt.ChargeState;
return(labeledTheorProfile);
}
public IsotopicProfile GetN15IsotopicProfile2(TargetBase mt, double lowPeakCutoff)
{
Check.Require(mt != null, "Mass tag not defined");
Check.Require(mt.IsotopicProfile != null, "Mass tag's theor isotopic profile not defined");
Check.Require(mt.ChargeState != 0, "Can't have a charge state of '0'");
var nitrogenCount = mt.GetAtomCountForElement("N");
_isotopicDistributionCalculator.SetLabeling("N", N14ISOTOPE_NUMBER, this.N14LabelingAmount, N15ISOTOPE_NUMBER, this.N15LabelingAmount);
var labeledTheorProfile = _isotopicDistributionCalculator.GetIsotopePattern(mt.EmpiricalFormula);
addMZInfoToTheorProfile(mt.IsotopicProfile, labeledTheorProfile, nitrogenCount, mt.ChargeState);
_isotopicDistributionCalculator.ResetToUnlabeled();
PeakUtilities.TrimIsotopicProfile(labeledTheorProfile, lowPeakCutoff);
labeledTheorProfile.ChargeState = mt.ChargeState;
return(labeledTheorProfile);
}
private IsotopicProfile GetUnlabeledIsotopicProfile(TargetBase mt)
{
IsotopicProfile iso;
try
{
iso = _tomIsotopicPatternGenerator.GetIsotopePattern(mt.EmpiricalFormula, _tomIsotopicPatternGenerator.aafIsos);
}
catch (Exception ex)
{
throw new Exception("Theoretical feature generator failed. Details: " + ex.Message);
}
PeakUtilities.TrimIsotopicProfile(iso, LowPeakCutOff);
iso.ChargeState = mt.ChargeState;
if (iso.ChargeState != 0)
{
calculateMassesForIsotopicProfile(iso, mt);
}
return(iso);
}
public void getIsotopicProfileTest1()
{
var utils = new PeptideUtils();
var formula = utils.GetEmpiricalFormulaForPeptideSequence("SAMPLERPAMPLERSAMPLERPAMPLERSAMPLERPAMPLERSAMPLERPAMPLER");
var iso1 = isotopicDistributionCalculator.GetIsotopePattern(formula);
PeakUtilities.TrimIsotopicProfile(iso1, 0.001);
var tomGen = new TomIsotopicPattern();
var iso2 = tomGen.GetIsotopePattern(formula);
PeakUtilities.TrimIsotopicProfile(iso2, 0.001);
for (var i = 0; i < iso1.Peaklist.Count; i++)
{
var roundedI1 = (decimal)Math.Round(iso1.Peaklist[i].Height, 2);
var roundedI2 = (decimal)Math.Round(iso2.Peaklist[i].Height, 2);
Assert.AreEqual(roundedI1, roundedI2);
}
TestUtilities.DisplayIsotopicProfileData(iso1);
}
public IsotopicProfile GetDHIsotopicProfile2(TargetBase mt, double lowpeakCutoff, double fractionLabeling, double molarMixingofH)
{
Check.Require(mt != null, "Mass tag not defined");
Check.Require(mt.IsotopicProfile != null, "Mass tag's theor isotopic profile not defined");
Check.Require(mt.ChargeState != 0, "Can't have a charge state of '0'");
//int numNitrogens = mt.GetAtomCountForElement("N");
var numDeuterium = 0;
//_isotopicDistributionCalculator.SetLabeling("H", H_ISOTOPE_NUMBER, this.HLabelingAmount, D_ISOTOPE_NUMBER, this.DLabelingAmount);
var hydrogenTheoreticalProfile = _isotopicDistributionCalculator.GetIsotopePattern(mt.EmpiricalFormula);
var deuteriumTheoreticalProfile = _isotopicDistributionCalculator.GetIsotopePattern(mt.EmpiricalFormula);
HLabelingAmount = molarMixingofH;
DLabelingAmount = 1 - molarMixingofH;
//convert to floats
var labelingAmountFraction = Convert.ToSingle(fractionLabeling);
var HLabelingAmountMix = Convert.ToSingle(HLabelingAmount);
var DLabelingAmountMix = Convert.ToSingle(DLabelingAmount);
//initialization
float maxHeightForNormalization = 0;
if (hydrogenTheoreticalProfile.Peaklist.Count > 0)
{
maxHeightForNormalization = hydrogenTheoreticalProfile.Peaklist[0].Height * HLabelingAmountMix;
}
//add deuterated peaks as an offset index
for (var i = 0; i < hydrogenTheoreticalProfile.Peaklist.Count; i++)
{
var peakH = hydrogenTheoreticalProfile.Peaklist[i];
MSPeak peakD;
if (i == 0) //initial peak where there is no D contribution
{
peakD = new MSPeak(0);
}
else
{
peakD = deuteriumTheoreticalProfile.Peaklist[i - 1];
}
var contributionH = peakH.Height * HLabelingAmountMix;
var contributionD = (1 - labelingAmountFraction) * peakD.Height * DLabelingAmountMix + labelingAmountFraction * peakD.Height * DLabelingAmountMix;
peakH.Height = contributionH + contributionD;
//peakH.Height = peakH.Height + (1-Convert.ToSingle(fractionLabeling)) * peakD.Height +Convert.ToSingle(fractionLabeling) * peakD.Height;
//find true hightes peak in combined distribusion
if (peakH.Height > maxHeightForNormalization)
{
maxHeightForNormalization = peakH.Height;
}
}
//rename for clarity
var labeledTheoreticalProfile = hydrogenTheoreticalProfile;
//normalize to 1
foreach (var peak in labeledTheoreticalProfile.Peaklist)
{
peak.Height /= maxHeightForNormalization;
}
//should be good up to here
addMZInfoToTheorProfile(mt.IsotopicProfile, labeledTheoreticalProfile, numDeuterium, mt.ChargeState);//Keep this as the H mass?
//_isotopicDistributionCalculator.ResetToUnlabeled();
PeakUtilities.TrimIsotopicProfile(labeledTheoreticalProfile, lowpeakCutoff);
labeledTheoreticalProfile.ChargeState = mt.ChargeState;
return(labeledTheoreticalProfile);
}
