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);
}
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 override void GetFitScores(IEnumerable <IsosResult> isosResults)
{
foreach (var result in isosResults)
{
//create a temporary mass tag, as a data object for storing relevant info, and using the CalculateMassesForIsotopicProfile() method.
var mt = new PeptideTarget
{
ChargeState = (short)result.IsotopicProfile.ChargeState,
MonoIsotopicMass = result.IsotopicProfile.MonoIsotopicMass
};
mt.MZ = (mt.MonoIsotopicMass / mt.ChargeState) + Globals.PROTON_MASS;
//TODO: use Josh's isotopicDistribution calculator after confirming averagine formula
mt.EmpiricalFormula = _tomIsotopicPatternGenerator.GetClosestAvnFormula(result.IsotopicProfile.MonoIsotopicMass, false);
mt.IsotopicProfile = _tomIsotopicPatternGenerator.GetIsotopePattern(mt.EmpiricalFormula, _tomIsotopicPatternGenerator.aafIsos);
TheorIsotopicProfile = mt.IsotopicProfile;
mt.CalculateMassesForIsotopicProfile(mt.ChargeState);
var theorXYData = mt.IsotopicProfile.GetTheoreticalIsotopicProfileXYData(result.IsotopicProfile.GetFWHM());
offsetDistribution(theorXYData, mt.IsotopicProfile, result.IsotopicProfile);
// Obsolete Class-wide variable: MercuryDistributionCreator distributionCreator;
//
//double resolution = result.IsotopicProfile.GetMZofMostAbundantPeak() / result.IsotopicProfile.GetFWHM();
//distributionCreator.CreateDistribution(result.IsotopicProfile.MonoIsotopicMass, result.IsotopicProfile.ChargeState, resolution);
//distributionCreator.OffsetDistribution(result.IsotopicProfile);
//XYData theorXYData = distributionCreator.Data;
var areaFitter = new AreaFitter();
var fitVal = areaFitter.GetFit(theorXYData, result.Run.XYData, 0.1, out _);
if (double.IsNaN(fitVal) || fitVal > 1)
{
result.IsotopicProfile.Score = 1;
}
else
{
result.IsotopicProfile.Score = fitVal;
}
}
}
public void GetUnsummedIntensitiesAndDetectSaturation(Run run, IEnumerable <IsosResult> resultList)
{
Check.Require(run != null, "SaturationDetector failed. Run is null");
if (run == null)
{
return;
}
if (_msGenerator == null)
{
_msGenerator = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
}
if (run is UIMFRun uimfRun)
{
if (uimfRun.CurrentScanSet == null)
{
throw new NullReferenceException("CurrentScanSet is null. You need to set it.");
}
if (uimfRun.CurrentIMSScanSet == null)
{
throw new NullReferenceException("CurrentIMSScanSet is null. You need to set it.");
}
//this creates a FrameSet containing only the primary frame. Therefore no summing will occur
var lcScanSet = new ScanSet(uimfRun.CurrentScanSet.PrimaryScanNumber);
//this creates a ScanSet containing only the primary scan. Therefore no summing will occur
var imsScanSet = new IMSScanSet(uimfRun.CurrentIMSScanSet.PrimaryScanNumber);
//get the mass spectrum +/- 5 da from the range of the isotopicProfile
uimfRun.CurrentScanSet = lcScanSet;
uimfRun.CurrentIMSScanSet = imsScanSet;
_msGenerator.Execute(run.ResultCollection);
}
else
{
if (run.CurrentScanSet == null)
{
throw new NullReferenceException("CurrentScanSet is null. You need to set it.");
}
//this creates a ScanSet containing only the primary scan. Therefore no summing will occur
var scanSet = new ScanSet(run.CurrentScanSet.PrimaryScanNumber);
run.CurrentScanSet = scanSet;
_msGenerator.Execute(run.ResultCollection);
}
foreach (var result in resultList)
{
var indexOfObsMostAbundant = result.IsotopicProfile.GetIndexOfMostIntensePeak();
var mzOfMostAbundant = result.IsotopicProfile.Peaklist[indexOfObsMostAbundant].XValue;
var indexOfUnsummedMostAbundantMZ = run.XYData.GetClosestXVal(mzOfMostAbundant);
if (indexOfUnsummedMostAbundantMZ >= 0)
{
result.IsotopicProfile.OriginalIntensity = run.XYData.Yvalues[indexOfUnsummedMostAbundantMZ];
result.IsotopicProfile.IsSaturated = (result.IsotopicProfile.OriginalIntensity >=
SaturationThreshold);
if (result.IsotopicProfile.IsSaturated)
{
//problem is that with these saturated profiles, they are often truncated because another
//isotopic profile was falsely assigned to the back end of it. So we need to find more peaks that should
//belong to the saturated profile.
var theorTarget = new PeptideTarget
{
ChargeState = (short)result.IsotopicProfile.ChargeState,
MonoIsotopicMass = result.IsotopicProfile.MonoIsotopicMass
};
theorTarget.MZ = (theorTarget.MonoIsotopicMass / theorTarget.ChargeState) + Globals.PROTON_MASS;
var averagineFormula = _tomIsotopicPatternGenerator.GetClosestAvnFormula(result.IsotopicProfile.MonoIsotopicMass, false);
theorTarget.IsotopicProfile = _tomIsotopicPatternGenerator.GetIsotopePattern(averagineFormula, _tomIsotopicPatternGenerator.aafIsos);
theorTarget.EmpiricalFormula = averagineFormula;
theorTarget.CalculateMassesForIsotopicProfile(result.IsotopicProfile.ChargeState);
AssignMissingPeaksToSaturatedProfile(run.PeakList, result.IsotopicProfile, theorTarget.IsotopicProfile);
//goal is to find the index of the isotopic profile peaks of a peak that is not saturated
var indexOfGoodUnsaturatedPeak = -1;
for (var i = indexOfObsMostAbundant + 1; i < result.IsotopicProfile.Peaklist.Count; i++)
{
var indexUnsummedData = run.XYData.GetClosestXVal(result.IsotopicProfile.Peaklist[i].XValue);
var unsummedIntensity = run.XYData.Yvalues[indexUnsummedData];
if (unsummedIntensity < _minRelIntTheorProfile * SaturationThreshold)
{
indexOfGoodUnsaturatedPeak = i;
break;
}
}
AdjustSaturatedIsotopicProfile(result.IsotopicProfile, theorTarget.IsotopicProfile,
indexOfGoodUnsaturatedPeak);
}
}
//double summedIntensity = 0;
//foreach (MSPeak peak in result.IsotopicProfile.Peaklist)
//{
// int indexOfMZ = result.Run.XYData.GetClosestXVal(peak.XValue);
// if (indexOfMZ >= 0)
// {
// summedIntensity += result.Run.XYData.Yvalues[indexOfMZ];
// }
//}
//result.IsotopicProfile.OriginalTotalIsotopicAbundance = summedIntensity;
}
}
public override void Deconvolute(ResultCollection resultList)
{
float[] xvals = new float[1];
float[] yvals = new float[1];
resultList.Run.XYData.GetXYValuesAsSingles(ref xvals, ref yvals);
int sizeOfRapidArray = 10000;
int[] chargeResults = new int[sizeOfRapidArray];
double[] intensityResults = new double[sizeOfRapidArray];
double[] mzResults = new double[sizeOfRapidArray];
double[] scoreResults = new double[sizeOfRapidArray];
double[] avgmassResults = new double[sizeOfRapidArray];
double[] massResults = new double[sizeOfRapidArray];
double[] mostAbundantMassResults = new double[sizeOfRapidArray];
if (resultList.Run.PeakList == null || resultList.Run.PeakList.Count == 0)
{
return;
}
rapidPeakList = ConvertPeakListToRapidPeakList(resultList.Run.PeakList);
if (rapidPeakList == null || rapidPeakList.Length == 0)
{
return;
}
double rapidsBackgroundIntensityParameter = (resultList.Run.CurrentBackgroundIntensity * minPeptideToBackgroundRatio);
Transformer.PerformTransform_cluster(Convert.ToSingle(rapidsBackgroundIntensityParameter),
ref xvals, ref yvals, ref rapidPeakList, ref chargeResults,
ref intensityResults, ref mzResults, ref scoreResults, ref avgmassResults,
ref massResults, ref mostAbundantMassResults);
GenerateResults(resultList, ref chargeResults, ref intensityResults,
ref mzResults, ref scoreResults,
ref avgmassResults, ref massResults,
ref mostAbundantMassResults, this.resultCombiningMode);
if (this.IsNewFitCalculationPerformed)
{
//HACK: RAPID doesn't return the peaks of the isotopic profile. And it's score is meaningless. So will iterate over
//the results and 1) get the peaks of the isotopic profile and 2) get a least-squares fit of the isotopic profile.
foreach (IsosResult result in resultList.IsosResultBin)
{
//create a temporary mass tag, as a data object for storing relevent info, and using the CalculateMassesForIsotopicProfile() method.
PeptideTarget mt = new PeptideTarget();
mt.ChargeState = (short)result.IsotopicProfile.ChargeState;
mt.MonoIsotopicMass = result.IsotopicProfile.MonoIsotopicMass;
mt.MZ = (mt.MonoIsotopicMass / mt.ChargeState) + Globals.PROTON_MASS;
mt.EmpiricalFormula = _TomIsotopicPatternCreator.GetClosestAvnFormula(result.IsotopicProfile.MonoIsotopicMass, false);
mt.IsotopicProfile = _TomIsotopicPatternCreator.GetIsotopePattern(mt.EmpiricalFormula, _TomIsotopicPatternCreator.aafIsos);
mt.CalculateMassesForIsotopicProfile(mt.ChargeState);
double toleranceInPPM = calcToleranceInPPMFromIsotopicProfile(result.IsotopicProfile);
//this finds the isotopic profile based on the theor. isotopic profile.
BasicTFF bff = new BasicTFF(toleranceInPPM, false);
IsotopicProfile iso = bff.FindMSFeature(resultList.Run.PeakList, mt.IsotopicProfile);
if (iso != null && iso.Peaklist != null && iso.Peaklist.Count > 1)
{
//start at the second peak... and add the newly found peaks
for (int i = 1; i < iso.Peaklist.Count; i++)
{
result.IsotopicProfile.Peaklist.Add(iso.Peaklist[i]);
}
//now that we have the peaks, we can get info for MonoPlusTwoAbundance
result.IsotopicProfile.MonoPlusTwoAbundance = result.IsotopicProfile.GetMonoPlusTwoAbundance();
}
XYData theorXYData = mt.IsotopicProfile.GetTheoreticalIsotopicProfileXYData(result.IsotopicProfile.GetFWHM());
//offset the theor isotopic profile
offsetDistribution(theorXYData, mt.IsotopicProfile, result.IsotopicProfile);
AreaFitter areafitter = new AreaFitter();
int ionCountUsed;
double fitval = areafitter.GetFit(theorXYData, result.Run.XYData, 0.1, out ionCountUsed);
if (fitval == double.NaN || fitval > 1)
{
fitval = 1;
}
result.IsotopicProfile.Score = fitval;
}
}
}
