protected virtual bool FindTransform(PeakData peakData, ref ThrashV1Peak peak, out HornTransformResults record,
double backgroundIntensity = 0)
{
SetIsotopeFitScorerOptions();
record = new HornTransformResults();
if (peak.SignalToNoiseDbl < MinSignalToNoise || peak.FWHM.Equals(0))
{
return(false);
}
//var resolution = peak.Mz / peak.FWHM;
/**/
var chargeState = AutoCorrelationChargeDetermination.GetChargeState(peak, peakData, ShowTraceMessages);
/*/
* // This chunk of code tries to use the DeconTools Patterson Algorithm Charge State Calculator, but it gets vastly different results.
* var xyData = new XYData();
* var mzArray = peakData.MzList.ToArray();
* var intensityArray = peakData.IntensityList.ToArray();
* xyData.SetXYValues(ref mzArray, ref intensityArray);
* var peakList = new List<Peak>();
* for (int i = 0; i < peakData.MzList.Count; i++)
* {
* peakList.Add(new Peak(peakData.MzList[i], (float)peakData.IntensityList[i], 1));
* }
* var chargeState = DeconTools.Backend.Algorithms.ChargeStateDetermination.PattersonAlgorithm.PattersonChargeStateCalculator.GetChargeState(xyData, peakList, convertDeconPeakToMSPeak(peak));
* /**/
if (chargeState == -1 && CheckPatternsAgainstChargeOne)
{
chargeState = 1;
}
if (ShowTraceMessages)
{
Console.Error.WriteLine("Deisotoping :" + peak.Mz);
Console.Error.WriteLine("Charge = " + chargeState);
}
if (chargeState == -1)
{
return(false);
}
if ((peak.Mz + ChargeCarrierMass) * chargeState > MaxMWAllowed)
{
return(false);
}
if (IsO16O18Data)
{
if (peak.FWHM < 1.0 / chargeState)
{
// move back by 4 Da and see if there is a peak.
var minMz = peak.Mz - 4.0 / chargeState - peak.FWHM;
var maxMz = peak.Mz - 4.0 / chargeState + peak.FWHM;
ThrashV1Peak o16Peak;
var found = peakData.GetPeak(minMz, maxMz, out o16Peak);
if (found && !o16Peak.Mz.Equals(peak.Mz))
{
// put back the current into the to be processed list of peaks.
peakData.AddPeakToProcessingList(peak);
// reset peak to the right peak so that the calling function may
// know that the peak might have changed in the O16/O18 business
peak = o16Peak;
peakData.RemovePeak(peak);
return(FindTransform(peakData, ref peak, out record, backgroundIntensity));
}
}
}
var peakCharge1 = new ThrashV1Peak(peak);
// Until now, we have been using constant theoretical delete intensity threshold..
// instead, from now, we should use one that is proportional to intensity, for more intense peaks.
// However this will not solve all problems. If thrashing occurs, then the peak intensity will
// change when the function returns and we may not delete far enough.
//double deleteThreshold = backgroundIntensity / peak.Intensity * 100;
//if (backgroundIntensity ==0 || deleteThreshold > _deleteIntensityThreshold)
// deleteThreshold = _deleteIntensityThreshold;
var deleteThreshold = DeleteIntensityThreshold;
int fitCountBasis;
var bestFit = _isotopeFitScorer.GetFitScore(peakData, chargeState, ref peak, out record, deleteThreshold,
MinIntensityForScore, LeftFitStringencyFactor, RightFitStringencyFactor, out fitCountBasis,
ShowTraceMessages);
// When deleting an isotopic profile, this value is set to the first m/z to perform deletion at.
double zeroingStartMz;
// When deleting an isotopic profile, this value is set to the last m/z to perform deletion at.
double zeroingStopMz;
_isotopeFitScorer.GetZeroingMassRange(out zeroingStartMz, out zeroingStopMz, record.DeltaMz, deleteThreshold,
ShowTraceMessages);
//bestFit = _isotopeFitter.GetFitScore(peakData, chargeState, peak, record, _deleteIntensityThreshold, _minTheoreticalIntensityForScore, DebugFlag);
//_isotopeFitter.GetZeroingMassRange(_zeroingStartMz, _zeroingStopMz, record.DeltaMz, _deleteIntensityThreshold, DebugFlag);
if (CheckPatternsAgainstChargeOne && chargeState != 1)
{
HornTransformResults recordCharge1;
int fitCountBasisCharge1;
var bestFitCharge1 = _isotopeFitScorer.GetFitScore(peakData, 1, ref peakCharge1, out recordCharge1,
deleteThreshold, MinIntensityForScore, LeftFitStringencyFactor,
RightFitStringencyFactor, out fitCountBasisCharge1, ShowTraceMessages);
//double bestFitCharge1 = _isotopeFitter.GetFitScore(peakData, 1, peakCharge1, recordCharge1, _deleteIntensityThreshold, _minTheoreticalIntensityForScore, DebugFlag);
//_isotopeFitter.GetZeroingMassRange(_zeroingStartMz, _zeroingStopMz, record.DeltaMz, _deleteIntensityThreshold, DebugFlag);
double startMz1 = 0;
double stopMz1 = 0;
_isotopeFitScorer.GetZeroingMassRange(out startMz1, out stopMz1, record.DeltaMz, deleteThreshold,
ShowTraceMessages);
if (bestFit > MaxFitAllowed && bestFitCharge1 < MaxFitAllowed)
{
bestFit = bestFitCharge1;
fitCountBasis = fitCountBasisCharge1;
peak = peakCharge1;
record = new HornTransformResults(recordCharge1);
zeroingStartMz = startMz1;
zeroingStopMz = stopMz1;
chargeState = 1;
}
}
if (bestFit > MaxFitAllowed) // check if fit is good enough
{
return(false);
}
if (ShowTraceMessages)
{
Console.Error.WriteLine("\tBack with fit = " + record.Fit);
}
// Applications using this DLL should use Abundance instead of AbundanceInt
record.Abundance = peak.Intensity;
record.ChargeState = chargeState;
ThrashV1Peak monoPeak;
var monoMz = record.MonoMw / record.ChargeState + ChargeCarrierMass;
// used when _reportO18Plus2Da is true.
ThrashV1Peak m3Peak;
var monoPlus2Mz = record.MonoMw / record.ChargeState + 2.0 / record.ChargeState + ChargeCarrierMass;
peakData.FindPeak(monoMz - peak.FWHM, monoMz + peak.FWHM, out monoPeak);
peakData.FindPeak(monoPlus2Mz - peak.FWHM, monoPlus2Mz + peak.FWHM, out m3Peak);
record.MonoIntensity = (int)monoPeak.Intensity;
record.MonoPlus2Intensity = (int)m3Peak.Intensity;
record.SignalToNoise = peak.SignalToNoiseDbl;
record.FWHM = peak.FWHM;
record.PeakIndex = peak.PeakIndex;
SetIsotopeDistributionToZero(peakData, peak, zeroingStartMz, zeroingStopMz, record.MonoMw, chargeState, true,
record, ShowTraceMessages);
if (ShowTraceMessages)
{
Console.Error.WriteLine("Performed deisotoping of " + peak.Mz);
}
return(true);
}
public virtual bool FindTransform(PeakData peakData, ref clsPeak peak, out clsHornTransformResults record,
double backgroundIntensity = 0)
{
record = new clsHornTransformResults();
if (peak.SignalToNoise < TransformParameters.MinS2N || peak.FWHM.Equals(0))
{
return(false);
}
//var resolution = peak.Mz / peak.FWHM;
var chargeState = AutoCorrelationChargeDetermination.GetChargeState(peak, peakData, DebugFlag);
if (chargeState == -1 && TransformParameters.CheckAllPatternsAgainstCharge1)
{
chargeState = 1;
}
if (DebugFlag)
{
Console.Error.WriteLine("Deisotoping :" + peak.Mz);
Console.Error.WriteLine("Charge = " + chargeState);
}
if (chargeState == -1)
{
return(false);
}
if ((peak.Mz + TransformParameters.CCMass) * chargeState > TransformParameters.MaxMW)
{
return(false);
}
if (TransformParameters.O16O18Media)
{
if (peak.FWHM < 1.0 / chargeState)
{
// move back by 4 Da and see if there is a peak.
var minMz = peak.Mz - 4.0 / chargeState - peak.FWHM;
var maxMz = peak.Mz - 4.0 / chargeState + peak.FWHM;
clsPeak o16Peak;
var found = peakData.GetPeak(minMz, maxMz, out o16Peak);
if (found && !o16Peak.Mz.Equals(peak.Mz))
{
// put back the current into the to be processed list of peaks.
peakData.AddPeakToProcessingList(peak);
// reset peak to the right peak so that the calling function may
// know that the peak might have changed in the O16/O18 business
peak = o16Peak;
peakData.RemovePeak(peak);
return(FindTransform(peakData, ref peak, out record, backgroundIntensity));
}
}
}
var peakCharge1 = new clsPeak(peak);
// Until now, we have been using constant theoretical delete intensity threshold..
// instead, from now, we should use one that is proportional to intensity, for more intense peaks.
// However this will not solve all problems. If thrashing occurs, then the peak intensity will
// change when the function returns and we may not delete far enough.
//double deleteThreshold = backgroundIntensity / peak.Intensity * 100;
//if (backgroundIntensity ==0 || deleteThreshold > _deleteIntensityThreshold)
// deleteThreshold = _deleteIntensityThreshold;
var deleteThreshold = TransformParameters.DeleteIntensityThreshold;
int fitCountBasis;
var bestFit = TransformParameters.IsotopeFitScorer.GetFitScore(peakData, chargeState, ref peak, out record, deleteThreshold,
TransformParameters.MinIntensityForScore, TransformParameters.LeftFitStringencyFactor, TransformParameters.RightFitStringencyFactor, out fitCountBasis,
DebugFlag);
// When deleting an isotopic profile, this value is set to the first m/z to perform deletion at.
double zeroingStartMz;
// When deleting an isotopic profile, this value is set to the last m/z to perform deletion at.
double zeroingStopMz;
TransformParameters.IsotopeFitScorer.GetZeroingMassRange(out zeroingStartMz, out zeroingStopMz, record.DeltaMz, deleteThreshold,
DebugFlag);
//bestFit = _isotopeFitter.GetFitScore(peakData, chargeState, peak, record, _deleteIntensityThreshold, _minTheoreticalIntensityForScore, DebugFlag);
//_isotopeFitter.GetZeroingMassRange(_zeroingStartMz, _zeroingStopMz, record.DeltaMz, _deleteIntensityThreshold, DebugFlag);
if (TransformParameters.CheckAllPatternsAgainstCharge1 && chargeState != 1)
{
clsHornTransformResults recordCharge1;
int fitCountBasisCharge1;
var bestFitCharge1 = TransformParameters.IsotopeFitScorer.GetFitScore(peakData, 1, ref peakCharge1, out recordCharge1,
deleteThreshold, TransformParameters.MinIntensityForScore, TransformParameters.LeftFitStringencyFactor,
TransformParameters.RightFitStringencyFactor, out fitCountBasisCharge1, DebugFlag);
//double bestFitCharge1 = _isotopeFitter.GetFitScore(peakData, 1, peakCharge1, recordCharge1, _deleteIntensityThreshold, _minTheoreticalIntensityForScore, DebugFlag);
//_isotopeFitter.GetZeroingMassRange(_zeroingStartMz, _zeroingStopMz, record.DeltaMz, _deleteIntensityThreshold, DebugFlag);
double startMz1 = 0;
double stopMz1 = 0;
TransformParameters.IsotopeFitScorer.GetZeroingMassRange(out startMz1, out stopMz1, record.DeltaMz, deleteThreshold, DebugFlag);
if (bestFit > TransformParameters.MaxFit && bestFitCharge1 < TransformParameters.MaxFit)
{
bestFit = bestFitCharge1;
fitCountBasis = fitCountBasisCharge1;
peak = peakCharge1;
record = new clsHornTransformResults(recordCharge1);
zeroingStartMz = startMz1;
zeroingStopMz = stopMz1;
chargeState = 1;
}
}
if (bestFit > TransformParameters.MaxFit) // check if fit is good enough
{
return(false);
}
if (DebugFlag)
{
Console.Error.WriteLine("\tBack with fit = " + record.Fit);
}
// Applications using this DLL should use Abundance instead of AbundanceInt
record.Abundance = peak.Intensity;
record.ChargeState = chargeState;
clsPeak monoPeak;
var monoMz = record.MonoMw / record.ChargeState + TransformParameters.CCMass;
// used when _reportO18Plus2Da is true.
clsPeak m3Peak;
var monoPlus2Mz = record.MonoMw / record.ChargeState + 2.0 / record.ChargeState + TransformParameters.CCMass;
peakData.FindPeak(monoMz - peak.FWHM, monoMz + peak.FWHM, out monoPeak);
peakData.FindPeak(monoPlus2Mz - peak.FWHM, monoPlus2Mz + peak.FWHM, out m3Peak);
record.MonoIntensity = (int)monoPeak.Intensity;
record.MonoPlus2Intensity = (int)m3Peak.Intensity;
record.SignalToNoise = peak.SignalToNoise;
record.FWHM = peak.FWHM;
record.PeakIndex = peak.PeakIndex;
SetIsotopeDistributionToZero(peakData, peak, zeroingStartMz, zeroingStopMz, record.MonoMw, chargeState, true,
record, DebugFlag);
if (DebugFlag)
{
Console.Error.WriteLine("Performed deisotoping of " + peak.Mz);
}
return(true);
}
