private IEnumerable <DeisotopedPeak> GetDeisotopedPeaks(List <Peak> specWindow, IEnumerable <Peak> peakList, int numDeisotopedPeaksToGet)
{
var peakListSortedByIntensity = new List <Peak>(peakList);
peakListSortedByIntensity.Sort(new IntensityComparer());
var remainingPeakList = new LinkedList <Peak>(peakListSortedByIntensity);
var deisotopedPeakSet = new SortedSet <DeisotopedPeak>();
while (remainingPeakList.Any())
{
var peakWithHighestIntensity = remainingPeakList.First.Value;
var peakMz = peakWithHighestIntensity.Mz;
var score = new double[_maxCharge + 1];
for (var charge = _maxCharge; charge >= _minCharge; charge--)
{
// check whether next isotope peak exists
var nextIsotopeMz = peakMz + Constants.C13MinusC12 / charge;
var nextIsotopePeak = PeakListUtils.FindPeak(specWindow, nextIsotopeMz, _tolerance);
if (nextIsotopePeak == null)
{
continue;
}
var mostAbundantIsotopeMass = (peakMz - Constants.Proton) * charge;
var averagineIsoEnv = Averagine.GetIsotopomerEnvelope(mostAbundantIsotopeMass);
var approxMostAbundantIsotopeIndex = averagineIsoEnv.MostAbundantIsotopeIndex;
var monoIsotopicMass = mostAbundantIsotopeMass - approxMostAbundantIsotopeIndex * Constants.C13MinusC12;
var averagineIsotopeProfile = Averagine.GetTheoreticalIsotopeProfile(monoIsotopicMass, charge);
var corr = PeakListUtils.GetPearsonCorrelation(specWindow, averagineIsotopeProfile, _comparer);
score[charge] = corr;
var isValid = true;
for (var mult = 2; mult <= _maxCharge / charge; mult++)
{
var multiple = charge * mult;
if (score[multiple] > 0.8 * corr)
{
isValid = false;
break;
}
}
if (!isValid)
{
continue;
}
deisotopedPeakSet.Add(new DeisotopedPeak(monoIsotopicMass, charge, corr));
if (deisotopedPeakSet.Count > numDeisotopedPeaksToGet)
{
deisotopedPeakSet.Remove(deisotopedPeakSet.Min);
}
}
remainingPeakList.RemoveFirst();
}
return(deisotopedPeakSet);
}
private void ApplyDeconvolution(List <Peak> specWindow, ref LinkedList <Peak> remainingPeakList, ref List <double> deisotopedMassList)
{
if (!remainingPeakList.Any())
{
return;
}
var peakWithHighestIntensity = remainingPeakList.First.Value;
var peakMz = peakWithHighestIntensity.Mz;
var score = new double[_maxCharge + 1];
for (var charge = _maxCharge; charge >= _minCharge; charge--)
{
// check whether next isotope peak exists
var nextIsotopeMz = peakMz + Constants.C13MinusC12 / charge;
var nextIsotopePeak = PeakListUtils.FindPeak(specWindow, nextIsotopeMz, _tolerance);
if (nextIsotopePeak == null)
{
continue;
}
var mostAbundantIsotopeMass = (peakMz - Constants.Proton) * charge;
var averagineIsoEnv = Averagine.GetIsotopomerEnvelope(mostAbundantIsotopeMass);
var approxMostAbundantIsotopeIndex = averagineIsoEnv.MostAbundantIsotopeIndex;
var monoIsotopicMass = mostAbundantIsotopeMass - approxMostAbundantIsotopeIndex * Constants.C13MinusC12;
var averagineIsotopeProfile = Averagine.GetTheoreticalIsotopeProfile(monoIsotopicMass, charge);
var corr = PeakListUtils.GetPearsonCorrelation(specWindow, averagineIsotopeProfile, _comparer);
score[charge] = corr;
var isValid = true;
for (var mult = 2; mult <= _maxCharge / charge; mult++)
{
var multiple = charge * mult;
if (score[multiple] > 0.8 * corr)
{
isValid = false;
break;
}
}
if (!isValid)
{
continue;
}
if (corr > _corrThreshold)
{
deisotopedMassList.Add(monoIsotopicMass);
}
}
remainingPeakList.RemoveFirst();
}
public void TestAveragine()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
const double monoMass = 10247.5293287335;
const int charge = 14;
var profile = Averagine.GetTheoreticalIsotopeProfile(monoMass, charge);
Console.WriteLine("Isotope ions:");
foreach (var p in profile)
{
Console.WriteLine("{0}\t{1}", p.Mz, p.Intensity);
}
Console.WriteLine();
}
/// <summary>
/// Read a line from the feature file containing a single feature.
/// </summary>
/// <param name="line">The line from the feature file.</param>
/// <param name="delimeter">The delimiter used in feature file.</param>
/// <param name="headers">The headers of the feature file columns.</param>
/// <returns>Parsed feature.</returns>
private static Feature ReadFeature(string line, char delimeter, IReadOnlyDictionary <string, int> headers)
{
var expectedHeaders = new List <string>
{
"MonoMass",
"Abundance",
"LikelihoodRatio",
"Envelope",
"MinCharge",
"MaxCharge",
////"SummedCorr",
"MinScan",
"MaxScan"
};
string likelihoodVarHeader = "LikelihoodRatio";
foreach (var header in expectedHeaders.Where(header => !headers.ContainsKey(header)))
{
if (header == "LikelihoodRatio" && headers.ContainsKey("Probability"))
{
likelihoodVarHeader = "Probability";
}
else
{
throw new KeyNotFoundException(string.Format("Missing expected column header \"{0}\" in feature file.", header));
}
}
var parts = line.Split(delimeter);
var mass = Convert.ToDouble(parts[headers["MonoMass"]]);
var abundance = Convert.ToDouble(parts[headers["Abundance"]]);
var score = Convert.ToDouble(parts[headers[likelihoodVarHeader]]);
var isotopes = ReadIsotopicEnvelope(parts[headers["Envelope"]]);
var minCharge = Convert.ToInt32(parts[headers["MinCharge"]]);
var maxCharge = Convert.ToInt32(parts[headers["MaxCharge"]]);
int id = -1;
if (headers.ContainsKey("FeatureID"))
{
id = Convert.ToInt32(parts[headers["FeatureID"]]);
}
var summedCorr = headers.ContainsKey("SummedCorr") ? Convert.ToDouble(parts[headers["SummedCorr"]]) : 0.0;
int mostAbundantIsotopeIndex = Averagine.GetIsotopomerEnvelope(mass).MostAbundantIsotopeIndex;
List <Peak> minIsotopicProfile = Averagine.GetTheoreticalIsotopeProfile(mass, minCharge, 0);
List <Peak> maxIsotopicProfile = Averagine.GetTheoreticalIsotopeProfile(mass, maxCharge, 0);
var minPoint = new Feature.FeaturePoint
{
Id = id,
Mass = mass,
Scan = Convert.ToInt32(parts[headers["MinScan"]]),
Mz = minIsotopicProfile[mostAbundantIsotopeIndex].Mz,
Charge = minCharge,
Abundance = abundance,
Score = score,
Isotopes = isotopes,
Correlation = summedCorr
};
var maxPoint = new Feature.FeaturePoint
{
Id = id,
Mass = mass,
Scan = Convert.ToInt32(parts[headers["MaxScan"]]),
Mz = maxIsotopicProfile[mostAbundantIsotopeIndex].Mz,
Charge = maxCharge,
Abundance = abundance,
Score = score,
Isotopes = isotopes,
Correlation = summedCorr,
};
return(new Feature(minPoint, maxPoint)
{
Id = id
});
}
private void SetLcMsMatches(double peakMz, int scanNum, IList <Peak> precursorSpecWindow, IList <Peak> nextMs1SpecWindow)
{
var xicThisPeak = _run.GetPrecursorExtractedIonChromatogram(peakMz, _tolerance, scanNum);
if (xicThisPeak.Count < 2)
{
return;
}
for (var charge = _maxCharge; charge >= _minCharge; charge--)
{
// check whether next isotope peak exists
var nextIsotopeMz = peakMz + Constants.C13MinusC12 / charge;
var xicNextIsotope = _run.GetPrecursorExtractedIonChromatogram(nextIsotopeMz, _tolerance, scanNum);
if (!xicNextIsotope.Any())
{
continue;
}
if (xicThisPeak.GetCorrelation(xicNextIsotope) < _mostAbundantPlusOneIsotopeCorrThreshold)
{
continue;
}
var mostAbundantIsotopeMass = (peakMz - Constants.Proton) * charge;
var averagineIsoEnv = Averagine.GetIsotopomerEnvelope(mostAbundantIsotopeMass);
var approxMostAbundantIsotopeIndex = averagineIsoEnv.MostAbundantIsotopeIndex;
var monoIsotopicMass = mostAbundantIsotopeMass - approxMostAbundantIsotopeIndex * Constants.C13MinusC12;
// Isotope correlation
var averagineIsotopeProfile = Averagine.GetTheoreticalIsotopeProfile(monoIsotopicMass, charge);
var precursorIsotopeCorr = precursorSpecWindow != null?PeakListUtils.GetPearsonCorrelation(precursorSpecWindow, averagineIsotopeProfile, _comparer) : 0;
var nextMs1IsotopeCorr = nextMs1SpecWindow != null?PeakListUtils.GetPearsonCorrelation(nextMs1SpecWindow, averagineIsotopeProfile, _comparer) : 0;
var isotopeCorr = Math.Max(precursorIsotopeCorr, nextMs1IsotopeCorr);
if (isotopeCorr < _isotopeCorrThresholdThreshold)
{
continue;
}
if (_chargeCorrThresholdThreshold > 0.0)
{
var mzChargePlusOne = Ion.GetIsotopeMz(monoIsotopicMass, charge + 1, approxMostAbundantIsotopeIndex);
var xicPlusOneCharge = _run.GetPrecursorExtractedIonChromatogram(mzChargePlusOne, _tolerance, scanNum);
var corrPlusOneCharge = xicPlusOneCharge.Count >= 3 ? xicThisPeak.GetCorrelation(xicPlusOneCharge) : 0;
double corrMinusOneCharge;
if (charge > 1)
{
var mzChargeMinusOne = Ion.GetIsotopeMz(monoIsotopicMass, charge - 1, approxMostAbundantIsotopeIndex);
var xicMinusOneCharge = _run.GetPrecursorExtractedIonChromatogram(mzChargeMinusOne, _tolerance, scanNum);
corrMinusOneCharge = xicMinusOneCharge.Count >= 3 ? xicThisPeak.GetCorrelation(xicMinusOneCharge) : 0;
}
else
{
corrMinusOneCharge = 0.0;
}
var chargeCorr = Math.Max(corrPlusOneCharge, corrMinusOneCharge);
if (chargeCorr < _chargeCorrThresholdThreshold)
{
continue;
}
}
_lcMsMatchMap.SetMatches(monoIsotopicMass, xicThisPeak[0].ScanNum, xicThisPeak[xicThisPeak.Count - 1].ScanNum);
}
}
