/// <summary>
/// Deconvolute mass spectrum using deconvolution algorithm described in Mann et al., Anal. Chem. 1989
/// </summary>
/// <returns>deconvoluted spectrum</returns>
public DeconvolutedSpectrum GetDeconvolutedSpectrum()
{
if (_deconvolutedSpectrum != null)
{
return(_deconvolutedSpectrum);
}
var minBinIndex = _massBinning.GetBinNumber(_minMass);
var maxBinIndex = _massBinning.GetBinNumber(_maxMass);
var massIntensity = new double[maxBinIndex - minBinIndex + 1];
foreach (var peak in _spectrum.Peaks)
{
for (var charge = _minCharge; charge <= _maxCharge; charge++)
{
var mass = (peak.Mz - Constants.Proton) * charge;
if (mass < _minMass)
{
continue;
}
if (mass > _maxMass)
{
break;
}
var massBinNum = _massBinning.GetBinNumber(mass);
massIntensity[massBinNum - minBinIndex] += peak.Intensity;
}
}
var deconvPeaks = new List <DeconvolutedPeak>();
for (var i = 0; i < massIntensity.Length; i++)
{
var intensity = massIntensity[i];
if (intensity < float.Epsilon)
{
continue;
}
var mass = _massBinning.GetMzAverage(i + minBinIndex);
deconvPeaks.Add(new DeconvolutedPeak(mass, intensity, 1, 0, 0));
}
_deconvolutedSpectrum = new DeconvolutedSpectrum(_spectrum, deconvPeaks.ToArray());
return(_deconvolutedSpectrum);
}
public CompositeScorerBasedOnDeconvolutedSpectrum(DeconvolutedSpectrum deconvolutedSpectrum, ProductSpectrum spec, Tolerance productTolerance, IMassBinning comparer)
: base(deconvolutedSpectrum, productTolerance)
{
ReferencePeakIntensity = GetRefIntensity(spec.Peaks);
_comparer = comparer;
_massBinToPeakMap = new Dictionary <int, DeconvolutedPeak>();
foreach (var p in deconvolutedSpectrum.Peaks)
{
var mass = p.Mz;
var deltaMass = productTolerance.GetToleranceAsDa(mass, 1);
var minMass = mass - deltaMass;
var maxMass = mass + deltaMass;
var binNum = comparer.GetBinNumber(mass);
if (binNum < 0)
{
binNum = comparer.GetBinNumber(minMass);
if (binNum < 0)
{
binNum = comparer.GetBinNumber(maxMass);
}
}
// filter out
if (binNum < 0)
{
continue;
}
UpdateDeconvPeak(binNum, p as DeconvolutedPeak);
// going up
for (var nextBinNum = binNum + 1; nextBinNum < comparer.NumberOfBins; nextBinNum++)
{
var nextBinMass = comparer.GetMassStart(nextBinNum);
if (minMass < nextBinMass && nextBinMass < maxMass)
{
UpdateDeconvPeak(nextBinNum, p as DeconvolutedPeak); //_ionMassChkBins[nextBinNum] = true;
}
else
{
break;
}
}
// going down
for (var prevBinNum = binNum - 1; prevBinNum < comparer.NumberOfBins; prevBinNum--)
{
var prevBinMass = comparer.GetMassEnd(prevBinNum);
if (minMass < prevBinMass && prevBinMass < maxMass)
{
UpdateDeconvPeak(prevBinNum, p as DeconvolutedPeak); //_ionMassChkBins[prevBinNum] = true;
}
else
{
break;
}
}
}
}
/// <summary>
/// Read a spectrum from the current position in <paramref name="reader"/>, with the option to only read the metadata.
/// </summary>
/// <param name="reader"></param>
/// <param name="includePeaks"></param>
/// <returns></returns>
protected internal override Spectrum ReadSpectrum(BinaryReader reader, bool includePeaks = true)
{
// Must reflect all changes to WriteSpectrum
var scanNum = reader.ReadInt32();
var c = new char[NativeIdLength];
reader.Read(c, 0, NativeIdLength);
var nativeId = (new string(c)).Trim();
var msLevel = reader.ReadByte();
var elutionTime = reader.ReadDouble();
var tic = reader.ReadSingle();
double?precursorMass = reader.ReadDouble();
if (Math.Abs(precursorMass.Value) < float.Epsilon)
{
precursorMass = null;
}
int?precursorCharge = reader.ReadInt32();
if (precursorCharge == 0)
{
precursorCharge = null;
}
var activationMethod = (ActivationMethod)reader.ReadByte();
var isolationWindowTargetMz = reader.ReadDouble();
var isolationWindowLowerOffset = reader.ReadDouble();
var isolationWindowUpperOffset = reader.ReadDouble();
var peakList = new List <DeconvolutedPeak>();
var numPeaks = reader.ReadInt32();
for (var i = 0; i < numPeaks; i++)
{
var mz = reader.ReadDouble();
var intensity = reader.ReadSingle();
var charge = reader.ReadInt32();
var corr = reader.ReadSingle();
var dist = reader.ReadSingle();
var peak = new DeconvolutedPeak(mz, intensity, charge, corr, dist);
var isoPeakCount = (int)reader.ReadByte();
peak.ObservedPeakIndices.Capacity = isoPeakCount;
for (var j = 0; j < isoPeakCount; j++)
{
peak.ObservedPeakIndices.Add(reader.ReadUInt16());
}
peakList.Add(peak);
}
var spec = new DeconvolutedSpectrum(peakList, scanNum)
{
ActivationMethod = activationMethod,
IsolationWindow = new IsolationWindow(
isolationWindowTargetMz,
isolationWindowLowerOffset,
isolationWindowUpperOffset,
precursorMass,
precursorCharge
),
MsLevel = msLevel,
ElutionTime = elutionTime,
NativeId = nativeId,
TotalIonCurrent = tic
};
return(spec);
}