public IEnumerable <int> GetMatchingMs2ScanNums(double sequenceMass)
{
var sequenceMassBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(sequenceMass);
IList <int> ms2ScanNums;
if (_sequenceMassBinToScanNumsMap.TryGetValue(sequenceMassBinNum, out ms2ScanNums))
{
return(ms2ScanNums);
}
ms2ScanNums = new List <int>();
var averagineEnvelope = Averagine.GetIsotopomerEnvelope(sequenceMass);
var mostAbundantIsotopeIndex = averagineEnvelope.MostAbundantIsotopeIndex;
for (var precursorCharge = _minCharge; precursorCharge <= _maxCharge; precursorCharge++)
{
var mostAbundantIsotopeMz = Ion.GetIsotopeMz(sequenceMass, precursorCharge, mostAbundantIsotopeIndex);
var binNumber = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(mostAbundantIsotopeMz);
IList <ChargeAndScanNum> chargeAndScanNumList;
if (!_mostAbundantIsotopeMzIndexToChargeAndScanNums.TryGetValue(binNumber, out chargeAndScanNumList))
{
continue;
}
foreach (var chargeAndScanNum in chargeAndScanNumList)
{
if (chargeAndScanNum.Charge == precursorCharge)
{
ms2ScanNums.Add(chargeAndScanNum.ScanNum);
}
}
}
_sequenceMassBinToScanNumsMap.Add(sequenceMassBinNum, ms2ScanNums);
return(ms2ScanNums);
}
internal DeisotopedPeak(double monoIsotopicMass, int charge, double score)
{
MonoIsotopicMass = monoIsotopicMass;
MonoIsotopicMassIndex = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(MonoIsotopicMass);
Charge = charge;
Score = score;
}
public IEnumerable <int> GetMatchingMs2ScanNums(double sequenceMass)
{
var sequenceMassBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(sequenceMass);
IList <int> ms2ScanNums;
if (_sequenceMassBinToScanNumsMap.TryGetValue(sequenceMassBinNum, out ms2ScanNums))
{
return(ms2ScanNums);
}
return(new int[0]);
}
private readonly Dictionary <int, IList <int> > _sequenceMassBinToScanNumsMap; // mass -> scan numbers
private void PrecomputePossibleSequenceMasses()
{
var ms2ScanNums = _run.GetScanNumbers(2);
foreach (var ms2ScanNum in ms2ScanNums)
{
var possibleSequenceMasses = GetPossibleSequenceMasses(ms2ScanNum);
var binNumHash = new HashSet <int>();
foreach (var sequenceMass in possibleSequenceMasses)
{
var dMass = sequenceMass * _ppmTolerance * 1e-6;
var minMass = sequenceMass - dMass;
var maxMass = sequenceMass + dMass;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
if (!binNumHash.Add(binNum))
{
continue;
}
IList <int> scanNums;
if (_sequenceMassBinToScanNumsMap.TryGetValue(binNum, out scanNums))
{
scanNums.Add(ms2ScanNum);
}
else
{
scanNums = new List <int> {
ms2ScanNum
};
_sequenceMassBinToScanNumsMap.Add(binNum, scanNums);
}
}
}
}
}
private void PrecomputeMostAbundantMzToMatches()
{
var ms2ScanNums = _run.GetScanNumbers(2);
_mostAbundantIsotopeMzIndexToChargeAndScanNums = new Dictionary <int, IList <ChargeAndScanNum> >();
foreach (var ms2ScanNum in ms2ScanNums)
{
var possibleSequenceMatches = GetPossibleSequenceMatches(ms2ScanNum);
foreach (var match in possibleSequenceMatches)
{
var mostAbundantIsotopeMz = match.MostAbundantIsotopeMz;
var charge = match.Charge;
var deltaMz = mostAbundantIsotopeMz * _ppmTolerance * 1e-6;
var minMz = mostAbundantIsotopeMz - deltaMz;
var maxMz = mostAbundantIsotopeMz + deltaMz;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minMz);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxMz);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
IList <ChargeAndScanNum> chargeAndScanNums;
if (_mostAbundantIsotopeMzIndexToChargeAndScanNums.TryGetValue(binNum,
out chargeAndScanNums))
{
chargeAndScanNums.Add(new ChargeAndScanNum(charge, ms2ScanNum));
}
else
{
chargeAndScanNums = new List <ChargeAndScanNum> {
new ChargeAndScanNum(charge, ms2ScanNum)
};
_mostAbundantIsotopeMzIndexToChargeAndScanNums.Add(binNum, chargeAndScanNums);
}
}
}
}
}
