private void SetLcMsMatches(double peakMz, int scanNum)
{
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;
}
var mostAbundantIsotopeMass = (peakMz - Constants.Proton) * charge;
var averagineIsoEnv = Averagine.GetIsotopomerEnvelope(mostAbundantIsotopeMass);
var approxMostAbundantIsotopeIndex = averagineIsoEnv.MostAbundantIsotopeIndex;
var monoIsotopicMass = mostAbundantIsotopeMass - approxMostAbundantIsotopeIndex * Constants.C13MinusC12;
_lcMsMatchMap.SetMatches(monoIsotopicMass, xicThisPeak[0].ScanNum, xicThisPeak[xicThisPeak.Count - 1].ScanNum);
}
}
private void Read(string msDeconvFileName)
{
var curScan = 0;
var isMs1 = false;
var minMass = double.MaxValue;
var maxMass = 0.0;
var featureCountUnfiltered = 0;
var featureCountFiltered = 0;
foreach (var line in File.ReadLines(msDeconvFileName))
{
if (line.StartsWith("SCANS="))
{
curScan = Convert.ToInt32(line.Substring(line.LastIndexOf('=') + 1));
isMs1 = _run.GetMsLevel(curScan) == 1;
}
else if (isMs1 && line.Length > 0)
{
var token = line.Split();
if (token.Length != 3)
{
continue;
}
featureCountUnfiltered++;
var charge = Convert.ToInt32(token[2]);
if (charge == 1)
{
continue;
}
var monoMass = Convert.ToDouble(token[0]);
if (minMass > monoMass)
{
minMass = monoMass;
}
if (maxMass < monoMass)
{
maxMass = monoMass;
}
featureCountFiltered++;
var minScan = _run.GetPrevScanNum(curScan, 1);
var maxScan = _run.GetNextScanNum(curScan, 1);
_lcMsMatchMap.SetMatches(monoMass, minScan, maxScan);
}
}
Console.Write(@"{0}/{1} features loaded...", featureCountFiltered, featureCountUnfiltered);
_lcMsMatchMap.CreateSequenceMassToMs2ScansMap(_run, _massTolerance, minMass, maxMass);
}
private void Read(string isosFileName)
{
var icrToolsparser = new TsvFileParser(isosFileName, ',');
var monoMassArr = icrToolsparser.GetData("monoisotopic_mw").Select(Convert.ToDouble).ToArray();
var scanArray = icrToolsparser.GetData("scan_num").Select(s => Convert.ToInt32(s)).ToArray();
var chargeArray = icrToolsparser.GetData("charge").Select(s => Convert.ToInt32(s)).ToArray();
var fitStringArr = icrToolsparser.GetData("fit");
var fitArray = fitStringArr == null ? null : icrToolsparser.GetData("fit").Select(Convert.ToDouble).ToArray();
var featureCountFiltered = 0;
var minMass = double.MaxValue;
var maxMass = 0.0;
for (var i = 0; i < monoMassArr.Length; i++)
{
if (fitArray != null && fitArray[i] > _fitScoreThreshold || chargeArray[i] <= 1)
{
continue;
}
featureCountFiltered++;
var scan = scanArray[i];
var monoMass = monoMassArr[i];
if (minMass > monoMass)
{
minMass = monoMass;
}
if (maxMass < monoMass)
{
maxMass = monoMass;
}
var minScan = _run.GetPrevScanNum(scan, 1);
var maxScan = _run.GetNextScanNum(scan, 1);
_lcMsMatchMap.SetMatches(monoMass, minScan, maxScan);
}
Console.Write(@"{0}/{1} features loaded...", featureCountFiltered, monoMassArr.Length);
_lcMsMatchMap.CreateSequenceMassToMs2ScansMap(_run, _massTolerance, minMass, maxMass);
}
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);
}
}
