public ObservedIsotopeEnvelope(double monoMass, int charge, int scanNum, Ms1Peak[] peaks, TheoreticalIsotopeEnvelope theoreticalEnvelope)
{
MonoMass = monoMass;
Charge = charge;
ScanNum = scanNum;
TheoreticalEnvelope = theoreticalEnvelope;
Peaks = new Ms1Peak[theoreticalEnvelope.Size];
Array.Copy(peaks, Peaks, theoreticalEnvelope.Size);
GoodEnough = false;
}
public ObservedIsotopeEnvelope(double monoMass, int charge, int scanNum, Ms1Peak[] peaks, TheoreticalIsotopeEnvelope theoreticalEnvelope)
{
MonoMass = monoMass;
Charge = charge;
ScanNum = scanNum;
TheoreticalEnvelope = theoreticalEnvelope;
Peaks = new Ms1Peak[theoreticalEnvelope.Size];
Array.Copy(peaks, Peaks, theoreticalEnvelope.Size);
GoodEnough = false;
}
public LcMsPeakCluster(LcMsRun run, TheoreticalIsotopeEnvelope theoreticalIsotopeEnvelope, double mass, int charge, double repMz, int repScanNum, double abundance)
: base(mass, charge, repMz, repScanNum, abundance)
{
_run = run;
TheoreticalEnvelope = theoreticalIsotopeEnvelope;
Flag = 0;
RepresentativeSummedEnvelop = new double[TheoreticalEnvelope.Size];
AbundanceDistributionAcrossCharge = new double[2];
BestCorrelationScoreAcrossCharge = new double[2];
BestDistanceScoreAcrossCharge = new double[2];
BestIntensityScoreAcrossCharge = new double[2];
EnvelopeDistanceScoreAcrossCharge = new double[2];
EnvelopeCorrelationScoreAcrossCharge = new double[2];
EnvelopeIntensityScoreAcrossCharge = new double[2];
BestCharge = new int[2];
XicCorrelationBetweenBestCharges = new double[2];
_initScore = false;
}
public LcMsPeakCluster(LcMsRun run, TheoreticalIsotopeEnvelope theoreticalIsotopeEnvelope, double mass, int charge, double repMz, int repScanNum, double abundance)
: base(mass, charge, repMz, repScanNum, abundance)
{
_run = run;
TheoreticalEnvelope = theoreticalIsotopeEnvelope;
Flag = 0;
RepresentativeSummedEnvelop = new double[TheoreticalEnvelope.Size];
AbundanceDistributionAcrossCharge = new double[2];
BestCorrelationScoreAcrossCharge = new double[2];
BestDistanceScoreAcrossCharge = new double[2];
BestIntensityScoreAcrossCharge = new double[2];
EnvelopeDistanceScoreAcrossCharge = new double[2];
EnvelopeCorrelationScoreAcrossCharge = new double[2];
EnvelopeIntensityScoreAcrossCharge = new double[2];
BestCharge = new int[2];
XicCorrelationBetweenBestCharges = new double[2];
_initScore = false;
}
private void SetTargetMass(double targetMass)
{
/*var chargeLowerBound = Math.Ceiling(targetMass / Run.MaxMs1Mz);
var chargeUpperBound = Math.Floor(targetMass / Run.MinMs1Mz);
if (targetMass > 2000) chargeLowerBound = Math.Max(chargeLowerBound, 2);
var rowLb = Math.Max(0, chargeLowerBound - MinScanCharge);
var rowUb = Math.Min(NRows - 1, chargeUpperBound - MinScanCharge);
*/
_targetMass = targetMass;
var chargeRange = GetDetectableMinMaxCharge(targetMass, Run.MinMs1Mz, Run.MaxMs1Mz);
_targetMinCharge = chargeRange.Item1;
_targetMaxCharge = chargeRange.Item2;
_rows = Enumerable.Range(0, _targetMaxCharge - _targetMinCharge + 1).ToArray();
_theoreticalEnvelope = new TheoreticalIsotopeEnvelope(targetMass, MaxEnvelopeLength, RelativeIsotopePeakIntensityThreshold);
}
public double GetMs1EvidenceScore(int ms2ScanNum, double targetMass, int charge)
{
var tolerance = new Tolerance(Comparer.Ppm*0.5);
if (_ms1Filter != null)
{
var ms2ScanNums = _ms1Filter.GetMatchingMs2ScanNums(targetMass);
if (ms2ScanNums.Any(ms2 => ms2 == ms2ScanNum)) return 1.0d;
}
var theoreticalEnvelope = new TheoreticalIsotopeEnvelope(targetMass, MaxEnvelopeLength, RelativeIsotopePeakIntensityThreshold);
var totalElutionTime = Run.GetElutionTime(Run.MaxLcScan);
var elutionTime = Run.GetElutionTime(ms2ScanNum);
var ms1ScanNums = Run.GetMs1ScanVector();
var minElutionTime = elutionTime - totalElutionTime * 0.002;
var maxElutionTime = elutionTime + totalElutionTime * 0.002;
var ms1ScanIndex = Run.GetPrevScanNum(ms2ScanNum, 1);
var bcDistances = new List<double>();
var correlations = new List<double>();
var maxSearchScans = (int)Math.Max(ms1ScanNums.Length - ms1ScanIndex + 1, ms1ScanIndex);
for (var i = 0; i <= maxSearchScans; i++)
{
for (var j = 0; j < 2; j++)
{
if (i == 0 && j > 0) continue;
var col = (j < 1) ? ms1ScanIndex + i : ms1ScanIndex - i;
if (col >= ms1ScanNums.Length || col < 0) continue;
if (Run.GetElutionTime(ms1ScanNums[col]) > maxElutionTime || Run.GetElutionTime(ms1ScanNums[col]) < minElutionTime) continue;
var ms1Spec = Ms1Spectra[col];
var observedPeaks = ms1Spec.GetAllIsotopePeaks(targetMass, charge, theoreticalEnvelope, tolerance);
var bcDist = theoreticalEnvelope.GetBhattacharyyaDistance(observedPeaks);
var corrCoeff = theoreticalEnvelope.GetPearsonCorrelation(observedPeaks);
if (bcDist < 0.05)
{
return 1 - bcDist;
}
if (corrCoeff > 0.7)
{
return corrCoeff;
}
bcDistances.Add(bcDist);
correlations.Add(corrCoeff);
}
}
if (bcDistances.Count < 1) return 0d;
return correlations.Max();
}
