public void UpdatePsmInformation(MSDataFile dataFile, bool is2dFDR = true, bool useMedian = true, double evalueThreshold = 1e-3)
{
List <double> errors = new List <double>();
MaximumPrecursorMassError = 0;
int count = 0;
int msms = 0;
int ms = 0;
int localMSMS = -1;
List <int> msmsBetweenMS = new List <int>();
List <double> injectionTimes = new List <double>();
for (int sn = dataFile.FirstSpectrumNumber; sn <= dataFile.LastSpectrumNumber; sn++)
{
int order = dataFile.GetMsnOrder(sn);
if (order == 1)
{
ms++;
if (localMSMS >= 0)
{
msmsBetweenMS.Add(localMSMS);
}
localMSMS = 0;
}
else
{
localMSMS++;
msms++;
injectionTimes.Add(dataFile.GetInjectionTime(sn));
}
}
MaxMSMSScansBetweenMS = msmsBetweenMS.Max();
AverageMSMSSCansBetweenMS = msmsBetweenMS.Average();
TotalMSMSscans = msms;
TotalMSscans = ms;
AverageMSMSInjectionTime = injectionTimes.Average();
MaxMSMSInjectionTime = injectionTimes.Max();
foreach (KeyValuePair <int, SortedMaxSizedContainer <PSM> > kvp in _data)
{
int scanNumber = kvp.Key;
SortedMaxSizedContainer <PSM> psms = kvp.Value;
double isolationMZ = dataFile.GetPrecusorMz(scanNumber);
Polarity polarity = dataFile.GetPolarity(scanNumber);
foreach (PSM psm in psms)
{
psm.Charge *= (int)polarity; // For negative mode ions
psm.IsolationMz = isolationMZ;
double isolationMass = Mass.MassFromMz(isolationMZ, psm.Charge);
double theoreticalMass = psm.MonoisotopicMass;
int nominalMassOffset;
double adjustedIsolationMass;
Tolerance tolerancePPM = Tolerance.CalculatePrecursorMassError(theoreticalMass,
isolationMass, out nominalMassOffset, out adjustedIsolationMass);
psm.AdjustedIsolationMass = adjustedIsolationMass;
psm.IsotopeSelected = nominalMassOffset;
if (!HasPPMInfo)
{
psm.PrecursorMassError = tolerancePPM.Value;
}
double positive = Math.Abs(psm.PrecursorMassError);
if (positive > MaximumPrecursorMassError)
{
MaximumPrecursorMassError = positive;
}
if (psm.FdrScoreMetric <= evalueThreshold)
{
errors.Add(psm.PrecursorMassError);
}
count++;
}
}
SystematicPrecursorMassError = useMedian ? GetMedianValue(errors) : errors.Average();
// Adjust all psms to
foreach (PSM psm in PeptideSpectralMatches)
{
psm.CorrectedPrecursorMassError = psm.PrecursorMassError - SystematicPrecursorMassError;
}
}
