public Ms2ScanWithSpecificMass(MsDataScan mzLibScan, double precursorMonoisotopicPeakMz, int precursorCharge, string fullFilePath, CommonParameters commonParam, IsotopicEnvelope[] neutralExperimentalFragments = null)
{
PrecursorMonoisotopicPeakMz = precursorMonoisotopicPeakMz;
PrecursorCharge = precursorCharge;
PrecursorMass = PrecursorMonoisotopicPeakMz.ToMass(precursorCharge);
FullFilePath = fullFilePath;
ChildScans = new List <Ms2ScanWithSpecificMass>();
NativeId = mzLibScan.NativeId;
TheScan = mzLibScan;
if (commonParam.DissociationType != DissociationType.LowCID)
{
ExperimentalFragments = neutralExperimentalFragments ?? GetNeutralExperimentalFragments(mzLibScan, commonParam);
}
if (ExperimentalFragments != null && ExperimentalFragments.Any())
{
DeconvolutedMonoisotopicMasses = ExperimentalFragments.Select(p => p.MonoisotopicMass).ToArray();
}
else
{
DeconvolutedMonoisotopicMasses = new double[0];
}
}
public Ms2ScanWithSpecificMass(MsDataScan mzLibScan, double precursorMonoisotopicPeakMz, int precursorCharge, string fullFilePath, CommonParameters commonParam, IsotopicEnvelope[] neutralExperimentalFragments = null)
{
PrecursorMonoisotopicPeakMz = precursorMonoisotopicPeakMz;
PrecursorCharge = precursorCharge;
PrecursorMass = PrecursorMonoisotopicPeakMz.ToMass(precursorCharge);
FullFilePath = fullFilePath;
ChildScans = new List <Ms2ScanWithSpecificMass>();
TheScan = mzLibScan;
ExperimentalFragments = neutralExperimentalFragments ?? GetNeutralExperimentalFragments(mzLibScan, commonParam);
if (ExperimentalFragments.Any())
{
DeconvolutedMonoisotopicMasses = ExperimentalFragments.Select(p => p.monoisotopicMass).ToArray();
}
}
//look for IsotopicEnvelopes which are in the range of acceptable mass
public IsotopicEnvelope[] GetClosestExperimentalIsotopicEnvelopeList(double minimumMass, double maxMass)
{
if (DeconvolutedMonoisotopicMasses.Length == 0)
{
return(null);
}
//if no mass is in this range, then return null
if (DeconvolutedMonoisotopicMasses[0] > maxMass || DeconvolutedMonoisotopicMasses.Last() < minimumMass)
{
return(null);
}
int startIndex = GetClosestFragmentMass(minimumMass);
int endIndex = GetClosestFragmentMass(maxMass);
//the index we get from GetClosestFragmentMass is the closest mass, while the acceptable mass we need is between minimumMass and maxMass
//so the startIndex mass is supposed to be larger than minimumMass, if not , then startIndex increases by 1;
//the endIndex mass is supposed to be smaller than maxMass, if not , then endIndex decreases by 1;
if (DeconvolutedMonoisotopicMasses[startIndex] < minimumMass)
{
startIndex = startIndex + 1;
}
if (DeconvolutedMonoisotopicMasses[endIndex] > maxMass)
{
endIndex = endIndex - 1;
}
int length = endIndex - startIndex + 1;
if (length < 1)
{
return(null);
}
IsotopicEnvelope[] isotopicEnvelopes = ExperimentalFragments.Skip(startIndex).Take(length).ToArray();
return(isotopicEnvelopes);
}
