public override PrecursorInfo GetPrecursorInfo(int scanNum)
{
m_spec = m_reader.GetSpectrum(scanNum);
var precursor = new PrecursorInfo();
var level = m_spec.MSLevelInfo;
if (level == MSLevel.MS)
{
precursor.MSLevel = 1;
}
else if (level == MSLevel.MSMS)
{
precursor.MSLevel = 2;
}
else
{
precursor.MSLevel = 1;
}
//this returns a list of precursor masses (not sure how there can be more than one)
var precursorMZlist = m_spec.GetPrecursorIon(out var precursorMassCount);
//if a mass is returned
if (precursorMassCount == 1)
{
//mass
precursor.PrecursorMZ = precursorMZlist[0];
//intensity
m_spec.GetPrecursorIntensity(out var precursorIntensity);
precursor.PrecursorIntensity = (float)precursorIntensity;
//charge
m_spec.GetPrecursorCharge(out var precursorCharge);
precursor.PrecursorCharge = precursorCharge;
//adjust scan number if needed
precursor.PrecursorScan = scanNum;
// TODO: Only CID possible in Agilent files?
precursor.FragmentationType = FragmentionType.CID;
}
else if (precursorMassCount > 1)
{
throw new NotImplementedException("Strange case where more than one precursor is used to generate one spectrum");
}
else
{
precursor.PrecursorMZ = 0;
precursor.PrecursorIntensity = 0;
precursor.PrecursorCharge = -1;
precursor.PrecursorScan = scanNum;
}
precursor.IonizationMode = m_spec.IonPolarity == IonPolarity.Negative ? IonizationMode.Negative : IonizationMode.Positive;
return(precursor);
}
public double[] GetPrecursorInfo(int scanNum)
{
PrecursorInfo infos = raws.GetPrecursorInfo(scanNum, path);
double[] mzCharge = new double[2];
double mz = infos.dMonoIsoMass;
int charge = infos.nChargeState;
mzCharge[0] = mz;
mzCharge[1] = charge;
return(mzCharge);
}
public override PrecursorInfo GetPrecursorInfo(int scanNum)
{
var scanInfo = GetScanInfo(scanNum);
XRawFileIO.ExtractParentIonMZFromFilterText(scanInfo, out var precursorMz, out var msLevel, out var fragmentationType);
var ionMode = XRawFileIO.DetermineIonizationMode(scanInfo);
var precursor = new PrecursorInfo
{
MSLevel = msLevel
};
// Get Precursor MZ
if (scanInfo == null)
{
precursor.PrecursorMZ = 0;
}
else
{
precursor.PrecursorMZ = precursorMz;
}
// Get the Parent scan if MS level is not MS1
if (precursor.MSLevel > 1)
{
var stepBack = 0;
while (scanNum - stepBack > 0)
{
if (scanNum - stepBack > 0)
{
var testScanLevel = GetMSLevel(scanNum - stepBack);
stepBack++;
if (testScanLevel == 1) //the first precursor scan prior
{
break;
}
}
}
precursor.PrecursorScan = scanNum - (stepBack - 1);
switch (fragmentationType)
{
case "hcd":
precursor.FragmentationType = FragmentionType.HCD;
break;
case "etd":
precursor.FragmentationType = FragmentionType.ETD;
break;
case "cid":
precursor.FragmentationType = FragmentionType.CID;
break;
default:
precursor.FragmentationType = FragmentionType.None;
break;
}
}
else
{
precursor.PrecursorScan = scanNum;
precursor.FragmentationType = FragmentionType.None;
}
precursor.IonizationMode = ionMode.Equals(IonModeConstants.Positive) ? IonizationMode.Positive : IonizationMode.Negative;
//TODO: we still need to get charge
//precursor.PrecursorCharge = 1;
return(precursor);
}
