public override int GetPrecusorCharge(int spectrumNumber, int msnOrder = 2)
{
IBDASpecData spectrum = _msdr.GetSpectrum(spectrumNumber - 1);
int precursor_charge;
spectrum.GetPrecursorCharge(out precursor_charge);
return((short)precursor_charge);
}
public override PrecursorInfo GetPrecursorInfo(int scanNum)
{
m_spec = m_reader.GetSpectrum(scanNum, null, null);
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;
}
int precursorMassCount;
//this returns a list of precursor masses (not sure how there can be more than one)
var precursorMZlist = m_spec.GetPrecursorIon(out precursorMassCount);
//if a mass is returned
if (precursorMassCount == 1)
{
//mass
precursor.PrecursorMZ = precursorMZlist[0];
//intensity
double precursorIntensity;
m_spec.GetPrecursorIntensity(out precursorIntensity);
precursor.PrecursorIntensity = (float)precursorIntensity;
//charge
int precursorCharge;
m_spec.GetPrecursorCharge(out precursorCharge);
precursor.PrecursorCharge = precursorCharge;
//adjust scan number if needed
precursor.PrecursorScan = scanNum;
// TODO: Only CID possible in Aglent files?
precursor.FragmentationType = FragmentionType.CID;
}
else if (precursorMassCount > 1)
{
throw new NotImplementedException("Strange case where more than one precursor is used to generate one spectra");
}
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);
}
/// <summary>
/// Get all Product Ion MS/MS scans and print out the precursor and collision energy.
/// </summary>
private void GetPrecursorInfo(IMsdrDataReader dataAccess)
{
//Create a chromatogram filter to let the scans that match
//the filter criteria to pass through
IBDAChromFilter chromFilter = new BDAChromFilter();
chromFilter.ChromatogramType = ChromType.TotalIon;
chromFilter.DesiredMSStorageType = DesiredMSStorageType.PeakElseProfile;//This means to use peak scans if available, otherwise use profile scans
chromFilter.MSLevelFilter = MSLevel.MSMS;
chromFilter.MSScanTypeFilter = MSScanType.ProductIon;
IBDAChromData[] chroms = dataAccess.GetChromatogram(chromFilter);//expect 1 chromatogram because we're not asking it to separate by scan segments, etc.
IBDAChromData chrom = chroms[0];
double[] retTime = chrom.XArray;
println("Get MS/MS spectra using retention time");
for (int i = 0; i < retTime.Length; i++)
{
//for each retention time, get the corresponding scan
//passing in null for peak filter means no peak threshold applied
IBDASpecData spec = dataAccess.GetSpectrum(retTime[i], MSScanType.ProductIon, IonPolarity.Mixed, IonizationMode.Unspecified, null);
print("RT=" + retTime[i] + ", ");
int precursorCount = 0;
double[] precursorIons = spec.GetPrecursorIon(out precursorCount);
if (precursorCount == 1)
{
print("Precursor Ions:");
for (int j = 0; j < precursorIons.Length; j++)
{
print(precursorIons[j] + " ");
}
println("");
int charge;
double intensity;
if (spec.GetPrecursorCharge(out charge))
{
println(" charge: " + charge);
}
else
{
println(" no charge avaialble");
}
if (spec.GetPrecursorIntensity(out intensity))
{
println(" intensity: " + intensity);
}
else
{
println(" no intensity available");
}
}
else
{
println("No precursor ions");
}
/*
* //Uncomment this if you want to print out x and y values of the spectrum.
* double[] mzVals = spec.XArray;
* float[] aboundanceVals = spec.YArray;
* println("RT=" + retTime[i]);
* for (int j = 0; j < mzVals.Length; j++)
* {
* println(mzVals[j] + ", " + aboundanceVals[j]);
* }
*/
}
}