/// <summary>
/// Illustrate how to make calls to deisotope a spectrum.
/// </summary>
/// <param name="dataAccess"></param>
private void DeisotopeTest(IMsdrDataReader dataAccess)
{
IMsdrPeakFilter filter1 = new MsdrPeakFilter();
filter1.AbsoluteThreshold = 10;
filter1.RelativeThreshold = 0.1;
filter1.MaxNumPeaks = 0;//no limit on max number of peaks
IMsdrChargeStateAssignmentFilter csaFilter = new MsdrChargeStateAssignmentFilter();
IBDASpecFilter f = new BDASpecFilter();
f.SpectrumType = SpecType.MassSpectrum;
IBDAMSScanFileInformation msscanFileInfo = dataAccess.MSScanFileInformation;
int numSpectra = (int)msscanFileInfo.TotalScansPresent;
int nNonEmptyCount = 0; // just deisotope the first 10 non-empty spectra
for (int i = 0; i < numSpectra; i++)
{
IBDASpecData spec = dataAccess.GetSpectrum(i, filter1, filter1);//same peak filter used for both MS and MS2 spectra (you can pass in 2 different filters)
println("Original spectrum has " + spec.TotalDataPoints + " points");
if (spec.XArray.Length > 0)
{
++nNonEmptyCount;
}
if (nNonEmptyCount > 10)
{
break;
}
dataAccess.Deisotope(spec, csaFilter);
println(" Deisotoped spectrum has " + spec.TotalDataPoints + " points");
}
}
private static bool GetAccurateMZAndIntensity(IDictionary <int, IBDASpecData> ms1s, IMsdrDataReader agilentD, int parentScanId, ref double mz, out double intensity)
{
IBDASpecData ms1;
lock (ms1s)
{
if (!ms1s.TryGetValue(parentScanId, out ms1))
{
IBDASpecFilter spec_filter = new BDASpecFilter();
spec_filter.SpectrumType = SpecType.MassSpectrum;
spec_filter.ScanIds = new int[] { parentScanId };
lock (agilentD)
{
ms1 = agilentD.GetSpectrum(spec_filter)[0];
}
ms1s.Add(parentScanId, ms1);
}
}
int index = -1;
for (int i = 0; i < ms1.TotalDataPoints; i++)
{
if (index < 0 || Math.Abs(ms1.XArray[i] - mz) < Math.Abs(ms1.XArray[index] - mz))
{
index = i;
}
}
if (index >= 0)
{
mz = ms1.XArray[index];
intensity = ms1.YArray[index];
return(true);
}
intensity = double.NaN;
return(false);
}
private static bool GetAccurateMZAndIntensity(IDictionary<int, IBDASpecData> ms1s, IMsdrDataReader agilentD, int parentScanId, ref double mz, out double intensity)
{
IBDASpecData ms1;
lock(ms1s)
{
if(!ms1s.TryGetValue(parentScanId, out ms1))
{
IBDASpecFilter spec_filter = new BDASpecFilter();
spec_filter.SpectrumType = SpecType.MassSpectrum;
spec_filter.ScanIds = new int[] { parentScanId };
lock(agilentD)
{
ms1 = agilentD.GetSpectrum(spec_filter)[0];
}
ms1s.Add(parentScanId, ms1);
}
}
int index = -1;
for(int i = 0; i < ms1.TotalDataPoints; i++)
{
if(index < 0 || Math.Abs(ms1.XArray[i] - mz) < Math.Abs(ms1.XArray[index] - mz))
{
index = i;
}
}
if(index >= 0)
{
mz = ms1.XArray[index];
intensity = ms1.YArray[index];
return true;
}
intensity = double.NaN;
return false;
}
