public override int GetMsnOrder(int spectrumNumber)
{
var spec = _activeMSExperiment.GetMassSpectrumInfo(spectrumNumber);
return(spec.MSLevel);
}
private static MzLite.Model.MassSpectrum GetSpectrum(
Batch batch,
MassSpectrometerSample sample,
MSExperiment msExp,
int sampleIndex,
int experimentIndex,
int scanIndex)
{
MassSpectrumInfo wiffSpectrum = msExp.GetMassSpectrumInfo(scanIndex);
MzLite.Model.MassSpectrum mzLiteSpectrum = new Model.MassSpectrum(ToSpectrumID(sampleIndex, experimentIndex, scanIndex));
// spectrum
mzLiteSpectrum.SetMsLevel(wiffSpectrum.MSLevel);
if (wiffSpectrum.CentroidMode)
{
mzLiteSpectrum.SetCentroidSpectrum();
}
else
{
mzLiteSpectrum.SetProfileSpectrum();
}
// scan
Scan scan = new Scan();
scan.SetScanStartTime(wiffSpectrum.StartRT)
.UO_Minute();
mzLiteSpectrum.Scans.Add(scan);
// precursor
if (wiffSpectrum.IsProductSpectrum)
{
Precursor precursor = new Precursor();
double isoWidth;
double targetMz;
if (GetIsolationWindow(wiffSpectrum.Experiment, out isoWidth, out targetMz))
{
precursor.IsolationWindow
.SetIsolationWindowTargetMz(targetMz)
.SetIsolationWindowUpperOffset(isoWidth)
.SetIsolationWindowLowerOffset(isoWidth);
}
SelectedIon selectedIon = new SelectedIon();
selectedIon.SetSelectedIonMz(wiffSpectrum.ParentMZ)
.SetChargeState(wiffSpectrum.ParentChargeState);
precursor.SelectedIons.Add(selectedIon);
precursor.Activation
.SetCollisionEnergy(wiffSpectrum.CollisionEnergy);
mzLiteSpectrum.Precursors.Add(precursor);
}
return(mzLiteSpectrum);
}
