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
IParamEdit paramEdit = mzLiteSpectrum.BeginParamEdit();
paramEdit.MS_MsLevel(wiffSpectrum.MSLevel);
if (wiffSpectrum.CentroidMode)
{
paramEdit.MS_CentroidSpectrum();
}
else
{
paramEdit.MS_ProfileSpectrum();
}
// scan
Scan scan = new Scan();
scan.BeginParamEdit()
.MS_ScanStartTime(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.BeginParamEdit()
.MS_IsolationWindowTargetMz(targetMz)
.MS_IsolationWindowUpperOffset(isoWidth)
.MS_IsolationWindowLowerOffset(isoWidth);
}
SelectedIon selectedIon = new SelectedIon();
selectedIon.BeginParamEdit()
.MS_SelectedIonMz(wiffSpectrum.ParentMZ)
.MS_ChargeState(wiffSpectrum.ParentChargeState);
precursor.SelectedIons.Add(selectedIon);
precursor.Activation.BeginParamEdit()
.MS_CollisionEnergy(wiffSpectrum.CollisionEnergy);
mzLiteSpectrum.Precursors.Add(precursor);
}
return(mzLiteSpectrum);
}
