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);
}
private MzLite.Model.MassSpectrum ReadMassSpectrum(int scanNo)
{
RaiseDisposed();
try
{
string spectrumID = GetSpectrumID(scanNo);
MassSpectrum spectrum = new MassSpectrum(spectrumID);
// spectrum
int msLevel = GetMSLevel(rawFile, scanNo);
spectrum.SetMsLevel(msLevel);
if (IsCentroidSpectrum(rawFile, scanNo))
{
spectrum.SetCentroidSpectrum();
}
else
{
spectrum.SetProfileSpectrum();
}
// scan
Scan scan = new Scan();
scan.SetFilterString(GetFilterString(rawFile, scanNo))
.SetScanStartTime(GetRetentionTime(rawFile, scanNo));
//.UO_Minute();
spectrum.Scans.Add(scan);
// precursor
if (msLevel > 1)
{
Precursor precursor = new Precursor();
double isoWidth = GetIsolationWindowWidth(rawFile, scanNo, msLevel) * 0.5d;
double targetMz = GetIsolationWindowTargetMz(rawFile, scanNo, msLevel);
double precursorMz = GetPrecursorMz(rawFile, scanNo, msLevel);
int chargeState = GetChargeState(rawFile, scanNo);
precursor.IsolationWindow
.SetIsolationWindowTargetMz(targetMz)
.SetIsolationWindowUpperOffset(isoWidth)
.SetIsolationWindowLowerOffset(isoWidth);
SelectedIon selectedIon = new SelectedIon();
selectedIon
.SetSelectedIonMz(precursorMz)
.SetChargeState(chargeState);
precursor.SelectedIons.Add(selectedIon);
spectrum.Precursors.Add(precursor);
}
return(spectrum);
}
catch (Exception ex)
{
throw new MzLiteIOException(ex.Message, ex);
}
}
private MassSpectrum ReadMassSpectrum(UInt64 spectrumId)
{
BafSqlSpectrum bafSpec = linq2BafSql.GetBafSqlSpectrum(this.linq2BafSql.Core, spectrumId);
if (bafSpec == null)
{
throw new MzLiteIOException("No spectrum found for id: " + spectrumId);
}
MassSpectrum ms = new MassSpectrum(spectrumId.ToString());
// determine ms level
BafSqlAcquisitionKey aqKey = linq2BafSql.GetBafSqlAcquisitionKey(this.linq2BafSql.Core, bafSpec.AcquisitionKey);
Nullable <int> msLevel = null;
if (aqKey != null && aqKey.MsLevel.HasValue)
{
// bruker starts ms level by 0, must be added by 1
msLevel = aqKey.MsLevel.Value + 1;
ms.SetMsLevel(msLevel.Value);
}
// determine type of spectrum and read peak data
// if profile data available we prefer to get profile data otherwise centroided data (line spectra)
if (bafSpec.ProfileMzId.HasValue && bafSpec.ProfileIntensityId.HasValue)
{
ms.SetProfileSpectrum();
}
else if (bafSpec.LineMzId.HasValue && bafSpec.LineIntensityId.HasValue)
{
ms.SetCentroidSpectrum();
}
if (msLevel == 1)
{
ms.SetMS1Spectrum();
}
else if (msLevel > 1)
{
ms.SetMSnSpectrum();
}
// scan
if (bafSpec.Rt.HasValue)
{
Scan scan = new Scan();
scan.SetScanStartTime(bafSpec.Rt.Value).UO_Second();
ms.Scans.Add(scan);
}
// precursor
if (msLevel > 1)
{
SpectrumVariableCollection spectrumVariables = SpectrumVariableCollection.ReadSpectrumVariables(linq2BafSql, bafSpec.Id);
Precursor precursor = new Precursor();
decimal value;
if (spectrumVariables.TryGetValue("Collision_Energy_Act", supportedVariables, out value))
{
precursor.Activation.SetCollisionEnergy(Decimal.ToDouble(value));
}
if (spectrumVariables.TryGetValue("MSMS_IsolationMass_Act", supportedVariables, out value))
{
precursor.IsolationWindow.SetIsolationWindowTargetMz(Decimal.ToDouble(value));
}
if (spectrumVariables.TryGetValue("Quadrupole_IsolationResolution_Act", supportedVariables, out value))
{
double width = Decimal.ToDouble(value) * 0.5d;
precursor.IsolationWindow.SetIsolationWindowUpperOffset(width);
precursor.IsolationWindow.SetIsolationWindowLowerOffset(width);
}
Nullable <int> charge = null;
if (spectrumVariables.TryGetValue("MSMS_PreCursorChargeState", supportedVariables, out value))
{
charge = Decimal.ToInt32(value);
}
IEnumerable <BafSqlStep> ions = linq2BafSql.GetBafSqlSteps(this.linq2BafSql.Core, bafSpec.Id);
foreach (BafSqlStep ion in ions)
{
if (ion.Mass.HasValue)
{
SelectedIon selectedIon = new SelectedIon();
precursor.SelectedIons.Add(selectedIon);
selectedIon.SetSelectedIonMz(ion.Mass.Value);
selectedIon.SetUserParam("Number", ion.Number.Value);
selectedIon.SetUserParam("IsolationType", ion.IsolationType.Value);
selectedIon.SetUserParam("ReactionType", ion.ReactionType.Value);
selectedIon.SetUserParam("MsLevel", ion.MsLevel.Value);
if (charge.HasValue)
{
selectedIon.SetChargeState(charge.Value);
}
}
}
// set parent spectrum as reference
if (bafSpec.Parent.HasValue)
{
precursor.SpectrumReference = new SpectrumReference(bafSpec.Parent.ToString());
}
ms.Precursors.Add(precursor);
}
return(ms);
}
