/// <summary>
/// Internal spectrum reader to eliminate excess calls to LoadPwizReader() when called from ReadAllSpectra()
/// </summary>
/// <param name="scanIndex"></param>
/// <param name="includePeaks"></param>
/// <returns></returns>
private Spectrum ReadSpectrum(int scanIndex, bool includePeaks = true)
{
var pwizSpec = _dataFile.run.spectrumList.spectrum(scanIndex - 1, includePeaks);
var msLevel = (int)(pwizSpec.cvParam(CVID.MS_ms_level).value);
var tic = (double)(pwizSpec.cvParam(CVID.MS_total_ion_current).value);
double[] mzArray = new double[0];
double[] intensityArray = new double[0];
foreach (var bda in pwizSpec.binaryDataArrays)
{
if (bda.hasCVParam(CVID.MS_m_z_array))
{
mzArray = bda.data.ToArray();
}
if (bda.hasCVParam(CVID.MS_intensity_array))
{
intensityArray = bda.data.ToArray();
}
}
double scanTime = 0;
foreach (var s in pwizSpec.scanList.scans)
{
if (s.hasCVParam(CVID.MS_scan_start_time))
{
scanTime = (double)(s.cvParam(CVID.MS_scan_start_time).value);
}
}
if (msLevel > 1)
{
double? thermoMonoMass = null;
foreach (var up in pwizSpec.userParams)
{
if (up.name == "[Thermo Trailer Extra]Monoisotopic M/Z:")
{
thermoMonoMass = (double)(up.value);
}
}
ActivationMethod am = ActivationMethod.Unknown;
Data.Spectrometry.IsolationWindow iw = null;
foreach (var precursor in pwizSpec.precursors)
{
var act = precursor.activation;
foreach (var param in act.cvParams)
{
switch (param.cvid)
{
case CVID.MS_collision_induced_dissociation:
am = ActivationMethod.CID;
break;
case CVID.MS_electron_transfer_dissociation:
am = ActivationMethod.ETD;
break;
case CVID.MS_beam_type_collision_induced_dissociation:
am = ActivationMethod.HCD;
break;
case CVID.MS_electron_capture_dissociation:
am = ActivationMethod.ECD;
break;
case CVID.MS_pulsed_q_dissociation:
am = ActivationMethod.PQD;
break;
}
}
var piw = precursor.isolationWindow;
var target = (double)(piw.cvParam(CVID.MS_isolation_window_target_m_z).value);
var lowOff = (double)(piw.cvParam(CVID.MS_isolation_window_lower_offset).value);
var uppOff = (double)(piw.cvParam(CVID.MS_isolation_window_upper_offset).value);
int? charge = null;
double selectedIonMz = 0;
foreach (var si in precursor.selectedIons)
{
if (si.hasCVParam(CVID.MS_charge_state))
{
charge = (int)(si.cvParam(CVID.MS_charge_state).value);
}
selectedIonMz = (double)(si.cvParam(CVID.MS_selected_ion_m_z).value);
}
if (thermoMonoMass == null || thermoMonoMass.Value.Equals(0))
{
thermoMonoMass = selectedIonMz;
}
iw = new Data.Spectrometry.IsolationWindow(target, lowOff, uppOff, thermoMonoMass, charge);
}
return new ProductSpectrum(mzArray, intensityArray, scanIndex)
{
NativeId = pwizSpec.id,
TotalIonCurrent = tic,
ActivationMethod = am,
IsolationWindow = iw,
MsLevel = msLevel,
ElutionTime = scanTime,
};
}
return new Spectrum(mzArray, intensityArray, scanIndex)
{
NativeId = pwizSpec.id,
TotalIonCurrent = tic,
ElutionTime = scanTime,
MsLevel = msLevel,
};
}
/// <summary>
/// Internal spectrum reader to eliminate excess calls to LoadPwizReader() when called from ReadAllSpectra()
/// </summary>
/// <param name="scanIndex"></param>
/// <param name="includePeaks"></param>
/// <returns></returns>
private Spectrum ReadSpectrum(int scanIndex, bool includePeaks = true)
{
var pwizSpec = _dataFile.run.spectrumList.spectrum(scanIndex - 1, includePeaks);
var msLevel = (int)(pwizSpec.cvParam(CVID.MS_ms_level).value);
var tic = (double)(pwizSpec.cvParam(CVID.MS_total_ion_current).value);
double[] mzArray = new double[0];
double[] intensityArray = new double[0];
foreach (var bda in pwizSpec.binaryDataArrays)
{
if (bda.hasCVParam(CVID.MS_m_z_array))
{
mzArray = bda.data.ToArray();
}
if (bda.hasCVParam(CVID.MS_intensity_array))
{
intensityArray = bda.data.ToArray();
}
}
double scanTime = 0;
foreach (var s in pwizSpec.scanList.scans)
{
if (s.hasCVParam(CVID.MS_scan_start_time))
{
scanTime = (double)(s.cvParam(CVID.MS_scan_start_time).value);
}
}
if (msLevel > 1)
{
double?thermoMonoMass = null;
foreach (var up in pwizSpec.userParams)
{
if (up.name == "[Thermo Trailer Extra]Monoisotopic M/Z:")
{
thermoMonoMass = (double)(up.value);
}
}
ActivationMethod am = ActivationMethod.Unknown;
Data.Spectrometry.IsolationWindow iw = null;
foreach (var precursor in pwizSpec.precursors)
{
var act = precursor.activation;
var activationMethods = new List <ActivationMethod>();
foreach (var param in act.cvParams)
{
switch (param.cvid)
{
case CVID.MS_collision_induced_dissociation:
activationMethods.Add(ActivationMethod.CID);
break;
case CVID.MS_electron_transfer_dissociation:
activationMethods.Add(ActivationMethod.ETD);
break;
case CVID.MS_beam_type_collision_induced_dissociation:
activationMethods.Add(ActivationMethod.HCD);
break;
case CVID.MS_electron_capture_dissociation:
activationMethods.Add(ActivationMethod.ECD);
break;
case CVID.MS_pulsed_q_dissociation:
activationMethods.Add(ActivationMethod.PQD);
break;
}
}
if (activationMethods.Count > 1 && activationMethods.Contains(ActivationMethod.ETD))
{
am = ActivationMethod.ETD;
}
else if (activationMethods.Count > 0)
{
am = activationMethods[0];
}
var piw = precursor.isolationWindow;
var target = (double)(piw.cvParam(CVID.MS_isolation_window_target_m_z).value);
var lowOff = (double)(piw.cvParam(CVID.MS_isolation_window_lower_offset).value);
var uppOff = (double)(piw.cvParam(CVID.MS_isolation_window_upper_offset).value);
int? charge = null;
double selectedIonMz = 0;
foreach (var si in precursor.selectedIons)
{
if (si.hasCVParam(CVID.MS_charge_state))
{
charge = (int)(si.cvParam(CVID.MS_charge_state).value);
}
selectedIonMz = (double)(si.cvParam(CVID.MS_selected_ion_m_z).value);
}
if (thermoMonoMass == null || thermoMonoMass.Value.Equals(0))
{
thermoMonoMass = selectedIonMz;
}
iw = new Data.Spectrometry.IsolationWindow(target, lowOff, uppOff, thermoMonoMass, charge);
}
return(new ProductSpectrum(mzArray, intensityArray, scanIndex)
{
NativeId = pwizSpec.id,
TotalIonCurrent = tic,
ActivationMethod = am,
IsolationWindow = iw,
MsLevel = msLevel,
ElutionTime = scanTime,
});
}
return(new Spectrum(mzArray, intensityArray, scanIndex)
{
NativeId = pwizSpec.id,
TotalIonCurrent = tic,
ElutionTime = scanTime,
MsLevel = msLevel,
});
}
