/// <summary>
/// Populate the instrument configuration list
/// </summary>
/// <param name="mzMl"></param>
private void ConstructInstrumentConfigurationList(mzMLType mzMl)
{
var instrumentData = _rawFile.GetInstrumentData();
// Referenceable param group for common instrument properties
mzMl.referenceableParamGroupList = new ReferenceableParamGroupListType
{
count = "1",
referenceableParamGroup = new ReferenceableParamGroupType[1]
};
mzMl.referenceableParamGroupList.referenceableParamGroup[0] = new ReferenceableParamGroupType
{
id = "commonInstrumentParams",
cvParam = new CVParamType[2]
};
// Instrument model
if (!OntologyMapping.InstrumentModels.TryGetValue(instrumentData.Name, out var instrumentModel))
{
instrumentModel = new CVParamType
{
accession = "MS:1000483",
name = "Thermo Fisher Scientific instrument model",
cvRef = "MS",
value = ""
};
}
mzMl.referenceableParamGroupList.referenceableParamGroup[0].cvParam[0] = instrumentModel;
// Instrument serial number
mzMl.referenceableParamGroupList.referenceableParamGroup[0].cvParam[1] = new CVParamType
{
cvRef = "MS",
accession = "MS:1000529",
name = "instrument serial number",
value = instrumentData.SerialNumber
};
// Add a default analyzer if none were found
if (_massAnalyzers.Count == 0)
{
_massAnalyzers.Add(MassAnalyzerType.Any, "IC1");
}
// Set the run default instrument configuration ref
mzMl.run.defaultInstrumentConfigurationRef = "IC1";
var instrumentConfigurationList = new InstrumentConfigurationListType
{
count = _massAnalyzers.Count.ToString(),
instrumentConfiguration = new InstrumentConfigurationType[_massAnalyzers.Count]
};
// Make a new instrument configuration for each analyzer
var massAnalyzerIndex = 0;
foreach (var massAnalyzer in _massAnalyzers)
{
instrumentConfigurationList.instrumentConfiguration[massAnalyzerIndex] = new InstrumentConfigurationType
{
id = massAnalyzer.Value,
referenceableParamGroupRef = new ReferenceableParamGroupRefType[1],
componentList = new ComponentListType(),
cvParam = new CVParamType[3]
};
instrumentConfigurationList.instrumentConfiguration[massAnalyzerIndex].referenceableParamGroupRef[0] =
new ReferenceableParamGroupRefType
{
@ref = "commonInstrumentParams"
};
instrumentConfigurationList.instrumentConfiguration[massAnalyzerIndex].componentList =
new ComponentListType
{
count = "3",
source = new SourceComponentType[1],
analyzer = new AnalyzerComponentType[1],
detector = new DetectorComponentType[1]
};
// Instrument source
if (_ionizationTypes.IsNullOrEmpty())
{
_ionizationTypes.Add(IonizationModeType.Any,
OntologyMapping.IonizationTypes[IonizationModeType.Any]);
}
instrumentConfigurationList.instrumentConfiguration[massAnalyzerIndex].componentList.source[0] =
new SourceComponentType
{
order = 1,
cvParam = new CVParamType[_ionizationTypes.Count]
};
var index = 0;
// Ionization type
foreach (var ionizationType in _ionizationTypes)
{
instrumentConfigurationList.instrumentConfiguration[massAnalyzerIndex].componentList.source[0]
.cvParam[index] =
ionizationType.Value;
index++;
}
// Instrument analyzer
// Mass analyzer type
instrumentConfigurationList.instrumentConfiguration[massAnalyzerIndex].componentList.analyzer[0] =
new AnalyzerComponentType
{
order = index + 1,
cvParam = new CVParamType[1]
};
instrumentConfigurationList.instrumentConfiguration[massAnalyzerIndex].componentList.analyzer[0]
.cvParam[0] =
OntologyMapping.MassAnalyzerTypes[massAnalyzer.Key];
index++;
// Instrument detector
instrumentConfigurationList.instrumentConfiguration[massAnalyzerIndex].componentList.detector[0] =
new DetectorComponentType
{
order = index + 1,
cvParam = new CVParamType[1]
};
// Try to map the instrument to the detector
var detectorCvParams = OntologyMapping.InstrumentToDetectors[instrumentModel.accession];
CVParamType detectorCvParam;
if (massAnalyzerIndex < detectorCvParams.Count)
{
detectorCvParam = detectorCvParams[massAnalyzerIndex];
}
else
{
detectorCvParam = OntologyMapping.InstrumentToDetectors["MS:1000483"][0];
}
instrumentConfigurationList.instrumentConfiguration[massAnalyzerIndex].componentList.detector[0]
.cvParam[0] = detectorCvParam;
massAnalyzerIndex++;
}
mzMl.instrumentConfigurationList = instrumentConfigurationList;
}
/// <summary>
/// Populate the precursor list element
/// </summary>
/// <param name="scanEvent">the scan event</param>
/// <param name="charge">the charge</param>
/// <returns>the precursor list</returns>
private PrecursorListType ConstructPrecursorList(IScanEventBase scanEvent, int?charge)
{
// Construct the precursor
var precursorList = new PrecursorListType
{
count = "1",
precursor = new PrecursorType[1]
};
var precursor = new PrecursorType
{
selectedIonList = new SelectedIonListType
{
count = 1.ToString(),
selectedIon = new ParamGroupType[1]
}
};
precursor.spectrumRef = ConstructSpectrumTitle(_precursorScanNumber);
precursor.selectedIonList.selectedIon[0] =
new ParamGroupType
{
cvParam = new CVParamType[3]
};
IReaction reaction = null;
var precursorMass = 0.0;
double? isolationWidth = null;
try
{
reaction = scanEvent.GetReaction(0);
precursorMass = reaction.PrecursorMass;
isolationWidth = reaction.IsolationWidth;
}
catch (ArgumentOutOfRangeException exception)
{
//do nothing
}
// Selected ion MZ
var ionCvParams = new List <CVParamType>
{
new CVParamType
{
name = "selected ion m/z",
value = precursorMass.ToString(CultureInfo.InvariantCulture),
accession = "MS:1000744",
cvRef = "MS",
unitCvRef = "MS",
unitAccession = "MS:1000040",
unitName = "m/z"
}
};
if (charge != null)
{
ionCvParams.Add(new CVParamType
{
name = "charge state",
value = charge.ToString(),
accession = "MS:1000041",
cvRef = "MS"
});
}
precursor.selectedIonList.selectedIon[0].cvParam = ionCvParams.ToArray();
precursor.isolationWindow =
new ParamGroupType
{
cvParam = new CVParamType[3]
};
precursor.isolationWindow.cvParam[0] =
new CVParamType
{
accession = "MS:1000827",
name = "isolation window target m/z",
value = precursorMass.ToString(CultureInfo.InvariantCulture),
cvRef = "MS",
unitCvRef = "MS",
unitAccession = "MS:1000040",
unitName = "m/z"
};
if (isolationWidth != null)
{
var offset = isolationWidth.Value / 2;
precursor.isolationWindow.cvParam[1] =
new CVParamType
{
accession = "MS:1000828",
name = "isolation window lower offset",
value = offset.ToString(CultureInfo.InvariantCulture),
cvRef = "MS",
unitCvRef = "MS",
unitAccession = "MS:1000040",
unitName = "m/z"
};
precursor.isolationWindow.cvParam[2] =
new CVParamType
{
accession = "MS:1000829",
name = "isolation window upper offset",
value = offset.ToString(CultureInfo.InvariantCulture),
cvRef = "MS",
unitCvRef = "MS",
unitAccession = "MS:1000040",
unitName = "m/z"
};
}
var activationCvParams = new List <CVParamType>();
if (reaction != null && reaction.CollisionEnergyValid)
{
activationCvParams.Add(
new CVParamType
{
accession = "MS:1000045",
name = "collision energy",
cvRef = "MS",
value = reaction.CollisionEnergy.ToString(CultureInfo.InvariantCulture),
unitCvRef = "UO",
unitAccession = "UO:0000266",
unitName = "electronvolt"
});
}
if (reaction != null)
{
if (!OntologyMapping.DissociationTypes.TryGetValue(reaction.ActivationType, out var activation))
{
activation = new CVParamType
{
accession = "MS:1000044",
name = "Activation Method",
cvRef = "MS",
value = ""
};
}
activationCvParams.Add(activation);
}
precursor.activation =
new ParamGroupType
{
cvParam = activationCvParams.ToArray()
};
precursorList.precursor[0] = precursor;
return(precursorList);
}
