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Write isolationWindow/selectedIon for PRM data #164

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Write isolationWindow/selectedIon for PRM data #164

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155 changes: 147 additions & 8 deletions Writer/MzMlSpectrumWriter.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -1359,14 +1359,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
}
else
{
spectrum.precursorList = new PrecursorListType
{
count = "0",
precursor = new PrecursorType[0]
};

Log.Error($"Failed finding precursor for {scanNumber}");
ParseInput.NewError();
spectrum.precursorList = ConstructPRMPrecursorList(scanEvent, charge, isolationWidth);
}
}
else
Expand Down Expand Up @@ -2424,6 +2417,152 @@ private PrecursorListType ConstructPrecursorList(int precursorScanNumber, IScanE

}

/// <summary>
/// Populate the precursor list element for PRM/MS2-only datasets (No MS1 scans)
/// </summary>
/// <param name="scanEvent">the scan event</param>
/// <param name="charge">the charge from trailer</param>
/// <param name="isolationWidth">the isolation width value from trailer</param>
/// <returns>the precursor list</returns>
private PrecursorListType ConstructPRMPrecursorList(IScanEventBase scanEvent, int? charge, double? isolationWidth)
{
List<PrecursorType> precursors = new List<PrecursorType>();


int msLevel = (int)scanEvent.MSOrder;
IReaction reaction = scanEvent.GetReaction(0);
double precursorMz = reaction.PrecursorMass;

//if isolation width was not found in the trailer, try to get one from the reaction
if (isolationWidth == null) isolationWidth = reaction.IsolationWidth;

var precursor = new PrecursorType
{
selectedIonList =
new SelectedIonListType { count = "1", selectedIon = new ParamGroupType[1] },
};

precursor.selectedIonList.selectedIon[0] = new ParamGroupType();

var ionCvParams = new List<CVParamType>
{
new CVParamType
{
name = "selected ion m/z",
value = precursorMz.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 = precursorMz.ToString(CultureInfo.InvariantCulture),
cvRef = "MS",
unitCvRef = "MS",
unitAccession = "MS:1000040",
unitName = "m/z"
};
if (isolationWidth != null)
{
var offset = isolationWidth.Value / 2 + reaction.IsolationWidthOffset;
precursor.isolationWindow.cvParam[1] =
new CVParamType
{
accession = "MS:1000828",
name = "isolation window lower offset",
value = (isolationWidth.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"
};
}

// Activation
var activationCvParams = new List<CVParamType>();
if (reaction != null)
{
if (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 (!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()
};

precursors.Add(precursor);

return new PrecursorListType
{
count = precursors.Count.ToString(),
precursor = precursors.ToArray()
};

}

private int GetParentFromScanString(string scanString)
{
var result = _filterStringIsolationMzPattern.Match(scanString);
Expand Down