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removed monoisotopic mass userparam when value is zero
changed selected ion mz in mzML to monoisotopic mass where available
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@nielshulstaert
nielshulstaert committed May 16, 2019
1 parent 5adf776 commit 534accb
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Showing 4 changed files with 81 additions and 67 deletions.
4 changes: 2 additions & 2 deletions Properties/AssemblyInfo.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@
// You can specify all the values or you can default the Build and Revision Numbers
// by using the '*' as shown below:
// [assembly: AssemblyVersion("1.0.*")]
[assembly: AssemblyVersion("1.1.5.0")]
[assembly: AssemblyFileVersion("1.1.5.0")]
[assembly: AssemblyVersion("1.1.6.0")]
[assembly: AssemblyFileVersion("1.1.6.0")]

[assembly: log4net.Config.XmlConfigurator(ConfigFile = "log4net.config")]
48 changes: 5 additions & 43 deletions Writer/MgfSpectrumWriter.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -15,9 +15,6 @@ public class MgfSpectrumWriter : SpectrumWriter

private const string PositivePolarity = "+";
private const string NegativePolarity = "-";
private const double PrecursorMzDelta = 0.0001;
private const double DefaultIsolationWindowLowerOffset = 1.5;
private const double DefaultIsolationWindowUpperOffset = 2.5;

// Precursor scan number for reference in the precursor element of an MS2 spectrum
private int _precursorScanNumber;
Expand Down Expand Up @@ -88,7 +85,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
// trailer extra data list
var trailerData = rawFile.GetTrailerExtraInformation(scanNumber);
int? charge = null;
double? monoisotopicMass = null;
double? monoisotopicMz = null;
double? isolationWidth = null;
for (var i = 0; i < trailerData.Length; i++)
{
Expand All @@ -99,7 +96,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc

if (trailerData.Labels[i] == "Monoisotopic M/Z:")
{
monoisotopicMass = double.Parse(trailerData.Values[i], NumberStyles.Any,
monoisotopicMz = double.Parse(trailerData.Values[i], NumberStyles.Any,
CultureInfo.CurrentCulture);
}

Expand All @@ -112,45 +109,10 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc

if (reaction != null)
{
var truePrecursorMass = reaction.PrecursorMass;

// take isolation width from the reaction if no value was found in the trailer data
if (isolationWidth == null || isolationWidth < ZeroDelta)
{
isolationWidth = reaction.IsolationWidth;
}

isolationWidth = isolationWidth / 2;

if (monoisotopicMass != null && monoisotopicMass > ZeroDelta
&& Math.Abs(
reaction.PrecursorMass - monoisotopicMass.Value) >
PrecursorMzDelta)
{
truePrecursorMass = monoisotopicMass.Value;

// check if the monoisotopic mass lies in the precursor mass isolation window
// otherwise take the precursor mass
if (isolationWidth <= 2.0)
{
if ((truePrecursorMass <
(reaction.PrecursorMass - DefaultIsolationWindowLowerOffset * 2)) ||
(truePrecursorMass >
(reaction.PrecursorMass + DefaultIsolationWindowUpperOffset)))
{
truePrecursorMass = reaction.PrecursorMass;
}
}
else if ((truePrecursorMass < (reaction.PrecursorMass - isolationWidth)) ||
(truePrecursorMass > (reaction.PrecursorMass + isolationWidth)))
{
truePrecursorMass = reaction.PrecursorMass;
}
}
var selectedIonMz = CalculateSelectedIonMz(reaction, monoisotopicMz, isolationWidth);

Writer.WriteLine("PEPMASS=" +
truePrecursorMass.ToString("0.0000000",
CultureInfo.InvariantCulture));
selectedIonMz.ToString(CultureInfo.InvariantCulture));
}

// charge
Expand Down Expand Up @@ -183,7 +145,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
centroidStream.Masses[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ centroidStream.Intensities[i].ToString("0.0000000",
+ centroidStream.Intensities[i].ToString("0.0000000000",
CultureInfo.InvariantCulture));
}
}
Expand Down
31 changes: 14 additions & 17 deletions Writer/MzMlSpectrumWriter.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -814,7 +814,7 @@ private SpectrumType ConstructSpectrum(int scanNumber)
// Trailer extra data list
var trailerData = _rawFile.GetTrailerExtraInformation(scanNumber);
int? charge = null;
double? monoisotopicMass = null;
double? monoisotopicMz = null;
double? ionInjectionTime = null;
double? isolationWidth = null;
for (var i = 0; i < trailerData.Length; i++)
Expand All @@ -829,7 +829,7 @@ private SpectrumType ConstructSpectrum(int scanNumber)

if (trailerData.Labels[i] == "Monoisotopic M/Z:")
{
monoisotopicMass = double.Parse(trailerData.Values[i], NumberStyles.Any,
monoisotopicMz = double.Parse(trailerData.Values[i], NumberStyles.Any,
CultureInfo.CurrentCulture);
}

Expand All @@ -847,7 +847,7 @@ private SpectrumType ConstructSpectrum(int scanNumber)
}

// Construct and set the scan list element of the spectrum
var scanListType = ConstructScanList(scanNumber, scan, scanFilter, scanEvent, monoisotopicMass,
var scanListType = ConstructScanList(scanNumber, scan, scanFilter, scanEvent, monoisotopicMz,
ionInjectionTime);
spectrum.scanList = scanListType;

Expand Down Expand Up @@ -892,7 +892,7 @@ private SpectrumType ConstructSpectrum(int scanNumber)

// Construct and set the precursor list element of the spectrum
var precursorListType =
ConstructPrecursorList(scanEvent, charge, scanFilter.MSOrder, isolationWidth);
ConstructPrecursorList(scanEvent, charge, scanFilter.MSOrder, monoisotopicMz, isolationWidth);
spectrum.precursorList = precursorListType;
break;
case MSOrderType.Ms3:
Expand All @@ -903,7 +903,8 @@ private SpectrumType ConstructSpectrum(int scanNumber)
name = "MSn spectrum",
value = ""
});
precursorListType = ConstructPrecursorList(scanEvent, charge, scanFilter.MSOrder, isolationWidth);
precursorListType = ConstructPrecursorList(scanEvent, charge, scanFilter.MSOrder, monoisotopicMz,
isolationWidth);
spectrum.precursorList = precursorListType;
break;
default:
Expand Down Expand Up @@ -1191,10 +1192,11 @@ private SpectrumType ConstructSpectrum(int scanNumber)
/// <param name="scanEvent">the scan event</param>
/// <param name="charge">the charge</param>
/// <param name="msLevel">the MS level</param>
/// <param name="monoisotopicMz">the monoisotopic m/z value</param>
/// <param name="isolationWidth">the isolation width</param>
/// <returns>the precursor list</returns>
private PrecursorListType ConstructPrecursorList(IScanEventBase scanEvent, int? charge, MSOrderType msLevel,
double? isolationWidth)
double? monoisotopicMz, double? isolationWidth)
{
// Construct the precursor
var precursorList = new PrecursorListType
Expand Down Expand Up @@ -1240,7 +1242,7 @@ private PrecursorListType ConstructPrecursorList(IScanEventBase scanEvent, int?
};

IReaction reaction = null;
var precursorMass = 0.0;
var precursorMz = 0.0;
try
{
switch (msLevel)
Expand All @@ -1253,26 +1255,21 @@ private PrecursorListType ConstructPrecursorList(IScanEventBase scanEvent, int?
break;
}

precursorMass = reaction.PrecursorMass;

// take isolation width from the reaction if no value was found in the trailer data
if (isolationWidth == null || isolationWidth < ZeroDelta)
{
isolationWidth = reaction.IsolationWidth;
}
precursorMz = reaction.PrecursorMass;
}
catch (ArgumentOutOfRangeException exception)
{
//do nothing
}

// Selected ion MZ
var selectedIonMz = CalculateSelectedIonMz(reaction, monoisotopicMz, isolationWidth);
var ionCvParams = new List<CVParamType>
{
new CVParamType
{
name = "selected ion m/z",
value = precursorMass.ToString(CultureInfo.InvariantCulture),
value = selectedIonMz.ToString(CultureInfo.InvariantCulture),
accession = "MS:1000744",
cvRef = "MS",
unitCvRef = "MS",
Expand Down Expand Up @@ -1320,7 +1317,7 @@ private PrecursorListType ConstructPrecursorList(IScanEventBase scanEvent, int?
{
accession = "MS:1000827",
name = "isolation window target m/z",
value = precursorMass.ToString(CultureInfo.InvariantCulture),
value = precursorMz.ToString(CultureInfo.InvariantCulture),
cvRef = "MS",
unitCvRef = "MS",
unitAccession = "MS:1000040",
Expand Down Expand Up @@ -1534,7 +1531,7 @@ private ScanListType ConstructScanList(int scanNumber, Scan scan, IScanFilter sc
};

// Monoisotopic mass
if (monoisotopicMass.HasValue)
if (monoisotopicMass.HasValue && monoisotopicMass.Value > ZeroDelta)
{
scanType.userParam = new UserParamType[1];
scanType.userParam[0] = new UserParamType
Expand Down
65 changes: 60 additions & 5 deletions Writer/SpectrumWriter.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,11 @@ namespace ThermoRawFileParser.Writer
{
public abstract class SpectrumWriter : ISpectrumWriter
{
private const double Tolerance = 0.01;
private const double Tolerance = 0.01;
protected const double ZeroDelta = 0.0001;
private const double PrecursorMzDelta = 0.0001;
private const double DefaultIsolationWindowLowerOffset = 1.5;
private const double DefaultIsolationWindowUpperOffset = 2.5;

/// <summary>
/// The parse input object
Expand Down Expand Up @@ -45,21 +48,23 @@ protected void ConfigureWriter(string extension)
var fullExtension = ParseInput.Gzip ? extension + ".gzip" : extension;
if (!ParseInput.Gzip || ParseInput.OutputFormat == OutputFormat.IndexMzML)
{
Writer = File.CreateText(ParseInput.OutputDirectory + "//" + ParseInput.RawFileNameWithoutExtension +
Writer = File.CreateText(ParseInput.OutputDirectory + "//" +
ParseInput.RawFileNameWithoutExtension +
extension);
}
else
{
var fileStream = File.Create(ParseInput.OutputDirectory + "//" + ParseInput.RawFileNameWithoutExtension + fullExtension);
var fileStream = File.Create(ParseInput.OutputDirectory + "//" +
ParseInput.RawFileNameWithoutExtension + fullExtension);
var compress = new GZipStream(fileStream, CompressionMode.Compress);
Writer = new StreamWriter(compress);
}
}
}
else
{
if (!ParseInput.Gzip || ParseInput.OutputFormat == OutputFormat.IndexMzML)
{
Writer = File.CreateText(ParseInput.OutputFile);
Writer = File.CreateText(ParseInput.OutputFile);
}
else
{
Expand All @@ -86,6 +91,56 @@ protected static string ConstructSpectrumTitle(int scanNumber)
return "controllerType=0 controllerNumber=1 scan=" + scanNumber;
}

/// <summary>
/// Calculate the selected ion m/z value. This is necessary because the precursor mass found in the reaction
/// isn't always the monoisotopic mass.
/// https://github.com/ProteoWizard/pwiz/blob/master/pwiz/data/vendor_readers/Thermo/SpectrumList_Thermo.cpp#L564-L574
/// </summary>
/// <param name="reaction">the scan event reaction</param>
/// <param name="monoisotopicMz">the monoisotopic m/z value</param>
/// <param name="isolationWidth">the scan event reaction</param>
protected static double CalculateSelectedIonMz(IReaction reaction, double? monoisotopicMz,
double? isolationWidth)
{
var selectedIonMz = reaction.PrecursorMass;

// take the isolation width from the reaction if no value was found in the trailer data
if (isolationWidth == null || isolationWidth < ZeroDelta)
{
isolationWidth = reaction.IsolationWidth;
}

isolationWidth = isolationWidth / 2;

if (monoisotopicMz != null && monoisotopicMz > ZeroDelta
&& Math.Abs(
reaction.PrecursorMass - monoisotopicMz.Value) >
PrecursorMzDelta)
{
selectedIonMz = monoisotopicMz.Value;

// check if the monoisotopic mass lies in the precursor mass isolation window
// otherwise take the precursor mass
if (isolationWidth <= 2.0)
{
if ((selectedIonMz <
(reaction.PrecursorMass - DefaultIsolationWindowLowerOffset * 2)) ||
(selectedIonMz >
(reaction.PrecursorMass + DefaultIsolationWindowUpperOffset)))
{
selectedIonMz = reaction.PrecursorMass;
}
}
else if ((selectedIonMz < (reaction.PrecursorMass - isolationWidth)) ||
(selectedIonMz > (reaction.PrecursorMass + isolationWidth)))
{
selectedIonMz = reaction.PrecursorMass;
}
}

return selectedIonMz;
}

/// <summary>
/// Get the spectrum intensity.
/// </summary>
Expand Down

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