MzMLWriter

Remarks

Builds an indexed mzML file from spectra. Describe the instrument, software and data processing with the Add methods, start a run with AddRun, add spectra with AddSpectrum, then call Write.

Order matters. A run must be started before any spectrum is added, and AddProcessingMethod does nothing unless AddDataProcessing has been called first.

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Constructors

Syntax	Description
MzMLWriter()	Creates a writer with the fixed mzML header in place.

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Methods

Method	Returns	Description
AddDataProcessing(string id)	void	Starts a data processing entry. Later AddProcessingMethod calls attach to it.
AddFileDescription(string fileName)	void	Not yet implemented. Has no effect on the written file.
AddInstrumentConfiguration(string id, string? refID)	void	Adds an instrument configuration entry. The refID parameter is unused.
AddProcessingMethod(string softwareRef)	void	Adds a processing method to the current data processing entry.
AddRun(string id, string instConf)	void	Starts a run. Spectra added afterward belong to it.
AddSoftware(string id, string version)	void	Adds a software entry. The ids “Xcalibur” and “pwiz” also get their standard CV terms.
AddSpectrum(Spectrum spec)	void	Converts a spectrum object into a spectrum element.
Write(string filename, bool validateSchema = false, string? schemaPath = null)	void	Writes the accumulated mzML content to the given path.

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Example

using Nova.Data;
using Nova.Io.Read;
using Nova.Io.Write;

MzMLWriter writer = new MzMLWriter();

// Describe how the file was produced. Ids given here are referred to
// by the entries that follow.
writer.AddSoftware("Nova", "1.1.0");
writer.AddInstrumentConfiguration("IC1", null);
writer.AddDataProcessing("DP1");
writer.AddProcessingMethod("Nova");

// A run must be started before any spectrum is added.
writer.AddRun("run1", "IC1");

FileReader reader = new FileReader("DDA.raw", MSFilter.MS1 | MSFilter.MS2);
foreach (Spectrum spectrum in reader)
{
  writer.AddSpectrum(spectrum);
}

writer.Write("converted.mzML");

Validation is off by default, because it needs a local copy of the schema and the output is usable either way.

writer.Write("converted.mzML", true, @"C:\schemas\mzML1.1.0.xsd");