Writing mzML¶

Using the psims library, ms_deisotope.output.mzml can write an mzML file with all associated metadata, including deconvoluted peak arrays, chromatograms, and data transformations. The MzMLSerializer class handles all facets of this process.

This module also contains a specialized version of MzMLLoader, ProcessedMzMLLoader, which can directly reconstruct each deconvoluted peak list and provides fast access to an extended index of metadata that MzMLSerializer writes to an external file.

import ms_deisotope
from ms_deisotope.test.common import datafile
from ms_deisotope.output.mzml import MzMLSerializer

reader = ms_deisotope.MSFileLoader(datafile("small.mzML"))
with open("small.deconvoluted.mzML", 'wb') as fh:
    writer = MzMLSerializer(fh, n_spectra=len(reader))

    writer.copy_metadata_from(reader)
    for bunch in reader:
        bunch.precursor.pick_peaks()
        bunch.precursor.deconvolute()
        for product in bunch.products:
            product.pick_peaks()
            product.deconvolute()
        writer.save(bunch)

    writer.close()

class ms_deisotope.output.mzml.MzMLSerializer(handle, n_spectra=200000, compression=None, deconvoluted=True, sample_name=None, build_extra_index=True, data_encoding=None, include_software_entry=True, close=None)[source]¶

Write ms_deisotope data structures to a file in mzML format.

base_peak_chromatogram_tracker¶

Accumulated mapping of scan time to base peak intensity. This is used to write the base peak chromatogram.

Type: OrderedDict

chromatogram_queue¶

Accumulate chromatogram data structures which will be written out after all spectra have been written to file.

Type: list

compression¶

The compression type to use for binary data arrays. Should be one of "zlib", "none", or None

Type: str

data_encoding¶

The encoding specification to specify the binary encoding of numeric data arrays that is passed to write_spectrum() and related methods.

Type: dict or int or numpy.dtype or str

data_processing_list¶

List of packaged DataProcessingInformation to write out

Type: list

deconvoluted¶

Indicates whether the translation should include extra deconvolution information

Type: bool

file_contents_list¶

List of terms to include in the <fileContents> tag

Type: list

handle¶

The file-like object being written to

Type: file-like

indexer¶

The external index builder

Type: ExtendedScanIndex

instrument_configuration_list¶

List of packaged InstrumentInformation to write out

Type: list

n_spectra¶

The number of spectra to provide a size for in the <spectrumList>

Type: int

processing_parameters¶

List of additional terms to include in a newly created DataProcessingInformation

Type: list

sample_list¶

List of SampleRun objects to write out

Type: list

sample_name¶

Default sample name

Type: str

sample_run¶

Description

Type: SampleRun

software_list¶

List of packaged Software objects to write out

Type: list

source_file_list¶

List of packaged SourceFile objects to write out

Type: list

total_ion_chromatogram_tracker¶

Accumulated mapping of scan time to total intensity. This is used to write the total ion chromatogram.

Type: OrderedDict

writer¶

The lower level writer implementation

Type: MzMLWriter

add_data_processing(data_processing_description: Union[ms_deisotope.data_source.metadata.data_transformation.DataProcessingInformation, ms_deisotope.data_source.metadata.data_transformation.ProcessingMethod])[source]¶

Add a new DataProcessingInformation or ProcessingMethod.

Creates a new <dataProcessing> entry describing one or more <processingMethod>`s for a single referenced :class:`~.Software instance.

Parameters: data_processing_description (DataProcessingInformation or ProcessingMethod) – Data manipulation sequence to add to the document

add_file_contents(file_contents: Union[str, collections.abc.Mapping, ms_deisotope.data_source.metadata.file_information.FileContent])[source]¶

Add a key to the resulting <fileDescription> of the output document.

Parameters: file_contents (str or Mapping) – The parameter to add

add_file_information(file_information: ms_deisotope.data_source.metadata.file_information.FileInformation)[source]¶

Add the information of a FileInformation to the output document.

Parameters: file_information (FileInformation) – The information to add.

add_instrument_configuration(configuration: ms_deisotope.data_source.metadata.instrument_components.InstrumentInformation)[source]¶

Add an InstrumentInformation object to the output document.

Parameters: configuration (InstrumentInformation) – The instrument configuration to add

add_processing_parameter(name: str, value: Optional[Union[str, int, float]] = None)[source]¶

Add a new processing method to the writer’s own <dataProcessing> element.

Parameters

name (str) – The processing technique’s name
value (obj) – The processing technique’s value, if any

add_software(software_description: ms_deisotope.data_source.metadata.software.Software)[source]¶

Add a Software object to the output document.

Parameters: software_description (Software) – The software description to add

add_software(software_description: ms_deisotope.data_source.metadata.software.Software)[source]¶

Add a Software object to the output document.

Parameters: software_description (Software) – The software description to add

add_source_file(source_file: ms_deisotope.data_source.metadata.file_information.SourceFile)[source]¶

Add the SourceFile to the output document.

Parameters: source_file (SourceFile) – The source fil to add

close()[source]¶

Finish writing scan data, write any pending metadata and close the file stream.

May call complete().

save(bunch: Union[ms_deisotope.data_source.scan.scan.Scan, ms_deisotope.data_source.scan.base.ScanBunch], **kwargs)¶

Save any scan information in bunch.

This method can handle ScanBunch or ScanBase instances, dispatching to the appropriate logic.

Parameters: bunch (ScanBunch or ScanBase) – The scan data to save. May be a collection of related scans or a single scan.