Writing mzMLb

Using the psims library, ms_deisotope.output.mzmlb can write an mzMLb file with all associated metadata. This uses the same machinery as ms_deisotope.output.mzml to accomplish this.

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

All behavior available for the ProcessedMzMLLoader are available for ProcessedMzMLbLoader.

import ms_deisotope
from ms_deisotope.test.common import datafile
from ms_deisotope.output.mzmlb import MzMLbSerializer

reader = ms_deisotope.MSFileLoader(datafile("small.mzML"))
with MzMLbSerializer('small.deconvoluted.mzMLb', n_spectra=len(reader)) as writer:
    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)
class ms_deisotope.output.mzmlb.MzMLbSerializer(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]
add_data_processing(data_processing_description: Union[ms_deisotope.data_source.metadata.data_transformation.DataProcessingInformation, ms_deisotope.data_source.metadata.data_transformation.ProcessingMethod])

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])

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)

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)

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)

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)

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)

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)

Add the SourceFile to the output document.

Parameters

source_file (SourceFile) – The source fil to add

close()

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.

See also

save_scan(), save_scan_bunch()

save_scan(scan: ms_deisotope.data_source.scan.base.ScanBase, **kwargs)

Write a Scan to the output document as a collection of related <spectrum> tags.

Note

If no spectra have been written to the output document yet, this method will call _add_spectrum_list() and writes all of the metadata lists out. After this point, no new document-level metadata can be added.

Parameters

  • scan (Scan) – The scan to write.

  • deconvoluted (bool) – Whether the scan to write out should include deconvolution information

save_scan_bunch(bunch: ms_deisotope.data_source.scan.base.ScanBunch, **kwargs)

Write a ScanBunch to the output document as a collection of related <spectrum> tags.

Note

If no spectra have been written to the output document yet, this method will call _add_spectrum_list() and writes all of the metadata lists out. After this point, no new document-level metadata can be added.

Parameters

bunch (ScanBunch) – The scan set to write.

class ms_deisotope.output.mzmlb.ProcessedMzMLbLoader(source_file, use_index=True, use_extended_index=True)[source]
get_index_information_by_scan_id(scan_id: str) → dict

Get the scan description from the extended index.

has_index_file() → bool

Checks if an extended index file exists for this reader.

Returns

Return type

bool