Writing MGF¶

ms_deisotope.output.mgf can write an MGF for centroided or deconvoluted spectra.

from ms_deisotope.output.mgf import MGFSerializer

def to_mgf(reader, outstream, msn_filters=None):
    if not msn_filters:
        msn_filters = []
    reader.make_iterator(grouped=False)
    writer = MGFSerializer(outstream, deconvoluted=False)
    with writer:
        for scan in reader:
            if scan.ms_level == 1:
                continue
            if msn_filters:
                scan = scan.transform(msn_filters)
            if scan.peak_set is None:
                scan.pick_peaks()
            writer.save_scan(scan)

Code for writing Mascot Generic Format files and for reading deconvoluted generic format files.

class ms_deisotope.output.mgf.MGFSerializer(stream, sample_name=None, deconvoluted=True)[source]¶

A MASCOT Generic Format writer which is deconvolution aware.

Implements :class:`~.HeaderedDelimitedWriter, as well as allowing global parameters to be included at the beginning of the file.

sample_name¶

The name of the sample. This value is currently ignored.

Type

str

started¶

Whether scans have been written out yet or not. Once started is true, it is no longer possible to add global parameters using add_global_parameter().

Type

bool

add_global_parameter(name, value)[source]¶

Add a global parameter at the beginning of the file, before scans are written.

Global parameters follow the same KEY=value format as scan-level parameters. New global parameters may not be added once a scan has been written.

Parameters

• name (str) – The parameter name. Will be made upper-case.

• value (object) – The parameter’s value. Will be converted to a string.

Raises

ValueError: – If scans have already been written, this method raises a ValueError

add_parameter(name, value)[source]¶

Add a parameter to the current block.

Parameters are written KEY=value format.

Parameters

• name (str) – The parameter name. Will be made upper-case.

• value (object) – The parameter’s value. Will be converted to a string.

save_scan_bunch(bunch, **kwargs)[source]¶

Save a single ScanBunch to the writing stream, recording any information relating the precursors and products to each other.

May call save_scan() multiple times.

Parameters

bunch (ScanBunch) – The scan bunch to save

ms_deisotope.output.mgf.ProcessedMGFDeserializer¶

alias of ms_deisotope.output.mgf.ProcessedMGFLoader