Data Access

ms_deisotope can read from mzML, mzXML and MGF files directly, using the pyteomics library. On Windows, it can also use comtypes to access Thermo Fisher’s MSFileReader to read RAW files and Agilent’s MassSpecDataReader to read .d directories. Whenever possible, the library provides a common interface to all supported formats.

To read from a supported file format, do one of the following:

import ms_deisotope

# automatically determine the appropriate reader type
# by inspecting the file
reader = ms_deisotope.MSFileReader("path/to/file.mzML")

# explicitly select the reader type to use if the file
# is compressed or ambiguous
reader = ms_deisotope.MzMLLoader("path/to/file.mzML")

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