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mzML file parser and converter to ISA-Tab

Project description

Extract metadata from mzML and imzML files and write them to an ISA-Tab document.

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mzml2isa is a Python3 program that can automatically generate ISA-Tab document structure metadata files from raw XML metabolomics data files (mzML open access data format). The mzml2isa tool provides the backbone of ISA-Tab metabolomics study which can then be edited with an ISA editing tool, ISAcreator (see MetaboLights pre-packaged ISA Creator)

  • Extract meta information from mzML files and stores it as a Python dictionary or serialize it into a JSON formatted document.

  • Create an ISA-Tab file structure with relevant meta information filled in.

  • Add additional metadata that cannot be parsed from mzML files to the ISA-Tab files through a JSON formatted dictionnary or an XLS file.


See the Installation page of the online documentation.



mzml2isa -i /path/to/mzml_files/ -o /path/to/out_folder/ -s name_of_study

Python Module

See the Usage page and the Examples page for more information.


To download some real data from MetaboLights studies to test the converter with, run

python scripts/ <size>

from inside the repository, where size is the maximum size in GiB you can allocate to download files. The script will download the files to the example_files/metabolights folder and then run mzml2isa on those files..

If you use a *NIX machine with curlftpfs and bash available, you can also run


to mount the database to the example directory and start converting mzML studies.



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