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Frequently Asked Questions

What metadata does mzml2isa extract from .mzML files ?

See :ref:`extracted_mzml`.

What metadata does mzml2isa extract from .imzML files ?

See :ref:`extracted_imzml`.

How do I report an issue / ask for a new feature ?

Go on the GitHub repository issue tracker of the program, check that no similar issue already exist, and if so, open a new issue and include the following information:

  • what software and software version you used (you can know the version of the program by running mzml2isa --version in a terminal)
  • one of the files you used (without this, nothing can be done to analyze the issue !)
  • any remark you might have on how you think your file may not be generic (special instrument, multiple instruments, special parameters, etc.)
  • the complete traceback of the error if you report a crash

The program crashed when I used it on my files, what should I do ?

While the mzML file format is supposed to be a standard, it so happens that depending on what hardware and software were used to generate .mzML files after a Mass Spectrometry study, some tags may not be named the same, and that some metadata may be absent or elsewhere than expected in the final .mzML file.

Even though the example files used to test mzml2isa are thought to be comprehensive, it might happen that the files you use are one of the special cases we did not consider. But a new version of the program may have corrected the bug that hit you already, so make sure you are running the latest version of mzml2isa.

To communicate that crash to us, see :ref:`issue`