mzx

Free and open conversion of mass spec data

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Installing

System Requirements:

  • Docker

  • Python3.10+ (Contains PEP 636 )

  • Your favorite Python package manager (uv, pip, poetry, …)

Install and update using pip:

pip install -U mzx

Usage

To run the cli command:

mzx --type mgf /path/to/data.mgf

This will convert the mgf data to mzml by default.

To run the gui:

mzx-gui

Note: The gui is experimental

You can also call the command from the module itself:

python -m mzx.cli /path/to/data.raw

python -m mzx.gui

Vendor Support

mzx utilizes proteowizard, and supports the following vendors: Agilent, Bruker, Sciex, Shimadzu, Thermo, and UIMF.

For more information, please see the proteowizard FAQ <https://proteowizard.sourceforge.io/faq.html>

Supported File Formats

  • .mgf

  • .mzML

  • .raw (Thermo)

  • .wiff (Sciex)

Features

  • Convert between various mass spectrometry file formats

  • Supports vendor formats: Agilent, Bruker, Sciex, etc.

  • CLI and experimental GUI for ease of use

Documentation

Full documentation is available at mzx.readthedocs.io

Developer setup

If you have uv installed, then you can a venv setup by running:

make setup

While making changes to mzx, you can install/uninstall it from your local

make install

make uninstall

Tests

make test