python-pymzml(1) mzML mass spectrometric data parsing


This manual page documents briefly the python-pymzml package that packages the pymzML Python extension.

pymzML is an extension to Python that offers:

- easy access to mass spectrometry (MS) data that allows the rapid development of tools;

- a very fast parser for mzML data, the standard in mass spectrometry data format;

- a set of functions to compare or handle spectra.

pymzML requires Python2.6.5+ and is fully compatible with Python3. The module is freely available on or pypi, published under LGPL and requires no additional modules to be installed.

The documentation of this Python extension is packaged in the python-pymzml-doc package.


A number of useful examples are shipped within the python-pymzml package and can be found at /usr/share/doc/python-pymzml/example_scripts. A number of the examples make use of functions contained in via an import of that file's contents. It is suggested to copy this directory to a temporary place and to run python from inside that new directory so as to gain access to the features contained in that file through an import (which would not work otherwise).


Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., and Fufezan, C. (2012) pymzML - Python module for high throughput bioinformatics on mass spectrometry data. Bioinformatics, UK,28:1052-1053. doi:10.1093/bioinformatics/bts066.


This manual page was written by Filippo Rusconi <[email protected]>. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3 (GPL-3+), published by the Free Software Foundation.

 On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'.