1. Introduction

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1.1. General information

Module to parse mzML data in Python based on cElementTree

Copyright 2010-2021 by:

M. Kösters,
J. Leufken,
T. Bald,
A. Niehues,
S. Schulze,
K. Sugimoto,
R.P. Zahedi,
M. Hippler,
S.A. Leidel,
C. Fufezan,

1.1.1. Contact information

Please refer to:

Dr. Christian Fufezan
Group Leader Experimental Bioinformatics
Cellzome GmbH
R&D Platform Technology & Science

1.2. Summary

pymzML is an extension to Python that offers
    1. easy access to mass spectrometry (MS) data that allows the rapid development of tools

    1. a very fast parser for mzML data, the standard mass spectrometry data format

    1. a set of functions to compare and/or handle spectra

    1. random access in compressed files

    1. interactive data visualization

1.3. Implementation

pymzML requires Python3.7+. The module is freely available on pymzml.github.com or pypi, published under MIT license and only requires numpy and regex, however there are several optional dependencies for extended functionality like interactive plotting and deconvolution.

1.4. Download

Get the latest version via github
The complete Documentation can be found as pdf

1.5. Citation

M Kösters, J Leufken, S Schulze, K Sugimoto, J Klein, R P Zahedi, M Hippler, S A Leidel, C Fufezan; pymzML v2.0: introducing a highly compressed and seekable gzip format, Bioinformatics, doi: https://doi.org/10.1093/bioinformatics/bty046

1.6. Installation

pymzML requires Python 3.7 or higher.


Consider to use a Python virtual environment for easy installation and use. Further, usage of python3.7+ is recommended.

Download pymzML using GitHub or the zip file:

  • GitHub version: Start by cloning the GitHub repository:

    user@localhost:~$ git clone https://github.com/pymzML/pymzml.git
    user@localhost:~$ cd pymzml
    user@localhost:~$ pip install -r requirements.txt
    user@localhost:~$ python setup.py install
  • pypi version:

    user@localhost:~$ pip install pymzml # install standard version
    user@localhost:~$ pip install "pymzml[plot]" # with plotting support
    user@localhost:~$ pip install "pymzml[pynumpress]" # with pynumpress support
    user@localhost:~$ pip install "pymzml[deconvolution]" # with deconvolution support using ms_deisotope
    user@localhost:~$ pip install "pymzml[full]" # full featured

If you have troubles installing the dependencies, install numpy first separately, since pynumpress requires numpy to be installed.

If you use Windows 7 please use the ‘SDK7.1 command prompt’ for installation of pymzML to assure correct compiling of the C extensions.

1.6.1. Testing

To test the package and correct installation:


1.7. Contributing

Please read the contribution guidelines before contributing here

1.8. Code of Conduct

Since pymzML is an open source project maintained by the community, we established a code of conduct in order to facilitate an inclusive environment for all users, contributors and project memebers. Before contributing to pymzML, please read the code of conduct here

The latest Documentation was generated on: Mar 01, 2024