# 1. Introduction

## 1.1. General information

Module to parse mzML data in Python based on cElementTree

Copyright 2010-2018 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
> GSK
> Germany
> eMail: christian@fufezan.net
> http:// <in transition >

## 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
  - 2. a very fast parser for mzML data, the standard mass spectrometry data format
  - 3. a set of functions to compare and/or handle spectra
  - 4. random access in compressed files
  - 5. interactive data visualization

## 1.3. Implementation

pymzML requires Python3.4+. The module is freely available on pymzml.github.com or pypi, published under GPL and requires no additional modules to be installed, but can optionally use numpy.

## 1.4. Download

Get the latest version via github
  https://github.com/pymzml/pymzML
The complete Documentation can be found as pdf
  http://pymzml.github.com/dist/pymzml.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 3.4 or higher.

Note

Consider to use a Python virtual environment for easy installation and use. Further, usage of python3.4+ 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

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:

    nosetests tests/*.py

The latest Documentation was generated on: Nov 05, 2018