Welcome to mzOS project

mzOS is a small library to perform deisotoping and feature annotation from an extracted feature list (commonly designed by peaklist) in LC-MS (Liquid Chromatography coupled to mass spectrometry) datasets.

Basically, you run first XCMS (using the classical pipeline), giving as a result a peaklist file. This is this result file that mzOS uses. Other feature extraction softwares might be supported later (OpenMS).


mzOS (last version 0.1.3) install should be pretty straightforward. The last version at the moment is 0.1.3. Simply using

  • pip install mzos

You can also download a zip archive from github for example. Unzip the archive then

  • cd mzOS
  • python setup.py install

The project is quite heavy (around 20Mo), actually it comes with LMSD and HMDB databases.

It is still in alpha stage and is not bug free.

Project layout

scripts/        # Scripts used to rebuild database sqlite files.
third_party/    # small utility to calculate efficiently theoritical isotopic pattern
        ...     # emass files
ressources/     # contains databases, isotopes and adducts list

...             # mzOS python modules