mzml2isa is available on PyPI, so if pip is installed on your machine, installing mzml2isa should be quite straightforward, without the need to worry about dependencies. It is also possible to install mzml2isa development version directly from the mzml2isa GitHub repository.


Windows users can either install mzml2isa as described below or use a ‘ready to go’ Windows executable (no python install required). The executables be found on the mzml2isa Github release section. See file mzml2isa_cli.exe.



Without pip you’ll have to install the requirements yourself, otherwise running will fail when trying to import mzml2isa for the first time.


an interface to ontology files (used to import the MS controled vocabulary)



an XML parser generally quicker than the builtin python xml.cElementTree (used as an alternative to parse the mzML files)


If installing lxml on windows, you can either:

  1. Compile it directly (requires Microsoft Visual C++ to be installed on the Windows machine): run the command set STATICBUILD=true && pip install lxml
  2. Install the unofficial windows binaries (whls)

PyPI (stable version) PyPI version

With pip

Just run one of the following commands in a terminal:

pip install mzml2isa        # install in /usr, needs super-user rights
pip install mzml2isa --user # install in ~/.local/

Without pip

This requires the python setuptools module to be installed, as well as the dependencies listed above. Download the latest stable release from the PyPI repository of mzml2isa , unpack it and install it by running the following commands:

tar xf mzml2isa-xx.yy.zz.tar.gz # replace with whatever version you downloaded
cd mzml2isa-xx.yy.zz.tar.gz
python install         # will require super-user rights

GitHub (development version) Build Status


Please check the current version of the program passes the Travis CI validation beforehand, or you could be installing a non-functional version of the program ! The program is working if the badge above displays Passing build.

With pip

pip install git+git://

Without pip

git clone
cd mzml2isa
python install