User Tutorials




This tutorial was designed to guide you through the use of our Community Contributions to the KNIME workflow system. It contains:

  • installation instructions,
  • a very small introduction to TOPPView in case you want to additionally install the OpenMS binaries for visualisation,
  • a basic introduction to KNIME and its graphical user interface
  • a guide to construct example workflows for proteomics, metabolomics, quality control …
  • a guide to the Python bindings pyOpenMS and DIA with OpenSWATH
  • a small “OpenMS in KNIME” Troubleshooting guide with an FAQ

Old versions

We will release new versions on our GitHub page for Tutorials. Older versions can be found there. It also contains releases for the versions used in different hands-on workshops (if you want to replicate it at home). The repository does not include data. Unless otherwise noted, the tutorials use the same (or a subset) of the tutorial data above.



For use with the binary installers of OpenMS. It describes how to use the OpenMS TOPP tools from the command line and has an extensive tutorial on visualisation with TOPPView. You need your own data to work through it. In case you do not have any, have a look at the data from the User Tutorial above.

Old versions

Old versions are available in the documentation of older OpenMS releases here.