Mass spectrometry has emerged as a key analytical tool in modern life sciences and the biotech industry. Modern instrumentation allows for comprehensive proteome and metabolome analyses. Innovative data analysis tools will become essential to transform the underlying data to biological insights. CodeMS combines mass spectrometry expertise with computer science and helps you to get the most out of your data.

We offer a wide range of services. If you have found whats right for you, contact us at and describe your problem. We will probably get back to you and figure out the details – during a cup of coffee if you are nearby.


We help you to set up a stable workflow, which is tailored to your data format and computing environment, allowing you to get the maximum amount of information out of your data.

Customized Tools

You find that a tool in your current analysis pipeline requires some new functionality or you need a completely new tool? We have a strong background in OpenMS and MaxQuant. While MaxQuant is closed source, there is still potential for optimizing the way it is used.
If you need more customized tools, we adapt existing OpenMS TOPP tools or create completely new ones, which neatly integrate with the KNIME or TOPPAS workflow engines.

If you find that your new tool is beneficial to the community, we can certainly make it available for everyone else, and even integrate it into the next official OpenMS release. These community-projects are offered with a discount, since we feel that giving back deserves reward.

Training Sessions and Workshops

We provide workshops for beginners and advanced scientists on mass spectrometry-based analyses of small and large molecules. Ranging from workshops which introduce the current status of the technology and our algorithmic solutions for data analysis to specialized seminars on specific workflows.
Our training courses are designed for individuals or for groups. The sessions will enable you to build your own analysis workflows and customize the existing tools to fit your requirements.

Sessions are offered online via webinars, or by face-to-face tutorials at your company.

Contact us at and request a quote.