pyOpenMS
Python bindings for mass spectrometry.
Python bindings to OpenMS-lib. Write custom analysis scripts and integrate OpenMS into Python workflows.
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Native algorithms
Run OpenMS-lib algorithms directly in Python
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DataFrame export
Pandas DataFrame export for common OpenMS data structures
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Scripts & notebooks
Run in scripts or Jupyter notebooks
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Scientific stack
Seamless integration with the scientific Python stack
Get started
Explore pyOpenMS
Documentation and resources to start building with pyOpenMS.
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Docs
Read Documentation
Tutorials and guides to help you get productive quickly.
Open docs -
Install
Installation
Install pyOpenMS from PyPI and verify your environment.
Install now -
API
API Reference
Full class and method reference for the Python bindings.
View reference -
pyOpenMS viz
Visualization
Interactive plotting and exploration for OpenMS data structures.
Explore viz -
No install needed
Try Online
Run pyOpenMS in the browser without a local install.
Open in Colab
For Developers
Contribute
Any class in OpenMS-lib can be wrapped and used from Python — your contributions help researchers worldwide.
Report an Issue
File bugs or request new features.
Open on GitHubBuild from Source
Compile pyOpenMS locally on your platform.
View build guideWrapping New Classes
Expose new OpenMS-lib classes to Python.
Follow the guideDeveloper manual
Architecture and contribution workflows.
Open docsReviewing Pull Requests
Help move contributions forward by reviewing open pull requests on GitHub.
Research impact