pyOpenMS
Python bindings for mass spectrometry.
Python bindings to OpenMS-lib. Write custom analysis scripts and integrate OpenMS into Python workflows.
Overview
What is pyOpenMS?
Python bindings to the OpenMS-lib C++ framework — script, prototype, and automate mass spectrometry analysis from Python.
Native algorithms
Run OpenMS-lib algorithms directly in Python
DataFrame export
Pandas DataFrame export for common OpenMS data structures
Scripts & notebooks
Run in scripts or Jupyter notebooks
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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Try Online
Open in Colab -
Installation
Install now -
Documentation
Open docs -
API Reference
View reference
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, request features, or discuss changes on the OpenMS tracker.
Open on GitHubBuild from Source
Platform-specific guides for compiling pyOpenMS locally.
View build guideWrapping New Classes
Step-by-step guide for exposing new OpenMS classes to Python.
Follow the guideDeveloper manual
Architecture and contribution workflows for pyOpenMS.
Open docs