Description
pyopenms is an agent skill for processing mass spectrometry data with pyOpenMS, the Python bindings to the OpenMS library. It supports proteomics and metabolomics workflows, including feature detection, peptide and protein identification, label-free quantification and end-to-end LC-MS/MS pipelines. It also reads and writes mass spectrometry file formats and processes raw spectra. The skill ships ready-to-run scripts for the most common high-level workflows. Each script is a parameterised command-line tool that handles loading, processing and export, so the skill advises running a script in preference to writing new code. It falls back to the Python API and its reference files only when no script fits the task. Use it when you have raw or processed spectra and need a standard pipeline for identification or quantification. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs. Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk. Install it with npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill pyopenms.…
Highlights
- Feature detection and quantification
- Peptide and protein identification
- Proteomics and metabolomics workflows
- Ready-to-run parameterised scripts
- Reads and writes MS file formats
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pyopenms FAQ
What does pyOpenMS do?
Python bindings to OpenMS, for processing mass spectrometry data in proteomics and metabolomics.
What workflows are included?
Feature detection, peptide and protein identification, label-free quantification and LC-MS/MS pipelines.
Should I write new code?
The skill advises running a bundled script where one fits, and using the Python API only when none does.
Which file formats?
Mass spectrometry formats that OpenMS reads and writes, handled in the scripts.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill pyopenms.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best pyopenms alternatives?
Popular alternatives to pyopenms include matchms, data-scraper-agent and django-celery. See all pyopenms alternatives