pyopenms

combined

Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets. Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.

When to use

Converting, validating, or batch-processing mass spectrometry files (e.g., mzML, mzXML, MGF) as part of a pipeline.
Cleaning raw spectra before downstream analysis (smoothing, baseline correction, denoising, peak picking).
Detecting and linking isotope patterns / features for proteomics or metabolomics feature tables.
Running identification-oriented steps where peptide/protein identification integration is required.
Building custom computational MS workflows in Python while leveraging OpenMS algorithms.

Skill page

Conflict

The K-Dense-AI copy is a distinct, high-fidelity implementation that ships a suite of parameterized CLI scripts (e.g., `detect_features_metabo.py`, `align_link_quantify.py`) and provides specific installation constraints (Python 3.11+, pyOpenMS 3.6.0). The other three copies (Vibe-Skills, medical-research-skills, and OpenClaw-Medical-Skills) are largely identical or near-identical generic API guides that lack these scripts and instead point to `references/` files. Because the K-Dense copy provides a different, more operational procedure (running scripts vs. writing API code) and the others provide a different, more conceptual procedure (API exploration), crowning one would hide the alternative approach. The Vibe-Skills and OpenClaw copies are effectively duplicates of each other, while the medical-research-skills copy is a simplified variant of the same API-focused approach.