alterlab-pyopenms

# PyOpenMS ## Overview PyOpenMS provides Python bindings to the OpenMS library for computational mass spectrometry, enabling analysis of proteomics and metabolomics data. Use for handling mass spectrometry file formats, processing spectral data, detecting features, identifying peptides/proteins, and performing quantitative analysis. ## Installation Install using uv (pyOpenMS 3.x — examples here are verified against 3.5): ```bash uv pip install "pyopenms>=3.4" ``` Verify installation: ```python import pyopenms print(pyopenms.__version__) ``` > Version note: pyOpenMS 3.x removed the old `FeatureFinder` facade. Use > `FeatureFinderAlgorithmPicked` (the former `"centroided"` algorithm) or, for > metabolomics, the `MassTraceDetection` → `ElutionPeakDetection` → > `FeatureFindingMetabo` chain. See `references/feature_detection.md`. ## When to Use This Skill Use this skill when the user wants to: - Read, convert, or inspect MS file formats (mzML, mzXML, idXML, featureXML, consensusXML, mzTab). - Process raw spectra — smoothing, baseline removal, centroiding/peak picking, normalization. - Run **feature detection** and label-free quantification on LC-MS runs. - Do **peptide/protein identification** and FDR control (search-engine adapters, PeptideIndexer, FalseDiscoveryRate) or build a full LC-MS/MS pipeline. - Do untargeted **metabolomics** feature finding (MassTraceDetection -> ElutionPeakDetection -> FeatureFindingMetabo) and adduct/formula work. - Drive OpenMS algorit...