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`. ## Core Capabilities PyOpenMS organizes functionality into these domains: ### 1. File I/O and Data Formats Handle mass spectrometry file formats and convert between representations. **Supported formats**: mzML, mzXML, TraML, mzTab, FASTA, pepXML, protXML, mzIdentML, featureXML, consensusXML, idXML Basic file reading: ```python import pyopenms as ms # Read mzML file exp = ms.MSExperiment() ms.MzMLFile().load("data.mzML", exp) # Access spectra for spectrum in exp: mz, intensity = spectrum.get_peaks() print(f"Spectrum: {len(mz)} peaks") ``` **For detailed file handling**: See `references/file_io.md` ### 2. Signal Processing Proce...