{"id":28093,"library":"pyopenms","title":"pyOpenMS","description":"pyOpenMS is the Python wrapper for OpenMS, a C++ library for LC-MS data analysis and computational proteomics. Current version 3.5.0. Release cadence is approximately bi-annual.","status":"active","version":"3.5.0","language":"python","source_language":"en","source_url":"https://github.com/OpenMS/OpenMS","tags":["proteomics","mass-spectrometry","bioinformatics","LC-MS"],"install":[{"cmd":"pip install pyopenms","lang":"bash","label":"pip install"}],"dependencies":[{"reason":"Required for numerical operations","package":"numpy","optional":false},{"reason":"Optional for plotting spectra","package":"matplotlib","optional":true}],"imports":[{"note":"","wrong":"","symbol":"MSExperiment","correct":"from pyopenms import MSExperiment"},{"note":"","wrong":"","symbol":"MZMLFile","correct":"from pyopenms import MZMLFile"}],"quickstart":{"code":"from pyopenms import MSExperiment, MZMLFile\n\nexp = MSExperiment()\nMZMLFile().load(\"input.mzML\", exp)\nprint(f\"Number of spectra: {exp.size()}\")\nms2 = [s for s in exp if s.getMSLevel() == 2]\nprint(f\"Number of MS2 spectra: {len(ms2)}\")","lang":"python","description":"Load an mzML file and count MS2 spectra."},"warnings":[{"fix":"Be patient; pre-built wheels are available on PyPI for many platforms. Use a virtual environment.","message":"Library is large and can take a long time to install or import; first import may appear to hang.","severity":"gotcha","affected_versions":"all"},{"fix":"Use pyopenms types like StringList or std::vector wrappers when expected.","message":"Some functions accept C++ types directly; passing Python lists of strings may fail silently or raise cryptic errors.","severity":"gotcha","affected_versions":"all"}],"env_vars":null,"last_verified":"2026-05-09T00:00:00.000Z","next_check":"2026-08-07T00:00:00.000Z","problems":[{"fix":"Run `pip install pyopenms` in your active Python environment. Ensure you are using Python 3.7+.","cause":"Library not installed or installed in wrong environment.","error":"ImportError: No module named pyopenms"},{"fix":"Install pyopenms via conda: `conda install -c conda-forge pyopenms`. This resolves shared library dependencies.","cause":"Missing OpenMS C++ runtime libraries (on Linux/macOS).","error":"OSError: libOpenMS.so: cannot open shared object file"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"install_tag":null,"quickstart_score":null,"quickstart_tag":null}