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matchms

Category: life-sciences · License: Apache-2.0 · Version: 2.1 · Includes scripts Tags: mass spectrometry, MS/MS, spectral matching, metabolomics, cheminformatics

When to use it

Process, clean, compare, and search tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity networks. Use pyopenms instead for LC-MS feature detection or proteomics pipelines.

Example requests

Ask your agent in plain language, for example:
  • “How do I get the top 5 library hits for each spectrum in my query MGF using matchms?”
  • “I’m running an old tutorial script on my GNPS export gnps_library.mgf and it fails with ImportError: cannot import name 'ModifiedCosine' from matchms.similarity. After I swapped that out, spectrum.add_losses() also breaks, and so does calling processor(spectrum) on my SpectrumProcessor. Can you fix the script so it runs on a current install?”
  • “I have about 40,000 MS/MS spectra from a plant extract in one file. I want to group the ones that look like they share a similar fragmentation pattern into a network so I can see which compounds are related. Where do I start, and how do I keep the computation from blowing up?”

Install

In Claude Code you can also add the marketplace with /plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.

Full playbook

Read SKILL.md for the complete workflow, references and any scripts. The agent installer copies the full skill folder.
Last modified on October 19, 2026