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matchms Mass Spectra Toolkit

A skill for cleaning, filtering, comparing, and library-searching MS/MS spectra with the current matchms 0.33.1 API.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

  • Loads and exports tandem MS data in MGF, MSP, mzML, mzXML, JSON, mzSpecLib, and metabolomics-USI formats.
  • Harmonizes metadata, handles precursor/adduct fields, and builds consistent peak-processing pipelines with SpectrumProcessor.
  • Guides the choice of similarity metric — cosine, modified cosine, neutral losses, BLINK, FlashSimilarity (entropy) — and builds score matrices.
  • Covers library search, top-hit extraction, sparse precursor gating, and molecular similarity networks.
  • Fixes breakages from pre-0.33 tutorials: ModifiedCosine removal, deprecated add_losses(), tuple return from process_spectra(), structured StackedSparseArray scores.

Who it's for

  • Metabolomics and natural-product researchers running MS/MS library searches.
  • Python users building molecular networking or spectral-similarity pipelines.
  • Anyone migrating older matchms code to the current API.

Example uses

  1. "Search queries.mgf against library.msp with modified cosine at 0.02 tolerance, keep the top 5 hits, export CSV" — uses the bundled scripts/library_search.py.
  2. "Apply identical preprocessing (normalize, 1% relative-intensity cut, min 5 peaks) to both references and queries, then compute the score matrix."
  3. "Estimate the pair count before an all-vs-all comparison and pre-filter candidates with PrecursorMzMatch."

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/matchms/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on AI Skill Mart.
Copy the skills/matchms folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/matchms/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/matchms ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills folder: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r scientific-agent-skills/skills/matchms ~/.claude/skills/
  4. Prepare a Python 3.10–3.14 environment and install the pinned release: uv pip install "matchms==0.33.1"
  5. Verify it: uv run python -c "import matchms; print(matchms.__version__)"
  6. Restart Claude Code and try a prompt like "search my MGF queries against this MSP library" to trigger the skill.
View source on GitHub ↗License: MIT