---
title: "Matchms - Air Market"
description: "You have tandem mass spectra and need them cleaned up and compared before they tell you anything. This handles reading the files, tidying the metadata, filtering peaks, and scoring one spectrum again…"
canonical: "https://airmarket.ai/app/matchms"
---

[Air Market](/) / [Data & Analytics](/category/data) / Matchms

Skill by [K-Dense](/@k-dense-ai)

# Matchms

Clean up MS/MS spectra and find out what matches what

## What this does

You have tandem mass spectra and need them cleaned up and compared before they tell you anything. This handles reading the files, tidying the metadata, filtering peaks, and scoring one spectrum against another or against a library. It also builds molecular-similarity networks. If your work is LC-MS feature detection or proteomics instead, this is not the one.

### Top 3 things it does for you

- Read and clean tandem mass spectra
- Match spectra against a library
- Compare spectra and build a score matrix

## Information

**Matchms at a glance**

|  |  |
| --- | --- |
| Kind | Skill |
| Publisher | [K-Dense](/@k-dense-ai) |
| Category | [Data & Analytics](/category/data) |
| Works with | Agent Skills - an open standard supported by 40+ agents |
| Version | 2.0 |
| Size | 87 KB |
| Licence | MIT |
| Repository | [k-dense-ai/scientific-agent-skills](https://github.com/k-dense-ai/scientific-agent-skills/tree/70a0d595e54b8d92ca54f216d4315e0ab8c7d967/skills/matchms) |
| GitHub stars | 34,239 (as of Nov 2026) |

## Security report

**Verified.** AIR scanned this exact version of Matchms and flagged nothing. AIR's verdict: **safe**.

**What Matchms's check was run against**

|  |  |
| --- | --- |
| Commit | 70a0d595e54b8d92ca54f216d4315e0ab8c7d967 |
| Content hash | 2cbaeb8693e2221f1944426d5b26f874fc93f8171f93ec1025d9f44f09a08160 |
| Files read | [Browse the files at this exact commit](https://github.com/k-dense-ai/scientific-agent-skills/blob/70a0d595e54b8d92ca54f216d4315e0ab8c7d967/skills/matchms/SKILL.md) |

A scan is named by the exact content it read, not by a version number. A different version is a different artifact, and nothing here applies to a version AIR has not scanned.

[Read the full security report for Matchms](/security/matchms)

## About Matchms

This works on tandem mass spectra with matchms: processing them, cleaning them, comparing them, and searching them. It covers MS/MS file input and output, harmonizing metadata, and filtering peaks.

On the comparison side it covers spectral similarity, library matching, score matrices, and molecular-similarity networks.

For LC-MS feature detection or proteomics pipelines, pyopenms is the one to use instead.

## What's inside

- SKILL.md - instructions
- references/filtering.md - reference
- references/importing_exporting.md - reference
- references/migration.md - reference
- references/similarity.md - reference
- references/sources.md - reference
- references/workflows.md - reference
- scripts/library_search.py - script

## Questions

### Is Matchms safe to install?

AIR scanned this exact version of Matchms and flagged nothing. AIR's verdict: safe. The verdict is named by the content that was read, at commit 70a0d595e54b, so it cannot drift onto a version nobody scanned. The full report is at https://airmarket.ai/security/matchms.

### How do I install Matchms?

Open https://airmarket.ai/app/matchms on Air Market and use the install action: Air Market hands Claude a prompt naming this exact skill, and Claude sets it up. Source, pinned to the exact commit this listing describes: https://github.com/k-dense-ai/scientific-agent-skills/tree/70a0d595e54b8d92ca54f216d4315e0ab8c7d967/skills/matchms. Install from that link, not the branch.

## Related on Air Market

- [More Data & Analytics listings](/category/data)
- [Everything by K-Dense](/@k-dense-ai)

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Canonical URL: <https://airmarket.ai/app/matchms>