matchms

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.

Quality

89%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

86%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A well-structured, highly actionable body with executable code throughout, real one-level-deep references, and a sequenced workflow with validation. The main slack is a small amount of inline catalog/date detail that could move to references and the absence of an explicit error-recovery loop.

Suggestions

Move the full similarity-method catalog ("Choose a Similarity Method") to references/similarity.md and keep only a 2-3 line pointer in the body to tighten conciseness.

Drop or relocate the hard release date "released 2026-06-08" — time-sensitive detail belongs in the migration/sources reference, not the overview.

Add an explicit validate-then-fix feedback loop to the Operating Workflow (e.g., 'If a require_* filter yields None, correct the offending metadata and re-run') to lift workflow clarity to 5.

Dimension	Reasoning	Score
Conciseness	Largely lean and free of basic-concept padding, but the full "Choose a Similarity Method" catalog and the dated "released 2026-06-08" detail could be trimmed or pushed to references; it is efficient with minor over-content, fitting the 4 anchor rather than the every-token-earns-its-place 5.	4 / 5
Actionability	Multiple copy-paste-ready, executable blocks (install/verify commands, the full load-and-score Quick Start, pair scoring, all-vs-all, the bundled CLI invocation) cover the common cases, matching the fully-executable 5 anchor.	5 / 5
Workflow Clarity	An 8-step Operating Workflow with explicit validation steps (drop invalid spectra, estimate pair count, validate top hits) and a Non-Negotiable Checks checklist avoids the batch-cap-at-3 rule, but lacks an explicit validate-fix-retry feedback loop, landing at the 4 anchor rather than 5.	4 / 5
Progressive Disclosure	The body is a clear overview that signals one-level-deep references (importing_exporting, filtering, similarity, workflows, migration, sources) plus scripts/library_search.py, all verified to exist, with each link annotated — matching the well-signaled-easy-navigation 5 anchor.	5 / 5
	Total	18 / 20 Passed

Description

92%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A tight, domain-specific description that states concrete capabilities, explicit use-for triggers, and a clear hand-off boundary to pyopenms. Its only gap is omitting the file-format extensions that would round out trigger-term coverage.

Dimension	Reasoning	Score
Specificity	Names the domain plus many concrete actions — "Process, clean, compare, and search tandem mass spectra" and "MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity networks" — giving comprehensive, not just minor-gap, coverage, which fits the 5 anchor over the 4.	5 / 5
Completeness	Explicitly answers what (the concrete action list) and when ("Use for MS/MS file I/O, metadata harmonization, peak filtering...") with concrete trigger phrases, and adds a negative boundary ("Use pyopenms instead for LC-MS feature detection..."), matching the 5 anchor rather than the 4 where 'when' is only loosely specified.	5 / 5
Trigger Term Quality	Strong domain keywords users would say ("tandem mass spectra", "MS/MS", "spectral similarity", "library matching", "molecular-similarity networks") but no file extensions/formats (.mgf, .msp, .mzml), so it stops short of the comprehensive-synonyms-plus-extensions 5 anchor.	4 / 5
Distinctiveness Conflict Risk	Clear niche (tandem mass spectrometry with matchms) with distinct triggers and an explicit don't-use-this-for pyopenms boundary, giving minimal conflict risk per the 5 anchor.	5 / 5
	Total	19 / 20 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: K-Dense-AI/scientific-agent-skills
Path: skills/matchms/SKILL.md
Commit: 36d8f13

Reviewed: about 6 hours ago

Table of Contents

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