Sources and Verification Record

This skill was refreshed on 2026-07-23 against matchms 0.33.1.

Version and Packaging

• matchms on PyPI — 0.33.1, released 2026-06-08; Python >=3.10,<3.15; release history and package metadata.
• matchms 0.33.1 release — Python 3.14 support and maintenance changes.
• matchms repository — source, pyproject.toml, tests, examples, and current README.
• matchms releases — complete upstream release history.

The 0.33.1 wheel was installed in an isolated uv environment and its public objects were inspected with inspect.signature. Runnable examples in this skill were checked against that environment.

Release Notes Used for Migration

• 0.27.0 — on-demand losses, removal of add_losses, and spectrums to spectra renaming.
• 0.30.0 — NumPy 2 baseline and Python 3.13 support.
• 0.31.0 — FlashSimilarity, BlinkCosine, min-max intensity scaling, and new filters.
• 0.32.0 — ModifiedCosineGreedy rename and ModifiedCosineHungarian.
• 0.33.0 — CosineLinear and preparation for the future 1.0 API.
• 0.33.1 — current verified release.

Current API Documentation

• Documentation home
• Core package, Pipeline, Spectrum, and Scores
• Spectrum
• Filtering
• Importing
• Exporting
• Similarity
• Networking

Read the Docs "latest" and the installed 0.33.1 source were treated as authoritative for class names, signatures, return values, and deprecations.

User Guides

• matchms user documentation
• Filtering tutorial
• Building an MS/MS analysis pipeline
• User-guide repository
• Latest recorded guide revision — 2024-06-13.

The tutorials are useful for workflow concepts but predate releases 0.27-0.33. In particular, the pipeline tutorial still uses ModifiedCosine. Current API docs and release notes supersede tutorial symbol names.

Primary Scientific References

• Huber et al., 2020 — matchms: processing and similarity evaluation of mass spectrometry data, Journal of Open Source Software 5(52), 2411, DOI 10.21105/joss.02411.
• Watrous et al., 2012 — Mass spectral molecular networking of living microbial colonies, PNAS 109, E1743-E1752, DOI 10.1073/pnas.1203689109.
• Harwood et al., 2023 — BLINK enables ultrafast tandem mass spectrometry cosine similarity scoring, Scientific Reports 13, 13462, DOI 10.1038/s41598-023-40496-9.
• Li & Fiehn, 2023 — Flash entropy search to query all mass spectral libraries in real time, Nature Methods 20, 1475-1478, DOI 10.1038/s41592-023-02012-9.
• Huber et al., 2021 — Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships, PLoS Computational Biology 17, e1008724, DOI 10.1371/journal.pcbi.1008724.

These papers motivate methods and interpretation. The matchms implementation and its exact defaults remain defined by the 0.33.1 API/source.

Ecosystem References

The current PyPI project description lists compatible or complementary tools:

• MS2DeepScore
• Spec2Vec
• matchmsextras
• MS2Query
• SimMS
• matchms organization

Check each project's current compatibility matrix before combining environments; matchms 0.33.1 uses NumPy 2 and Python 3.10-3.14.

Research Queries

Focused web searches and extracts covered:

• current matchms stable version, Python support, dependencies, and release history;
• breaking changes and deprecated/removed APIs since 2023;
• current core, filtering, I/O, similarity, Pipeline, Scores, and networking documentation;
• current upstream tutorials and their last revision;
• primary publications for matchms, modified cosine/molecular networking, BLINK, Flash Entropy, and Spec2Vec.

No research JSON artifacts were committed to the repository.