Model type
Mass-spectral processing and similarity software
Method
matchms
matchms provides reproducible processing and comparison of tandem mass spectra.
Sources
matchms/matchms: README.rst · README.rst: introductory description and LicenseHow it worksmatchms workflow
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Sources
matchms/matchms: README.rst · README.rst: introductory description and LicenseAt a glance
Inputs
MS/MS spectra in supported formats such as mzML, mzXML, MSP, MGF and JSON.
Sources
matchms/matchms: README.rst · README.rst: introductory description and LicenseOutputs
Processed spectra and pairwise similarity scores.
Sources
matchms/matchms: README.rst · README.rst: introductory description and LicenseSource reviewed · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.
No evaluations linked in this release.
How it works
How it works
matchms provides reproducible processing and comparison of tandem mass spectra. Modular import, metadata/peak processing and pairwise-similarity pipeline; classical cosine and external learned measures are distinct options. The documented inputs are MS/MS spectra in supported formats such as mzML, mzXML, MSP, MGF and JSON. The output consists of processed spectra and pairwise similarity scores.
Sources
matchms/matchms: README.rst · README.rst: introductory description and LicenseVersions and reproducibility
matchms version plus the exact filter/similarity pipeline. Spectral peaks and workflow memory requirements; no universal token context.
Sources
matchms/matchms: README.rst · README.rst: introductory description and LicenseStrengths and limitations
Strengths supported by sources
- Separates preprocessing from the similarity measure and supports custom metrics and sparse result storage.
Sources
matchms/matchms: README.rst · README.rst: introductory description and License
Limitations and conditions
- matchms is a framework, not one universal scoring model. Filter order, thresholds and selected similarity function must be recorded.
Sources
matchms/matchms: README.rst · README.rst: introductory description and License
Profile review details
Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.
Stable record: discovery-model-matchmsSpecifications
Inputs, training, access and other details
Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Model type | Mass-spectral processing and similarity softwareSourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Architecture | Modular import, metadata/peak processing and pairwise-similarity pipeline; classical cosine and external learned measures are distinct options.Sourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Inputs | MS/MS spectra in supported formats such as mzML, mzXML, MSP, MGF and JSON.Sourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Outputs | Processed spectra and pairwise similarity scores.Sourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Parameters | Inapplicable for the framework; external learned similarity plugins have separate parameters. · Not applicableSourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Known versions | matchms version plus the exact filter/similarity pipeline.Sourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Training data | No universal pretraining; selected learned plugins must provide their own training provenance.Sourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Training cutoff | Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicableSourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Context limits | Spectral peaks and workflow memory requirements; no universal token context.Sourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Weights licence | Inapplicable to core classical processing; external learned plugins have separate weight terms. · Not applicableSourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Access | Official project documentation and implementation: https://github.com/matchms/matchmsSourcesmatchms/matchms: README.rst · README.rst: introductory description and License |
| Code licence | Apache-2.0Sourcesmatchms/matchms: LICENSE · LICENSE: licence text |
| Assumptions | Not extracted or verified for this record. |
Applicable tests and references
Applicability is distinct from a completed evaluation.
- MassSpecGym · Proposed association
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
20 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | matchms/matchms: README.rst README.rst: introductory description and License Version: 066608589587c8d089afd2e8d55ceadb2766ea62 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram steps ["Imported MS/MS spectra","Metadata and peak processing","Selected similarity function","Similarity matrix"] Individual claims | matchms/matchms: README.rst README.rst: introductory description and License Version: 066608589587c8d089afd2e8d55ceadb2766ea62 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title matchms workflow Individual claims | matchms/matchms: README.rst README.rst: introductory description and License Version: 066608589587c8d089afd2e8d55ceadb2766ea62 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Model type Mass-spectral processing and similarity software Individual claims | matchms/matchms: README.rst README.rst: introductory description and License Version: 066608589587c8d089afd2e8d55ceadb2766ea62 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Architecture Modular import, metadata/peak processing and pairwise-similarity pipeline; classical cosine and external learned measures are distinct options. Individual claims | matchms/matchms: README.rst README.rst: introductory description and License Version: 066608589587c8d089afd2e8d55ceadb2766ea62 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Access Official project documentation and implementation: https://github.com/matchms/matchms Individual claims | matchms/matchms: README.rst README.rst: introductory description and License Version: 066608589587c8d089afd2e8d55ceadb2766ea62 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Code licence Apache-2.0 Individual claims | matchms/matchms: LICENSE LICENSE: licence text Version: 066608589587c8d089afd2e8d55ceadb2766ea62 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Inputs MS/MS spectra in supported formats such as mzML, mzXML, MSP, MGF and JSON. Individual claims | matchms/matchms: README.rst README.rst: introductory description and License Version: 066608589587c8d089afd2e8d55ceadb2766ea62 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Outputs Processed spectra and pairwise similarity scores. Individual claims | matchms/matchms: README.rst README.rst: introductory description and License Version: 066608589587c8d089afd2e8d55ceadb2766ea62 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Parameters Inapplicable for the framework; external learned similarity plugins have separate parameters. Individual claims | matchms/matchms: README.rst README.rst: introductory description and License Version: 066608589587c8d089afd2e8d55ceadb2766ea62 | inapplicable automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: discovered
3 source records and release history
- matchms/matchms official source · Original source · 066608589587c8d089afd2e8d55ceadb2766ea62
- matchms/matchms: README.rst · Original source · 066608589587c8d089afd2e8d55ceadb2766ea62
- matchms/matchms: LICENSE · Original source · 066608589587c8d089afd2e8d55ceadb2766ea62
Technical metadata and extraction receipts
Stable ID: discovery-model-matchms
- areas
- metabolomics
- access
- official_source_linked
- benchmark applicability
- candidate; not evidence of a reported evaluation
- candidate benchmark ids
- discovery-benchmark-massspecgym
- entity level
- method
- reported name
- matchms
- version
- Not reported
- historical missing metadata
- checkpoint: unextracted; code licence: unextracted; parameters: unextracted; training cutoff: unextracted; training data: unextracted; version: unextracted; weights licence: unextracted
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: The cited architecture/procedure describes an algorithm, representation recipe or software toolkit, rather than a single released learned biological model. Fitted models, selected reference databases and concrete runs remain separate configurations.; source ids: evidence-official-e508b40498c3a3ba53d5; source locator: README.rst: introductory description and License; ambiguities: The toolkit can build pipelines and call learned similarity models; this record identifies the toolkit rather than one fixed composed pipeline.
Related records
- applicable to: MassSpecGym
- model: Mass spectral cosine matching