Overview
matchms provides composable processing filters and similarity functions for spectral collections, supporting reproducible comparison and downstream library-search workflows.
What can this tool do?
Common uses
- Harmonize spectral metadata before comparison.
- Calculate similarity scores between query and reference spectra.
Scientific fit
Primary function
Spectral processing and comparison
Data compatibility
Inputs
Mass spectra, Spectral library
Outputs
Mass spectra, Statistical results
Input formats
MGF, MSP
Output formats
Other, Spectra, similarity scores and pipeline reports
Scope and considerations
Designed for
- Harmonize spectral metadata before comparison.
Not designed for
- Equating a similarity score with an independently confirmed structure.
Important requirements
- Python, supported spectral data and an explicitly configured preprocessing pipeline.
Considerations
- Precursor metadata, mass tolerance and peak filtering influence scores; retain the settings used for comparisons.
Access and documentation
Open-source software; use the official installation, license and citation guidance for the selected release.
Evidence and review
Documentation-based editorial review on 7 September 2026. Scope and limitations summarize the linked official sources; software execution and developer verification were not assessed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Huber, Verhoeven, Meijer, et al. matchms - processing and similarity evaluation of mass spectrometry data. Journal of Open Source Software 5, 2411 (2020). doi:10.21105/joss.02411
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-08 · Entry update
Audit core publications across existing tools
View change · Entry at this revision - 2026-09-07 · First committed entry
Add 50 documented metabolomics resources
View change · Entry at this revision