Overview
MSnLib combines reference-compound measurements, curated metadata and mzmine processing to generate spectral libraries organized as fragmentation trees. The 2025 publication describes more than two million spectra from 30,008 compounds; these are publication-version figures, not a live count.
What can this tool do?
Common uses
- Use reference fragmentation spectra for annotation or method development.
- Generate libraries from measured reference compounds using mzmine.
Scientific fit
Primary function
Reference data and database search
Other functions
Spectral processing and comparison
Data compatibility
Inputs
Mass spectra, Compound list or annotations
Outputs
Spectral library
Input formats
Reference measurements and curated compound metadata
Output formats
Release-specific spectral-library files and multistage fragmentation trees
Scope and considerations
Designed for
- Reference spectral resources and reproducible library generation.
Not designed for
- A standalone end-to-end statistical analysis of biological cohorts.
Important requirements
- Compatible library-search software for using released spectra; mzmine and suitable measurements for generation.
Considerations
- Match polarity, fragmentation stage and acquisition conditions when interpreting spectral similarity.
- Confirm library-release formats and licensing before reuse.
Access and documentation
Generation uses open-source mzmine. MERLIN metadata and acquisition resources carry an MIT license; consult the selected library release for data reuse terms.
Evidence and review
Primary publication identity and MERLIN MSnLib documentation verified. Desktop interface refers to mzmine generation, not a separate MSnLib application. Downloads and generation were not independently executed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Brungs C, Schmid R, Heuckeroth S, et al. MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries. Nature Methods 22, 2028-2031 (2025). doi:10.1038/s41592-025-02813-0
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-28 · First committed entry
Add MALDI-FISH and bioactivity fractionation strategies plus MSnLib (#67)
View change · Entry at this revision