Overview
microbeMASST is a domain-specific repository search resource that contextualizes known or unknown tandem mass spectra against a curated reference collection of microbial monoculture extracts. Searches use accelerated GNPS/FASST infrastructure and organize matches in taxonomic trees, helping users ask which cultured microorganisms have produced a compound or a spectrally related molecule. Batch-search code is also available for larger analyses.
What can this tool do?
Common uses
- Associate unknown or known MS/MS spectra with potential microbial producers represented in monoculture reference data.
- Explore exact and analog spectral matches across bacterial, fungal, and archaeal taxonomy.
- Batch-query many spectra to annotate microbial context in larger untargeted datasets.
- Use taxonomic matches to prioritize cultured organisms for targeted follow-up experiments.
Scientific fit
Primary function
Reference data and database search
Other functions
Spectral processing and comparison, Data management and sharing
Analysis types
Untargeted metabolomics, Metabolite profiling
MS level
MS/MS
Acquisition
Data-dependent acquisition (DDA), Targeted MS/MS, General or unspecified acquisition
Ion mobility
Ion mobility not required
Data compatibility
Inputs
Mass spectra
Outputs
Mass spectra, Sample metadata, Human-readable report
Input formats
MGF, Universal Spectrum Identifier (USI) or peak list
Output formats
CSV or TSV
Scope and considerations
Designed for
- Microbial-origin hypothesis generation and taxonomic contextualization of MS/MS features.
Not designed for
- Assigning the producer of a molecule in a mixed community solely from a monoculture spectral match.
Important requirements
- A query MS/MS spectrum provided as a USI, library identifier, peak list, or compatible batch input.
Considerations
- A spectral occurrence in a cultured microorganism supports producer/context hypotheses but does not establish biosynthetic origin in every sample.
- Reference coverage is uneven across taxa and reflects community deposition and metadata curation.
- Inspect medium and blank controls in the source study; a cultured-organism association can include compounds from growth media.
Access and documentation
Hosted access and any account or usage requirements should be checked at the linked service. Access to a web service does not establish the license of its code or reference data.
Evidence and review
Documentation-based editorial pass on 6 September 2026: scope, interpretation limits and practical use reviewed against the linked official documentation and cited literature. Software execution, service availability and developer verification were not assessed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Zuffa S, Schmid R, Bauermeister A, et al. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol 9, 336-345 (2024). doi:10.1038/s41564-023-01575-9
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 · Entry update
Expand and document 31 metabolomics tools and resources
View change · Entry at this revision - 2026-08-24 · First committed entry
Complete GNPS SIRIUS and MZmine tool ecosystems
View change · Entry at this revision