Documented workflows
Published software workflows and their original methodological context. Check current software documentation for version-specific changes.
Repository-scale MS/MS searching with MASST
MASST turns a single tandem mass spectrum into a repository-scale query. Matches can reveal datasets, files, organisms, environments, or sample types in which the query spectrum or close analogues occur, providing a route from spectral observation to biological or environmental context.
- Choose a query MS/MS spectrum
Select a representative centroided MS/MS spectrum for the molecule or unknown feature of interest and confirm precursor and fragment information.
- Configure the MASST search
Submit the spectrum to MASST and set precursor/fragment tolerances and spectral-similarity thresholds appropriate to the data.
- Search public repositories and libraries
Search public small-molecule MS/MS data and spectral libraries for related spectra and retrieve matching datasets/files.
- Contextualize public matches
Use dataset/sample metadata, optionally through ReDU, to examine organism, biospecimen, disease, environment, or other contexts associated with matches.
- Validate the resulting hypothesis
Confirm candidate occurrence or biological associations with orthogonal evidence, targeted analyses, standards, or independent samples as appropriate.
Requirements
- A representative centroided MS/MS query spectrum with suitable precursor information.
Considerations
- Repository composition and metadata completeness bias which contexts can be discovered.
- Spectral similarity alone does not prove chemical identity; matches should be interpreted with mass accuracy, metadata, and orthogonal evidence.
Wang M, Jarmusch AK, Vargas F, et al. Mass spectrometry searches using MASST. Nature Biotechnology 38, 23–26 (2020).
Read the source methodOverview
MASST (Mass Spectrometry Search Tool) searches a query tandem mass spectrum against public metabolomics data and spectral libraries to locate matching or related spectra and the files in which they occur. The current GNPS2 implementation uses accelerated indexing and supports current pan-repository metabolomics indexes, programmatic API access, command-line access, and GNPS2 workflow execution.
Also known as: Mass Spectrometry Search Tool
What can this tool do?
Common uses
- Search a query MS/MS spectrum across public metabolomics datasets and spectral libraries.
- Identify datasets, files, or sample contexts in which a molecule or close spectral analogue may occur.
- Use repository-scale matches as a starting point for biological, environmental, natural-product, or reverse-metabolomics hypotheses.
- Locate public datasets containing spectra similar to an unknown feature for follow-up reanalysis.
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
- Repository-scale contextualization of individual MS/MS spectra.
Not designed for
- Quantitative comparison across unrelated public studies or proof of biosynthetic origin.
Important requirements
- A centroided query MS/MS spectrum with precursor information.
Considerations
- Search tolerances, cosine/similarity thresholds, and repository composition affect which matches are returned.
- A spectral match indicates MS/MS similarity and possible occurrence; it is not by itself definitive structural confirmation.
- The current GNPS2 implementation is substantially faster than the original MASST workflow and also supports programmatic access described in the current documentation.
- Current pan-repository indexes extend beyond the original GNPS/MassIVE-only implementation; the exact indexed collections can change over time.
- Retain the query spectrum identifier and inspect matched files and their study metadata before drawing an occurrence conclusion.
Education
Learn this tool
External tutorials and workshops collected by Navigator. Entries marked Needs review have not been checked end to end.
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.
From tool to strategy
Strategies using MASST
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.
- Wang M, Jarmusch AK, Vargas F, et al. Mass spectrometry searches using MASST. Nat Biotechnol 38, 23-26 (2020). doi:10.1038/s41587-019-0375-9
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 · Entry update
Complete GNPS SIRIUS and MZmine tool ecosystems
View change · Entry at this revision - 2026-08-24 · Entry update
Add GNPS, SIRIUS, and MZmine content batch
View change · Entry at this revision - 2026-08-24 · Entry update
Apply v5.2 pre-population hardening
View change · Entry at this revision - 2026-08-21 · First committed entry
Add files via upload
View change · Entry at this revision