Overview
ModiFinder compares tandem mass spectra from structurally related known and unknown molecules, focusing on shifted fragment peaks that can indicate which part of the known structure contains a modification. It aggregates fragment-level evidence into atom-level scores that highlight likely modification sites. Current implementations include an interactive GNPS2 web interface, high-throughput workflows, and programmatic components.
What can this tool do?
Common uses
- Localize likely atom-level positions of a structural modification between a known molecule and a related unknown spectrum.
- Interpret analog-library or molecular-network neighbors with a known reference structure.
- Prioritize structural hypotheses for modified natural products, metabolites, or transformation products.
- Prioritize likely modification regions on a known analog for further structural investigation.
Scientific fit
Primary function
Metabolite annotation and identification
Other functions
Spectral processing and comparison
Analysis types
Untargeted metabolomics, Metabolite profiling
MS level
MS/MS
Acquisition
Data-dependent acquisition (DDA), Targeted MS/MS
Ion mobility
Ion mobility not required
Data compatibility
Inputs
Mass spectra, Molecular structures
Outputs
Molecular structures, Human-readable report
Input formats
SMILES or InChI
Output formats
JSON
Scope and considerations
Designed for
- MS/MS pairs representing structurally related molecules where one structure is known and the other differs by a modification.
Not designed for
- Complete de novo elucidation of an unrelated molecule or confident stereochemical assignment.
Important requirements
- Paired MS/MS spectra and a known chemical structure for the reference molecule.
Considerations
- Localization is computational evidence and does not establish a complete unknown structure or stereochemistry.
- Performance depends on informative shared/shifted fragments and spectral quality.
- Inspect whether the known and unknown spectra are compatible in polarity and fragmentation conditions before interpreting atom-level scores.
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.
- Shahneh MRZ, Strobel M, Vitale GA, et al. ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization. J Am Soc Mass Spectrom 35, 2564-2578 (2024). doi:10.1021/jasms.4c00061
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