Editorial additions pending. This submission has been accepted into the catalogue. Detailed metadata and editorial review may follow in later updates. Missing information does not mean a capability is unsupported.
Overview
An R package for Taxonomically Informed Metabolite Annotation. The workflow combines processed feature information and fragmentation spectra with organism metadata and structure-organism evidence. External annotations and custom libraries can supplement the workflow; resulting candidates require interpretation rather than being treated as confirmed identities.
What can this tool do?
Common uses
- Prioritize candidate annotations using organism taxonomy alongside MS/MS evidence.
- Combine compatible SIRIUS or GNPS annotations with a processed feature dataset.
Scientific fit
Primary function
Metabolite annotation and identification
Data compatibility
Inputs
Feature or peak table, Mass spectra, Sample metadata
Outputs
Compound list or annotations, Human-readable report
Input formats
CSV or TSV, MGF
Output formats
Other, Workflow files in .tima/data; exact tables depend on the selected workflow.
Scope and considerations
Designed for
- Downstream annotation of processed LC-MS/MS features with organism context.
Not designed for
- Replacing raw-data feature extraction or confirming chemical identity from taxonomy alone.
Important requirements
- Feature table with feature IDs, retention time, m/z and sample intensities; MGF spectra; sample-to-organism metadata when multiple organisms are analyzed.
Considerations
- Taxonomic context and reference-library coverage affect candidate prioritization.
- External annotations and custom libraries are optional inputs; check documented version and column conventions.
Access and documentation
Install through the documented R-universe repository; the documentation also describes a local Shiny interface and a Docker distribution. Consult the current setup instructions and terms for external resources.
Evidence and review
Draft editorial additions based on the official tima documentation. Original submitter attribution is retained. Software execution was not tested.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Rutz A, Dounoue-Kubo M, Ollivier S, et al. Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation. Frontiers in Plant Science 10:1329 (2019). doi:10.3389/fpls.2019.01329
Foundational method cited by the official tima documentation; it does not describe every later R-package update.
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
Original submission and discussion
- 2026-09-15 · Entry update
Add foundational TIMA method citation
View change · Entry at this revision - 2026-09-15 · Entry update
Draft timaR scope and input documentation
View change · Entry at this revision - 2026-09-14 · First committed entry
Add draft tool entry for timaR
View change · Entry at this revision