Overview
RHermes implements the HERMES formula-oriented workflow for LC-MS characterization and targeted follow-up. It finds formula/adduct signals in MS1 data, identifies signals of interest and generates acquisition inclusion lists for subsequent MS2 analysis.
What can this tool do?
Common uses
- An R package for broad-scoped targeted and semi-targeted LC-MS metabolomics analysis designed to deeply characterize biological and environmental samples.
Scientific fit
Primary function
Metabolite annotation and identification
Other functions
Data acquisition and instrument control, Spectral processing and comparison
Analysis types
Targeted metabolomics, Semi-targeted metabolomics
Data compatibility
Inputs
Raw instrument data, Compound list or annotations
Outputs
Feature or peak table, Compound list or annotations
Input formats
mzML LC-MS data and R molecular-formula/adduct databases
Output formats
R signal/annotation objects, inclusion lists and interactive plots
Scope and considerations
Designed for
- An R package for broad-scoped targeted and semi-targeted LC-MS metabolomics analysis designed to deeply characterize biological and environmental samples.
Not designed for
- Confirming exact structures from an MS1 formula match or automatically executing the follow-up experiment.
Important requirements
- R/Bioconductor dependencies, centroided compatible LC-MS data, a formula/adduct database and suitable processing parameters; inclusion-list follow-up requires access to a compatible MS acquisition method.
Considerations
- Formula-database selection constrains coverage and ambiguity. Inspect signals and MS2 evidence; distinguish inclusion-list generation from quantitative calibration or complete structural identification.
Access and documentation
GPL-3.0 source distribution. External datasets, dependent packages and any hosted routes retain their own terms; software operation was not tested.
License: GPL-3.0
Evidence and review
Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch2.md.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- HERMES: a molecular-formula-oriented method to target the metabolome. Nature Methods (2021). doi:10.1038/s41592-021-01307-z
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-27 · First committed entry
Add 24 reviewed Enveda tools in a separate second batch
View change · Entry at this revision