RHermes
is a broad-scoped targeted metabolomics package designed to
analyse LC-MS and LC-MS/MS data to identify compounds in biological or
environmental samples.
The RHermes
workflow works with both Orbitrap and qTOF instrument data
and comes with an interactive GUI to process and visualize the data.
Whether it’s natural products, biomedical or enviormental samples,
RHermes
can help you improve your matrix characterization. By
selecting an appropiate formula database, you can focus on just the
compounds you are interested in and improve your coverage.
With RHermes
you can see the metabolites in your data and much
more. There’s no need to manually calculate m/z’s to plot the XIC of
different adducts: with the GUI you are just one click away from a
metabolite-centric plot.
For more info, check out the documentation here and our article here.
You can download the development version from GitHub with:
if(!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("RogerGinBer/RHermes")
Once installed, you can use RHermes
programmatically like this:
library(RHermes)
#Generate a Exp object
example <- RHermesExp()
#Set your formula and adduct database
example <- setDB(example, db = "hmdb")
#Process your MS1 files
example <- processMS1(example,
system.file("extdata", "MS1TestData.mzML",
package = "RHermes"))
#Generate SOIs
example <- findSOI(example, getSOIpar(), 1)
#Generate an IL (Inclusion List)
example <- generateIL(example, 1, ILParam())
With the generated inclusion list, you can export it and run a Parallel Reaction Monitoring (PRM) MS2 experiment to reveal coeluting isomers or use any other MS2 mode you see fit.
Or start the interactive GUI typing:
RHermesGUI()
In the GUI you will find abundant help pages to guide you along the processing 👍
Please check the User Guide vignette for more detailed info and real examples.
We have compiled some molecular formula open databases ready to be used with RHermes for all sorts of samples: HMDB, ChEBI, NORMAN, LipidMaps, COCONUT, etc. They are freely available at this Zenodo repository.
Suggestions and bug reports are more than welcome at: https://github.com/RogerGinBer/RHermes/issues
Please cite this package as:
Giné, R., Capellades, J., Badia, J.M. et al. HERMES: a molecular-formula-oriented method to target the metabolome. Nat Methods 18, 1370–1376 (2021). https://doi.org/10.1038/s41592-021-01307-z