README.md

In RogerGinBer/RHermes: Improving metabolome characterization using molecular formula databases

RHermes

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.

Installation

You can download the development version from GitHub with:

if(!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("RogerGinBer/RHermes")

Analyzing LC-MS data with 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 :+1:

Please check the User Guide vignette for more detailed info and real examples.

Database availability

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.

Bug reporting

Suggestions and bug reports are more than welcome at: https://github.com/RogerGinBer/RHermes/issues

Citation

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

RogerGinBer/RHermes documentation built on Nov. 6, 2022, 11:34 a.m.