This R package is designed to perform metabolite annotation of features from LC-MS All-ion fragmentation (AIF) datasets, using ion fragment databases. It requires raw LC-MS AIF chromatograms acquired/transformed in centroid mode or processed data outputs obtained using RAMClustR.

For more details on how the software works, further testing and performance please read the full publication in Analytical Chemistry journal: https://pubs.acs.org/doi/10.1021/acs.analchem.1c03032

To install via Github, run the following code in R console:

install.packages("devtools", repos = "http://cran.us.r-project.org", dependencies = TRUE)

library(devtools)

install_github("gggraca/MetaboAnnotatoR", dependencies = TRUE)

In some environments, some errors might occur durring installation due to some of the package dependencies, being the most common "mzR has been built against a different Rcpp version". This issue can be easily fixed as suggested here. The following environment variable can be changed before installing using install_github:

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")

An example of usage using one LC-MS AIF chromatogram is provided in the introductory vignette. An illustration of the generation of Metabolite database records for MetaboAnnotatoR from text files is given here. MS/MS spectra can also be imported from .msp files as exemplified here.