ASICS User's Guide
In ASICS: Automatic Statistical Identification in Complex Spectra

This user's guide provides an overview of the package ASICS. ASICS is a fully automated procedure to identify and quantify metabolites in $^1$H NMR spectra of biological mixtures. It will enable empowering NMR-based metabolomics by quickly and accurately helping experts to obtain metabolic profiles.

library(ASICS)

Library of pure NMR metabolite spectra

A dataset with spectra of 175 pure metabolites is available in the package. It is automatically loaded at package start and available metabolites are displayed with:

head(pure_library$name, n = 20)

Identification and quantification of metabolites on one Bruker files with ASICS

The identification and the quantification are carried out using only one function ASICS directly from raw files (Bruker files):

# part of the spectrum to exclude (water)
to_exclude <- matrix(c(4.5,5.1,5.5,6.5), ncol = 2, byrow = TRUE)
result <- ASICS(path = system.file("extdata", "example_spectra",
                                   "AG_faq_Beck01", package = "ASICS"),
                exclusion.areas = to_exclude)
result

The quality of the results can be assessed by stacking the original and the recomposed spectra on one plot. A pure metabolite spectrum can also be added for visual comparison.

plot(result, xmin = 1, xmax = 1.5, ymax = 10, add_metab = "Lactate")

Relative concentrations of identified metabolites are saved in:

head(present_metabolites(result), 10)

Identification and quantification of metabolites on multiple Bruker files with ASICS

Usually, many spectra are available for one experience. With the ASICS_multiFiles function, quantification is launched on all spectra present in the specified folder (name.dir). The arguments of this function are the same than for ASICS function with the addition of ncores for parallel computation (if wanted).

res_multi <- ASICS_multiFiles(name.dir = system.file("extdata",
                                                     "example_spectra",
                                                     package = "ASICS"),
                              exclusion.areas = to_exclude, ncores = 4)

For further analyses, it is possible to extract concentrations of all spectra in a data-frame:

quantification <- extract_concentrations(res_multi)
head(quantification)

Reference

Tardivel P., Canlet C., Lefort G., Tremblay-Franco M., Debrauwer L., Concordet D., Servien R. (2017). ASICS: an automatic method for identification and quantification of metabolites in complex 1D 1H NMR spectra. Metabolomics, 13(10): 109. https://doi.org/10.1007/s11306-017-1244-5