ASICS

Gaëlle Lefort

2017-10-06

This vignette 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 metabolites 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)
##  [1] "1-Methyl-L-Histidine"           "1-Methylhydantoin"             
##  [3] "1,3-Diaminopropane"             "1,6-Anhydro-Beta-D-Glucose"    
##  [5] "2-AminoAdipicAcid"              "2-Aminobutyric Acid"           
##  [7] "2-deoxyadenosine"               "2-deoxycytidine"               
##  [9] "2-deoxyguanosine"               "2-deoxyguanosinemonophosphate" 
## [11] "2-HydroxyphenylAceticAcid"      "2-MethylglutaricAcid"          
## [13] "2-Oxobutyrate"                  "2-oxoglutarate"                
## [15] "2-PicolinicAcid"                "2,3-Pyridine dicarboxylic Acid"
## [17] "3-hydroxybutyrate"              "3-HydroxyphenylAceticAcid"     
## [19] "3-Methyl-L-Histidine"           "3-MethyladipicAcid"

Identification and quantification of metabolites on one or more 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
## Number of identified metabolites: 40 
## 
## Most concentrated metabolites: 
##                   Name Relative_Concentration
## 1            D-Glucose            0.025222765
## 2              Lactate            0.012571970
## 3       L-GlutamicAcid            0.008477737
## 4 DehydroAscorbic Acid            0.006028531
## 5              Taurine            0.005801350
## 6         Myo-Inositol            0.005675374

The quality of the results can be assessed by stacking the original and the recomposed spectrum 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:

present_metabolites(result)
##                         Name Relative_Concentration
## 1                  D-Glucose           0.0252227652
## 2                    Lactate           0.0125719704
## 3             L-GlutamicAcid           0.0084777365
## 4       DehydroAscorbic Acid           0.0060285310
## 5                    Taurine           0.0058013499
## 6               Myo-Inositol           0.0056753742
## 7               GlycericAcid           0.0053064883
## 8           D-GlucuronicAcid           0.0044623605
## 9                L-Threonine           0.0042456411
## 10                 D-Maltose           0.0040387420
## 11                 D-Mannose           0.0035036763
## 12     D-Glucose-6-Phosphate           0.0033814590
## 13                  Glycerol           0.0032563733
## 14                   Lactose           0.0031045187
## 15                 L-Proline           0.0030488700
## 16 trans-4-Hydroxy-L-Proline           0.0030219995
## 17                 Succinate           0.0027844317
## 18           CholineChloride           0.0027185555
## 19               L-Carnitine           0.0026062322
## 20                 L-Alanine           0.0025850374
## 21                L-Arabitol           0.0025712611
## 22                   Xylitol           0.0016947488
## 23          7-Methylxanthine           0.0016411650
## 24                  L-Serine           0.0012552302
## 25            CitraconicAcid           0.0011680861
## 26          PyroglutamicAcid           0.0010357808
## 27                 Adenosine           0.0009325115
## 28              Beta-Alanine           0.0009293748
## 29       2-Aminobutyric Acid           0.0007289741
## 30                   Betaine           0.0007006266
## 31                   Inosine           0.0006998606
## 32                      UDPG           0.0006708075
## 33                Cadaverine           0.0006324015
## 34    L-Glutathione-oxidized           0.0006271095
## 35                 L-Leucine           0.0005506930
## 36     Glycerophosphocholine           0.0005482748
## 37                 L-Cystine           0.0004585576
## 38            Phosphocholine           0.0004265864
## 39      O-Acetyl-L-Carnitine           0.0002676703
## 40           PantothenicAcid           0.0002230727

User’s guide

More details on ASICS functionnalities can be obtain in the user’s guide :

ASICSUsersGuide()

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

Session information

This vignette has been created with the following system configuration

sessionInfo()
## R version 3.4.1 (2017-06-30)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.1 LTS
## 
## Matrix products: default
## BLAS: /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
## 
## locale:
##  [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
##  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
##  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ASICS_1.0.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.13       knitr_1.17         magrittr_1.5      
##  [4] munsell_0.4.3      colorspace_1.3-2   lattice_0.20-35   
##  [7] rlang_0.1.2        quadprog_1.5-5     stringr_1.2.0     
## [10] plyr_1.8.4         tools_3.4.1        grid_3.4.1        
## [13] gtable_0.2.0       htmltools_0.3.6    yaml_2.1.14       
## [16] lazyeval_0.2.0     rprojroot_1.2      digest_0.6.12     
## [19] tibble_1.3.4       ggplot2_2.2.1.9000 evaluate_0.10.1   
## [22] rmarkdown_1.6      labeling_0.3       stringi_1.1.5     
## [25] compiler_3.4.1     scales_0.5.0.9000  backports_1.1.1   
## [28] zoo_1.8-0