Retrieve and Use Mass Spectrometry Data from MetaboLights (original) (raw)

Introduction

The Spectra package provides a central infrastructure for the handling of Mass Spectrometry (MS) data in Bioconductor. The package supports interchangeable use of different backends to import and represent MS data from a variety of sources and data formats. The MsBackendMetaboLights package allows to retrieve MS data files directly from theMetaboLights repository. MetaboLights is one of the main public repositories for deposition of metabolomics experiments including (raw) MS and/or NMR data files and the related experimental and analytical results. The MsBackendMetaboLights package downloads and locally caches MS data files for a MetaboLights data set and enables further analyses of this data directly in R.

Installation

The package can be installed from within R with the commands below:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RforMassSpectrometry/MsBackendMetaboLights")

Session information

sessionInfo()
## R version 4.5.0 RC (2025-04-04 r88126)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] MsBackendMetaboLights_1.2.0 Spectra_1.18.0             
## [3] BiocParallel_1.42.0         S4Vectors_0.46.0           
## [5] BiocGenerics_0.54.0         generics_0.1.3             
## [7] BiocStyle_2.36.0           
## 
## loaded via a namespace (and not attached):
##  [1] sass_0.4.10            MsCoreUtils_1.20.0     RSQLite_2.3.9         
##  [4] hms_1.1.3              digest_0.6.37          magrittr_2.0.3        
##  [7] evaluate_1.0.3         bookdown_0.43          fastmap_1.2.0         
## [10] blob_1.2.4             jsonlite_2.0.0         progress_1.2.3        
## [13] ProtGenerics_1.40.0    mzR_2.42.0             DBI_1.2.3             
## [16] BiocManager_1.30.25    httr_1.4.7             purrr_1.0.4           
## [19] codetools_0.2-20       jquerylib_0.1.4        cli_3.6.4             
## [22] crayon_1.5.3           rlang_1.1.6            dbplyr_2.5.0          
## [25] Biobase_2.68.0         bit64_4.6.0-1          withr_3.0.2           
## [28] cachem_1.1.0           yaml_2.3.10            tools_4.5.0           
## [31] parallel_4.5.0         memoise_2.0.1          dplyr_1.1.4           
## [34] ncdf4_1.24             filelock_1.0.3         curl_6.2.2            
## [37] vctrs_0.6.5            R6_2.6.1               BiocFileCache_2.16.0  
## [40] lifecycle_1.0.4        fs_1.6.6               IRanges_2.42.0        
## [43] bit_4.6.0              clue_0.3-66            MASS_7.3-65           
## [46] cluster_2.1.8.1        pkgconfig_2.0.3        bslib_0.9.0           
## [49] pillar_1.10.2          Rcpp_1.0.14            glue_1.8.0            
## [52] xfun_0.52              tibble_3.2.1           tidyselect_1.2.1      
## [55] knitr_1.50             htmltools_0.5.8.1      rmarkdown_2.29        
## [58] compiler_4.5.0         prettyunits_1.2.0      MetaboCoreUtils_1.16.0