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