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metabolomics2018

Workshop material for the xcms (version >= 3) workshop at the Metabolomics Society conference 2018 in Seattle (http://metabolomics2018.org). The workshop provides an overview of recent developments in Bioconductor to work with mass spectrometry (MSnbase) and specifically LC-MS data (xcms) and walks through the preprocessing of a toy data set emphasizing on selection of data-dependent settings for the individual pre-processing steps.

Covered topics are:

  • Data import and representation.
  • Accessing, subsetting and visualizing data.
  • Centroiding of profile MS data.
  • Chromatographic peak detection.
  • Empirically determine appropriate settings for the analyzed data set.
  • Evaluation of identified peaks.
  • Alignment (retention time correction).
  • Correspondence (grouping of chromatographic peaks across samples).

The full R code of all examples along with comprehensive descriptions is provided in the xcms-preprocessing.Rmd file. This file can be opened with e.g. RStudio which allows execution of the individual R commands (see section below for additionally required R packages). The R command rmarkdown::render("xcms-preprocessing.Rmd") would generate the html file xcms-preprocessing.html.

For those that can not attend the workshop: you can have a look at the presentation online xcms-preprocessing-ioslides.html.

Prerequisites

The analysis in this document requires an R version >= 3.5.0 and recent versions of the MSnbase and xcms (version >= 3.3.1 is needed) packages. The code below installs all packages for the analysis.

source("https://bioconductor.org/biocLite.R")
biocLite(c("xcms", "MSnbase", "doParallel", "msdata", "magrittr", "devtools"))
## Need xcms version > 3.3.1
if (packageVersion("xcms") < "3.3.1")
    devtools::install_github("sneumann/xcms", ref = "master")

Files

  • xcms-preprocessing.Rmd: file containing the complete R code and expanded description. Can be converted to a html file with rmarkdown::render("xcms-preprocessing.Rmd").

  • xcms-preprocessing-ioslides.Rmd: R markdown file that is rendered (with rmarkdown::render("xcms-preprocessing-ioslides.Rmd") into the html (ioslides-based) presentation for the conference. This file contains most of the R commands from xcms-preprocessing.Rmd but only few descriptions.

  • xcms-preprocessing-bullets.Rmd: file with complete R code but strongly reduced descriptive content (in form of bullet points). This file is thought to be used for an interactive presentation with RStudio (i.e. live execution of commands).