• 2021-03-25: provide a description on the good practice to define a phenodata/data files table containing also the names of the raw data files along with all sample information.
• 2020-06-15: use new more data-driven gap-filling approach: fillChromPeaks with ChromPeakAreaParam.
• 2020-02-04: add refineChromPeaks to allow refinement of peak detection results. Also, add the quantify method to extract the preprocessing results as SummarizedExperiment. Both required xcms version >= 2.9.2.
• 2019-09-29: More updates and expansion of descriptions.
• 2019-06-20: Updated to match xcms functionality available with Bioconductor version 3.9.

LC-MS data pre-processing with xcms

This 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. The present workshop represents an updated version of the workshop given at the Metabolomics Society conference 2018 in Seattle (http://metabolomics2018.org).

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 >= 3.6.0 and recent versions of the MSnbase and xcms (version >= 3.3.1 is needed) packages. The code below installs all packages for the analysis.

install("BiocManager")
BiocManager::install(c("xcms",
                       "MSnbase",
                       "msdata",
                       "magrittr",
                       "devtools",
                       "BiocParallel"))

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. (outdated!)

• 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). (outdated!)