Metabolomics data pre-processing using xcms

Workflow illustrating mass spectrometry (MS) data handling and access using Bioconductor’s MSnbase package (Gatto and Lilley 2012) and preprocessing of an (untargeted) LC-MS toy data set using the xcms package (Smith et al. 2006). The preprocessing comprises chromatographic peak detection, sample alignment and peak correspondence. Particular emphasis is given on defining data-set dependent values for the most important settings of popular preprocessing methods.

The source code of the workflow is available on github: https://github.com/jorainer/metabolomics2018