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CHAPTER 8

Pre-processing and Analysis of Metabolomics Data with XCMS/R and XCMS Online

The evaluation of metabolomics data sets involves multiples steps of data processing, statistical analysis and interpretation. XCMS is a commonly employed program for analyzing metabolomics data. It exists in two distinct variants: XCMS/R and XCMS Online. XCMS/R is a package for the statistics and graphics language R which requires manual coding, allowing for highly customized workflows. In contrast, XCMS Online provides a user-friendly web interface with modules for statistics and metabolic pathway integration. We demonstrate the step-by-step use of both platforms through the analysis of a liquid-chromatography/high-resolution mass spectrometry dataset of flowers of Arabidopsis thaliana (accessions Col and Ws). Both workflows identify common features in the twelve samples (2 accessions × 6 biological replicates). However, the general purpose of the programs is different. XCMS/R is more focused on optimizing the parameter settings and statistical testing/visualization. In contrast, XCMS Online performs most of the tasks automatically and supports the mapping of results on biochemical pathways.

Publication details

Print publication date
19 Mar 2020
Copyright year
2020
Print ISBN
978-1-78801-721-3
PDF eISBN
978-1-78801-988-0
ePub eISBN
978-1-78801-990-3