Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide
CHAPTER 8: Pre-processing and Analysis of Metabolomics Data with XCMS/R and XCMS Online1
Published:16 Mar 2020
Laila Pamela Partida-Martínez, Robert Winkler, 2020. "Pre-processing and Analysis of Metabolomics Data with XCMS/R and XCMS Online1", Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide, Robert Winkler
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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.