Data Analysis Strategies in CE–MS for Metabolomics

Abstract

This chapter covers all the steps of capillary electrophoresis (CE)–mass spectrometry (MS) data treatment with a focus on untargeted metabolomics, from both qualitative and quantitative points of view, to extract the most relevant biological information from the samples. Untargeted CE–MS acquisitions produce massive datasets containing three-dimensional matrices for each sample. Data-processing pipelines involve a number of steps aiming to convert such raw data into a single table containing peak area values for each feature in each analysis. Despite its ability to separate polar metabolites and deal with minute amounts of sample, the adoption of CE–MS in metabolomics remains fairly limited. One of the major reasons for this is the difficulty of dealing with the variability of compound migration time, which hampers its straightforward use for annotation and comparison purposes.

Authors 4

1. Nicolas Drouin Aachen Metabolomics and Analytics Centre Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Leiden University, Metabolomics and Analytics Centre, Leiden Academic Centre for Drug research, Einsteinweg 55, 2333 CC, Leiden, the Netherlands

2. Julien Boccard

   University of Geneva · Swiss Centre for Applied Human Toxicology

   Affiliation as printed

   Swiss Centre for Applied Human Toxicology, Missionsstrasse 64, 4055, Basel, Switzerland

   University of Geneva, Institute of Pharmaceutical Sciences of Western Switzerland, Analytical Sciences, Rue Michel-Servet 1, Geneva, 1211 Geneva 4 Switzerland

   University of Geneva, School of Pharmaceutical Sciences, Rue Michel-Servet 1, Geneva, 1211 Geneva 4 Switzerland

3. Serge L. Rudaz

   University of Geneva · Swiss Centre for Applied Human Toxicology

   Affiliation as printed

   Swiss Centre for Applied Human Toxicology, Missionsstrasse 64, 4055, Basel, Switzerland

   University of Geneva, Institute of Pharmaceutical Sciences of Western Switzerland, Analytical Sciences, Rue Michel-Servet 1, Geneva, 1211 Geneva 4 Switzerland

   University of Geneva, School of Pharmaceutical Sciences, Rue Michel-Servet 1, Geneva, 1211 Geneva 4 Switzerland

4. Víctor González‐Ruiz

   University of Geneva · Swiss Centre for Applied Human Toxicology

   Affiliation as printed

   Swiss Centre for Applied Human Toxicology, Missionsstrasse 64, 4055, Basel, Switzerland

   University of Geneva, Institute of Pharmaceutical Sciences of Western Switzerland, Analytical Sciences, Rue Michel-Servet 1, Geneva, 1211 Geneva 4 Switzerland

   University of Geneva, School of Pharmaceutical Sciences, Rue Michel-Servet 1, Geneva, 1211 Geneva 4 Switzerland