CHAPTER 3: Metabolomics
Published:16 Mar 2020
D. S. Wishart, J. Godzien, A. Gil-de-la-Fuente, R. Mandal, R. Rajabzadeh, H. Pirimoghadam, ... C. Barbas, in Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide, ed. R. Winkler, The Royal Society of Chemistry, 2020, pp. 41-95.
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Metabolomics is a rapidly growing area of omics science that employs analytical chemistry techniques such as liquid chromatography (LC), gas chromatography (GC), capillary electrophoresis (CE), mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy to identify large numbers of metabolites from cells, tissues or biofluids. The key to the success of metabolomics has been the development of specialized data processing software and large spectral databases to help researchers comprehensively identify and quantify metabolites. This chapter provides a brief introduction to metabolomics along with a general overview of the different ‘flavours’ of metabolomics, including targeted and untargeted metabolomics. It also describes standard workflows, software, data processing and database needs for each of the main platforms commonly used in modern MS-based metabolomics, including liquid chromatography mass spectrometry (LC-MS), gas chromatography mass spectrometry (GC-MS), capillary electrophoresis mass spectrometry (CE-MS) and lipidomics (the metabolomic study of lipids). In all cases the focus of the chapter is on describing free, open-source or open-access software and databases.