Metabolomics in practice

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This guide addresses the challenges and critical parameters in conducting metabolomics studies, emphasizing often-overlooked aspects such as sample preparation, method selection, data recording, evaluation, and validation. It systematically covers the entire workflow, from sample preparation to data processing, providing insights and advice that help overcome obstacles to achieve high-quality data in every experiment. Drawing on over a decade of practical experience in developing, optimizing, and validating metabolomics techniques for academic and industrial research, the lessons presented are pertinent to all systems-level approaches in fields such as systems biology, biotechnology, toxicology, and pharmaceutical sciences. Key topics include sampling and preparation in microbial metabolomics, various mass spectrometry techniques (HPLC, UHPLC, GC-MS, LC-MS, CE-MS, and FTICR-MS), NMR-based analysis, the potential of microfluidics and single-cell analysis, data processing, validation, and the role of metabolomics in studying mammalian systems and plant sciences, as well as its applications in biotechnology and nutritional metabolomics.