Methods of Extraction, Detection, and Identification of Different Metabolites—A Metabolomics Approach

Metabolic dynamics in attack and defense mechanisms are fascinating topics that illustrate the complex ways organisms adapt to their environments. Attack mechanisms involve several functions, including energy production and metabolic adaptation, where some organisms change their appearance or behavior to balance into their environment. Defense mechanisms involve stress response, immune system activation, repair, and recovery. This chapter provides an overview of the methods applied in modern metabolomics, including single-cell metabolomics and targeted/untargeted approaches, emphasizing how metabolite production rapidly shifts in response to environmental and cellular changes. To effectively monitor these spontaneous effects, it is essential to conduct metabolomics studies with a carefully controlled experimental design. This includes meticulous sample collection, efficient metabolite extraction, and optimization of parameters for the most relevant analytical platform. This chapter outlines the most relevant and commonly used methods for metabolite extraction, aiming to maximize the number of metabolites recovered. This is followed by a summary of the advantages and limitations of the most frequently employed analytical tools, with a particular focus on nuclear magnetic resonance (NMR) and various types of mass spectrometry (MS). Finally, we emphasize the importance of integrating different omics sciences to achieve a comprehensive understanding of biological systems.