Metabolic Profiling of Plants by GC-MS

Different genetic, physiological, and environmental conditions are likely to alter the metabolic composition of plants. Metabolomics aims to provide a comprehensive and unbiased analysis of all metabolites with a low molecular weight present in a biological sample and is therefore a very powerful tool for characterizing the plant metabolome. These studies are of great interest to plant scientists, since a systematic analysis of metabolites and metabolic pathways helps to elucidate how plants respond to genetic and environmental changes. Because of the diversity of structural classes of metabolites, ranging from primary metabolites to very complex secondary metabolites, there is no single methodology that can measure the complete metabolome in one step. By employing a combination of different instrument platforms and techniques, the differences in the metabolite profiles can be revealed. In particular, gas chromatography-mass spectrometry (GC-MS), one of the oldest hybrid techniques in analytical chemistry, is considered to be one of the most developed, robust, and highly sensitive instrument platforms for metabolite analysis. GC-MS-based methodologies were among the first to be applied for metabolite profiling and target analysis, and offer established protocols for machine setup, data mining, and interpretation as well as commercially and publicly available EI ionization spectral libraries. This chapter first provides an overview of plant metabolite analysis, pointing out the advantages and limitations of GC-MS. Subsequently, the most relevant sections of the experimental workflow for plant metabolic profiling using GC-MS, including state-of-the-art sample handling, GC-MS instrument setup, and data processing, are described in detail. Finally, the chapter turns to the implementation of GC-MS in plant metabolomics, portraying various examples of applications and new developments of this technology.