Gas Chromatography–Mass Spectrometry (GC-MS) in the Plant Metabolomics Toolbox: Sample Preparation and Instrumental Analysis

Metabolomics, which is typically referred to as the post-genomic methodology addressing low-molecular-weight metabolites, became a powerful tool in post-genomic research over the last two decades. Indeed, the state-of-the-art metabolomics relies on several well-established complementary platforms-nuclear magnetic resonance (NMR) spectroscopy, liquid and gas chromatography coupled on-line with mass spectrometry (LC- and GC-MS, respectively), and capillary electrophoresis-mass spectrometry (CE-MS). Among them, GC-MS represents one of the oldest and most well-established techniques currently employed in the metabolomics of volatile compounds and non-volatiles-polar low-molecular-weight metabolites, which can be efficiently converted in volatile form by comprehensive derivatization of polar functional groups. Currently, GC-MS is established as the principal analytical method for characterizing primary plant metabolism, although other methods also contribute significantly to determining the complete metabolite profile. Therefore, here, we address the role of GC-MS in plant metabolomics and its potential for the profiling of low-molecular-weight metabolites. Further, we comprehensively review the methods of sample preparation with special emphasis on extraction and derivatization approaches, which are currently employed to improve the method performance and its metabolome coverage.