GC-MS-based metabolomics – Part 1 Gas chromatography-mass spectrometry (GC-MS) and its place in the plant metabolomics toolbox

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 complemen-tary platforms – nuclear magnetic resonance (NMR) spectroscopy, liquid and gas chromatog-raphy coupled on-line to mass spectrometry (LC- and GC-MS, respectively), capillary electropho-resis-mass spectrometry (CE-MS). Among them, GC-MS represents one of the oldest and most well-established techniques currently employed in 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 recog-nized as the core analytical technique in characterization of plant primary metabolome, although the other methods contribute to the whole metabolite profile essentially. Therefore, here we ad-dress the role of GC-MS in plant metabolomics and its potential for profiling of low molecular weight metabolites. Further, we comprehensively review the methods of sample preparation with a special emphasis on the extraction and derivatization approaches, which are currently employed to improve the method performance and its metabolome coverage.