Gas chromatography-mass spectrometry (GC-MS) in the plant metabolomics toolbox. Part 2: Analysis of polar low molecular weight metabolites

Decades ago, the introduction of GC-MS marked a significant advancement in primary plant metabolites studies. Here, in Part 2 of the review, we will delve into critical aspects of the workflow, spanning the selection of an analytical platform, sample preparation, analytical acquisition, and data processing and interpretation. The exceptional separation capabilities of GC, characterized by remarkable chromatographic resolution, rendered it ideal for analysis of the complex plant metabolome, including the separation of isomeric compounds. The diversity in analytical platforms allows the investigation of plant metabolomes using targeted and non-targeted approaches. GC-MS, equipped with efficient extraction methods and reliable derivatization protocols for semi- and non-volatile compounds, enables qualitative and quantitative analysis of these molecules. The stability of derivatives forms the foundation for the robustness and reproducibility of GC-MS methods, and their mass spectra provide characteristic fragments for confident identification and sensitive quantification of individual metabolites. Ongoing advancements in all stages have elevated GC-MS-based metabolomics to an indispensable tool for unraveling the intricacies of plant metabolism. However, it is imperative to conduct careful validations and address potential artifacts at each step, especially derivatization, and further investigations of the aroused problems are needed.