Metabolomics analysis insight into medicinal plant science

The plant-based metabolomics studies are increasing rapidly to identify new active compounds, determine the vegetation period, investigate adulteration, evaluate correlation activity and metabolite levels, and monitor quality control of medicinal plants. Despite remarkable technological advances in metabolite separation and analysis, the chemical differences of primary and secondary metabolites of complex natural products present extraordinary challenges for analysis. The difficulties in plant metabolomics studies range from sample collection to preparation and continue from analysis to metabolite annotation and quantification. A comprehensive metabolomics analysis evaluation of current and new trends in plant metabolomics will guide researchers holistically in designing their research. Therefore, in this review, all necessary steps (extraction strategies, sample preparation, data acquisition and pre-processing, and metabolite annotation) to effectively complete plant metabolomics studies using different analytical platforms (nuclear magnetic resonance, gas chromatography-mass spectrometry, and liquid chromatography-high-resolution mass spectrometry) were evaluated. •Potential usage of metabolomics in medicinal plant science.•The challenges in medicinal plant metabolomics studies.•Precautions and tips from sample collection to preparation and analysis to metabolite annotation.•Comparison of GC-MS and LC-MS-based metabolomics analysis for plants.•Imaging techniques to decipher the spatial distribution of the plant metabolome.