Optimum extraction conditions differ for different types of metabolites. To extract carbohydrates, amino acids, and fatty acids from tomato tissues using GC-MS, an extraction protocol originally developed for potato tuber (Roessner et al. 2000) has been widely used. To extract secondary metabolites for non-targeted analysis by liquid chromatography MS (LC-MS), a methanol extraction has been widely applied (Bino et al. 2005; Moco et al. 2006). A lipophilic solvent (e.g., chloroform) is required for extracting non-polar secondary metabolites, such as carotenoids. To extract volatile metabolites, solid phase micro-extraction (Tikunov et al. 2005) or solvent extraction (e.g., propanol, pentane) (Schmelz et al. 2003) have been reported.

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