This review describes the usefulness of supercritical fluid chromatography (SFC) in the analysis of hydrophobic metabolites. The use of SFC for the analysis of naturally occurring polyprenols markedly improves the chromatographic resolution of polyprenol homologues and their geometric isomers as compared to conventional HPLC. Under optimized SFC conditions, individual homologues with 10-100-mers were separated. Furthermore, we established an analytical system for the fingerprinting and profiling of diverse lipids through the usage of SFC-MS. When a cyanopropylated silica gel packed column was used for the separation, 14 lipids were successfully detected, and the time required for analysis was less than 15 min. The use of an octadecylsilylated column for the separation depended on the differences in the fatty acid side chains. SFC is a useful separation technology for hydrophobic metabolites, which are difficult to be separated by HPLC.
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