Effects of freeze-drying of samples on metabolite levels in metabolome analyses

Freeze-drying (FD) is a useful technique for removing water from biological tissues, such as food samples. Cellular components freeze at once, and the ice sublimates under conditions of high vacuum and low temperatures. Because biological activity is restricted during FD, the degradation of cellular metabolites is often believed to be limited. However, the cellular structure is damaged by several factors, such as the increase in cell volume during freezing, and this has serious effects on the levels of some cellular metabolites. We studied these effects of FD on metabolite levels when using it as a sample preparation step in metabolome analysis. We observed significant decreases in the levels of some metabolites, such as succinate and choline, in Arabidopsis and pear, respectively. We also found that the effects of FD on certain metabolite levels differed between Arabidopsis plants and pear fruits. These results suggest that it is necessary to confirm the metabolite recovery in each sample species when FD is used for sample preparation.