SE155:/DS1

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Sample Set Information

ID	TSE1311
Title	Effects of freeze-drying of samples on metabolite levels in metabolome analyses.
Description	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.
Authors	Oikawa A, Otsuka T, Jikumaru Y, Yamaguchi S, Matsuda F, Nakabayashi R, Takashina T, Isuzugawa K, Saito K, Shiratake K.
Reference	J Sep Sci. 2011 Dec;34(24):3561-7. doi: 10.1002/jssc.201100466. Epub 2011 Aug 24.
Comment

ID	DS1
Title	Data processing and analysis (CE-MS)
Description	Raw metabolome data were analyzed using the proprietary software MasterHands. In brief, peaks were detected from sliced electropherograms (0.02 m/z width), and the accurate m/z value for each peak was calculated by Gaussian curve fitting. Migration times of the peaks were normalized by a dynamic time-warping method: numerical parameters were optimized using the simplex method and matching peaks across multiple data sets by dynamic programming. Peaks were picked and aligned using this software. Metabolites in the standard compounds were assigned to the remaining features by matching their m/z values and normalized migration times using the software described above. Data analysis For normalization, the area of the peak from the CE-MS analysis was divided by the area of the internal standard peak. The relative peak areas were used for comparing the metabolite levels between F and FD samples. For principal component analysis (PCA), the relative areas of ionic metabolites and the amounts of plant hormones were standardized by subtracting the mean amount of metabolite (from a sequence of experiments) from the calculated amount for each sample. The resulting value was divided by the standard deviation of each metabolite (z-score). PCA was processed with the software DrDMASS1 (http://kanaya.naist.jp/DrDMASSplus/).
Comment_of_details