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The ReSpect (RIKEN MS/MS spectra database … The ReSpect (RIKEN MS/MS spectra database for phytochemicals; 2011 January version), KNApSAcK (2010.12.24 version; Shinbo et al., 2006; Takahashi et al., 2008), and PRIMe standard compound database (2009 November version) were used in this study. The genetic polymorphism data from 20 Arabidopsis accessions were downloaded from the TAIR web site (Clark et al., 2007; Poole, 2007). All data processing procedures were conducted using the in-house script written with Perl. Structural elucidation work was performed in-batch search for all metabolite signals.
In the automated structural elucidation procedure, several thresholds were required to conduct the database searches. The thresholds used in this study are described in Figures 2 and 3. To search the MS/MS spectra, the similarity scores were determined by employing dot product method with mass tolerance at 0.5 Da (Stein and Scott, 1994). The two spectra were considered to be the similar when the similarity score was greater than 0.6. For hierarchical clustering analysis, log2-transformed Z-scored signal intensity data were processed using MEV version 4.4 (Saeed et al., 2003, 2006). EV version 4.4 (Saeed et al., 2003, 2006).
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