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The scans were repeated for 19.5 min in a … The scans were repeated for 19.5 min in a single run. The raw data were recorded with the aid of MassLynx version 4.1 software (Waters).The raw chromatogram data were processed to produce a data matrix consisting of 1,589 metabolite signals (773 from positive and 816 from negative ion mode; Supplemental Data S1) using MetAlign (Lommen, 2009). The parameters used for data processing were as follows: maximum amplitude, 10,000; peak slope factor, 1; peak threshold factor, 6; average peakwidth at half weight, 8; scaling options, none; maximum shift per scan, 35; select min nr per peak set, 4. The data matrix generated by MetAlign was processed with inhouse software written in Perl/Tk (Matsuda et al., 2009). By this procedure, the metabolite signals eluted before 0.85 min and after 12.0 min were discarded, original peak intensity values were divided with those of the internal standards (lidocaine: m/z = 235 [M + H]+, eluted at 4.19 min; camphor-10-sulfonic acid: m/z = 231 [M 2 H]2, eluted at 3.84 min, for the positive and negative ion modes, respectively) to normalize the peak intensity values, discarding low-intensity data (under signal-to-noise ratio , 5), and isotope peaks were removed by employing specific parameters (rthres . 0.8, DRt = 0.5 s, and Dm/z = 2 D). Metabolite signals were assigned unique accession codes, such as adn031026 (representing AtMetExpress Development negative ion mode data, peak number 31026).
MS2T data were acquired from nine tissues of Arabidopsis and processed to create 36 MS2T libraries using previously described methods (Matsuda et al., 2009). Each MS2T entry was assigned a unique accession code, such as ATH10n03690, in which ATH10n is the name of the library and 03690 is the entry number. A total of 36 MS2T libraries with 476,120 accession codes were created in this study (Supplemental Table S2). The MS2T libraries contain a high volume of redundant and low-quality data (Matsuda et al., 2009). Since the metabolic profile data and the MS2T libraries were acquired using compatible analytical conditions, a metabolite signal obtained in the profile can be tagged with MS2Ts obtained from a corresponding metabolite with identical unit mass eluting at a similar retention time. By this method, approximately 95% of the metabolite signals were tagged with at least one MS2T. The mean number of MS2Ts tagged to each metabolite peak was 13.5. s tagged to each metabolite peak was 13.5.
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