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Sample Set Information

Title MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites
Description We obtained structural information for the detected peaks in the metabolic profile data without performing additional MS/MS analysis; this was achieved by searching for the corresponding MS2T accession in the library. In the case of metabolic profile data for Arabidopsis tissues containing more than 1000 peaks, approximately 50% of the peaks were tagged by MS2Ts, and 90 peaks were identified or tentatively annotated with metabolite information by searching the metabolite databases and manually interpreting the MS2Ts. A comparison of metabolic profiles among the Arabidopsis tissues revealed that many unknown metabolites accumulated in a tissue-specific manner, some of which were deduced to be unusual Arabidopsis metabolites based on the MS2T data. Candidate genes responsible for these biosyntheses could be predicted by projecting the results to the transcriptome data. The method was also used for metabolic phenotyping of a subset of Ds transposon-inserted lines of Arabidopsis, resulting in clarification of the functions of reported genes involved in glycosylation of flavonoids. Thus, non-targeted metabolic profiling analysis using MS2T annotation methods could prove to be useful for investigating novel functions of secondary metabolites in plants.
Authors Fumio Matsuda, Keiko Yonekura-Sakakibara, Rie Niida, Takashi Kuromori, Kazuo Shinozaki, Kazuki Saito
Reference Matsuda F et al. (2009) The Plant Journal 57: 555-577

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The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

Analytical Method Details Information

Title Metabolic profiling analysis using LC-ESI-MS
Instrument Waters Acquity UPLC system and Waters Q-Tof Premie
Instrument Type UPLC-QTOF-MS
Ionization ESI
Ion Mode Negative
Description The frozen tissues were homogenized in five volumes of 80% aqueous methanol containing 0.5 mg l)1 lidocaine and D-camphor sulfonic acid (Tokyo Kasei) using a mixer mill (MM 300, Retsch, with a zirconia bead for 6 min at 20 Hz. Following centrifugation of 15 000 g for 10 min and filtration.

The sample extracts (2 μl) were analyzed using an LC-MS system equipped with an electrospray ionization (ESI) interface (HPLC, Waters Acquity UPLC system; MS, Waters Q-Tof Premier, The analytical conditions were as follows. HPLC: column, Acquity bridged ethyl hybrid (BEH) C18 (pore size 1.7 μm, length 2.1 · 100 mm, Waters); solvent system, acetonitrile (0.1% formic acid):water (0.1% formic acid); gradient program,1 : 99 v/v at 0 min, 1 : 99 v/v at 0.1 min, 99.5 : 0.5 at 15.5 min, 99.5 : 0.5 at 17.0 min, 1 : 99 v/v at 17.1 min and 1 : 99 at 20 min; flow rate, 0.3 ml min-1; temperature, 38℃; MS detection: capillary voltage, +3.0 keV; cone voltage, 22.5 V; source temperature, 120℃; desolvation temperature, 450℃; cone gas flow, 50 l h-1; desolvation gas flow, 800 l h-1; collision energy, 2 V; detection mode, scan (m/z 100–2000; dwell time 0.45 sec; interscan delay 0.05 sec, centroid). The scans were repeated for 19.5 min in a single run. The data were recorded using MASSLYNX version 4.1 software (Waters).

<MS2T data acquisition by LC-Q-TOF-MS>

The sample extracts prepared by the method above (2 μl) were subjected to the same LC-Q-TOF-MS system operated under the same conditions mentioned above, except for the following changes: gradient program, 1 : 99 v/v at 0 min, 1 : 99 v/v at 0.2 min, 99.5 : 0.5 at 31 min, 99.5 : 0.5 at 34.0 min, 1 : 99 v/v at 34.2 min and 1 : 99 at 40 min; flow rate 0.15 ml min-1; survey detection mode for MS detection. In this mode, following acquisition of the MS spectrum (m/z 100–1000; dwell time 0.45 sec, inter-scan delay 0.05 sec), the MS/MS data of the most abundant ions were automatically obtained (m/z 50–1000; dwell time 2.5 sec; inter-scan delay 0.5 sec, data acquisition, centroid mode; collision energy ramped from 5 to 60 V). The mass/charge ratio (m/z) was calibrated using the lock-mass function with leucine enkephalin. The analyses were repeated 25 times by shifting the m/z ranges of the target ion selection window for the MS/MS analysis (m/z 100–160, 130–190, 160–220 … 880–940, 940–1000).The data were converted into ASCII format using DataBridge (Waters). The information in each MS/MS spectrum was formatted to the MS2T libraries using in-house Perl scripts. Low-intensity signals of fewer than 5 counts/sec were discarded in this process. The original retention time values were divided by two to compensate for the difference in peak elution conditions.


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The peak data files of this analysis are available at MS2T.

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