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Sample preparation
Sample processing and extraction: Vacuole solution (200μL) was collected and diluted with water for the liquid-liquid distribution. Frozen cytoplasm was homogenized with zirconia beads using a Mixer Mill (Retsch, Haan, http://www.retsch.com) at 27 Hz for 2 min. The solution was suspended in 200μL of water and used as the cytoplasmic solution.
Liquid-liquid distribution: To exclude proteins and hydrophobic compounds such as lipids, which can have a negative effect on the reproducibility of electrophoresis, extracts were separated by adding methanol and chloroform to samples. Chloroform (200 μL) and methanol (500μL), including 8μM of internal standards (methionine sulfone for cation analysis and camphor 10-sulfonic acid for anion analysis), were used for compensation of the peak area after CE-MS analysis. The solution was added to 200μL samples, and the mixture was homogenized at 27 Hz for 1 min. The sample solution was then centrifuged at 20,400 x g for 3 min at 4°C. For further purification of the solution and reduction in volume, the upper layer was evaporated for 30 min at 45°C with a centrifugal concentrator and then separated into 2 layers.
Ultracentrifugation: Because high molecular weight compounds, such as oligo-sugars, may reduce CE performance, the upper layer was centrifugally filtered through a Millipore 5-kDa cutoff filter at 9,100 x g for 120 min. Sample concentration: The filtrate was dried for 120 min with a centrifugal concentrator. The residue was dissolved in 20μL water containing 200μM of internal standards (3-aminopyrrolidine for cation analysis and trimesic acid for anion analysis) to compensate for migration time in the peak annotation step. This solution was used for CE-MS analyses.
CE-TOFMS conditions
CE-TOF MS instruments: All CE-TOFMS experiments were performed using an Agilent CE capillary electrophoresis system (Agilent Technologies, www.home.agilent.com), an Agilent G3250AA LC/MSD TOF System, an Agilent 1100 series binary HPLC pump, a G1603A Agilent CE-MS adapter, and a G1607A Agilent CE-ESI-MS sprayer kit. For systems control and data acquisition, we used the G2201AA Agilent ChemStation software for CE data and Analyst QS software for Agilent TOFMS.
Separation column and electrolytes: Separations were carried out in a fused silica capillary (50μm i.d. x 100 cm total length) filled with 1 M formic acid as the electrolyte for cation analysis and 20 mM ammonium formate (pH 10.0) as the electrolyte for anion analyses. The capillary temperature was maintained at 20°C.
Sample injection: The samples were injected with a pressure injection of 50 mbar for 15 s (15 nL). The sample tray was cooled below 4°C.
Separation parameters: Prior to each run, the capillary was flushed with the electrolyte for 5 min. The applied voltage for separation was set at 30 kV. Methanol-water (50% v/v) containing 0.5μM reserpine was delivered as the sheath liquid at 10 μL/min.
Ionization: ESI-TOFMS was conducted in the positive ion mode for cation analyses and in the negative ion mode for anion analyses, and the capillary voltage was set at 4 kV.
Dry gas condition: A flow rate of heated dry nitrogen gas (heater temperature, 300°C) was maintained at 10 psig.
Voltage settings in TOFMS: The fragmentor, skimmer, and Oct RFV voltage were set at 110 V, 50 V, and 160 V for cation analysis, and at 120 V, 60 V, and 220 V for anion analysis, respectively.
Mass calibration: Automatic recalibration of each acquired spectrum was performed using reference masses of reference standards. For lock mass correction and subsequent exact mass measurement, the methanol dimer ion ([2M+H]+, m/z = 65.0597) and reserpine ([M+H]+, m/z = 609.2806) were used for cation analysis, and the formic acid dimer ion ([2M-H]-, m/z = 91.0037) and reserpine ([M-H]-, m/z = 607.2661) were used for anion analysis.
Mass data acquirement: Exact mass data were acquired at a rate of 1.5 cycles/s over a 50–1000 m/z range.
LC-MS conditions: LC-MS analysis was performed according to Matsuda et al., 2009.
Quality control: We analyzed the standard compound mixture at the beginning and end of each CE-MS sequence analysis (maximum 36 samples). To confirm reproducible sensitivity, the detected peak area was compared with that of a standard compound mixture. The standard compound mixture was composed of major detectable metabolites, such as amino acids and organic acids, and a new mixture was prepared at least every 6 months. For all of the analyses in this study, no differences were observed in the sensitivity of the standard compound mixture.
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