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Qual Browser module of Xcalibur 2.0 (Therm … Qual Browser module of Xcalibur 2.0 (Thermo Fisher) for data browsing. In house built MSGet program, programmed using Microsoft Visual C++ and XRawfile OCX modules (Thermo Fisher) for text data extraction. DrDMASS (Oikawa et al., 2006, Plant Physiol. 142: 398-413) for mass correction by IS. Microsoft Excel for peak detection, mass estimation etc. Data Preprocessing: A text file including retention time, scan number, m/z and intensities of each detected ions was exported from the data file generated by Xcalibur 2.0 (XRAW file) using MSGet. The m/z values of all ions in each scan were bulk-calibrated with observed m/z values of internal calibration standards in the same scan by DrDMASS. Peak Detection: If the common m/z were obtained in more than 30% of total scans number, we regarded them as artificial noise derived from internal standard, solvent, and instrument, and exclude from further analyses. After removing noise, quasi-molecular ions which were detected with 13C isotopic ions that were detected at m/z 1.003 higher in the same scans. Ions detected in more than five consecutive scans at the same m/z were recognized as a quasi-molecular peak. Estimation of Peak Characteristics: The accurate m/z value for each peak was calculated as a mean of m/z of the top five ions which had largest intensities but less than 1,000,000 in the peak. Detected 13C or 34S isotopic ions along with quasi-molecular ions in each peak group were collected and sorted by scan number. The relative intensity of 13C1 and 34S1 isotopic ion to quasi-molecular ion in each same scan number was calculated. The mean of relative intensities in five scan numbers nearest the top of each peak group were obtained and used for estimation of the number of C and S in the molecular formula. We set a relative intensity tolerance at 5%. Peak alignment: Peaks in multiple measurements of same sample (S) were compared. Peaks with reproducibility were merged as aligned peak and registered in KomicMarket. ligned peak and registered in KomicMarket.
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