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Sample Set Information

Title Comparison of fruit metabolites among developmental stages of tomato
Description Investigation of Solanum lycopersicum fruit metabolites. 2 tisseus (flesh and peel), 4 developmental stages (breaker, green, orange, red) data are examined.
Authors Yoko Iijima 1, Yukiko Nakamura 2, Yoshiyuki Ogata 1, Kenichi Tanaka 3, Nozomu Sakurai 1, Kunihiro Suda 1, Tatsuya Suzuki 1, Hideyuki Suzuki 1, Koei Okazaki 1, Masahiko Kitayama 2, Shigehiko Kanaya 3, Koh Aoki 1, Daisuke Shibata 1, 1: Kazusa DNA Research Institute, 2: Ehime Women’s College, 3:Nara Institute of Science and Technology
Reference Iijima Y et al. (2008) Plant J. 54: 949-962 [PMID: 18266924]
Comment version 1

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The web resources and information related to the species used in this study are available at Plant Genome Database Japan (PGDBj).

Raw data of S01_M04,M05,M06, S02_M04,M05,M06, S03_M05,M06,M07,M08, S04_M02,M03,M04,M05 S07_M03 are not registered in MassBase yet.

Sample Information

ID S04
Title Solanum lycopersicum Micro-Tom RP
Organism - Scientific Name Solanum lycopersicum
Organism - ID NCBI taxonomy:4081
Compound - ID
Compound - Source
Preparation Solanum lycopersicum cv. Micro-Tom WT, self polinated over 8 generations is used in this study. Seeds were sawn in the pot (500 ml) filled with mixture of vermiculite and Powersoil (mix ratio 1 to 1, Kureha Chemical Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan) and kept in the controlled room at 25C. Until germination, seeds were covered with plastic film and kept dark. After 4 days of germination, they were grown with photoperiod of 16 hr light(7000 lux) / 8 hr dark. Hyponex(R) (Hyponex Ltd., Osaka, Japan), 1000 times diluted, was applied to plants once a week as a nutrient. Peel of fruit at the stage of red (approx. 45-48 days after anthesis) is harvested as sample "RP".
Sample Preparation Details ID
Comment [KomicMarket ID] 4

Analytical Method Information

ID M101
Title LC-FTICR-MS, ESI Negative analysis
Method Details ID MS2
Sample Amount 3.3-5.3 mg
Comment M101 was assigned for convenience of description about the data analysis D01 where all of the analyzed data in negative mode M01 - M02 were used for the characterization and annotation of the peaks.

Analytical Method Details Information

Title LC-FT-ICR-MS ESI negative method 1
Instrument Agilent1100 HPLC (Agilent), LTQ-FT (Thermo Fisher Scientific)
Instrument Type LC-FTICR-MS
Ionization ESI
Ion Mode Negative
Description Peel and Flesh of fruits were separated by razor blade. Each sample was sliced and frozen in liquid nitrogen immediately and ground to powder by a homogenizer, Shake Master (Biomedical Science, Tokyo, Japan). The powdered samples were stored in -80C freezer for no longer than 3 months before extraction of metabolites. Powdered samples (50–70 mg) were extracted with three volumes of methanol containing formononetin (20 μg/ml) as an internal standard. After homogenize twice with Mixer Mill MM300 (QIAGEN, Hilden, Germany) at 27 Hz for 2min, homogenate was centrifuged(12,000xg, 10 min, 4C). The supernatant was filtered with PVDF membrane, 0.2 um (Whatman, Brentford, UK), and the filtrate was used for LC-FTICR-MS analysis. 20uL sample is injected into HPLC after 0.2um membrane filter treatment. HPLC conditions: Agilent 1100 series (Agilent), Column: TSKgel-100V (4.6 x 250 mm, 5 micrometer; TOSOH), Solvent: A; 0.1% formic acid aq. B; ACN (containing 10 mM ammonium formate), Gradient: (B);10 to 50% (0.0 to 50.0 min), 50 to 90% (50.0 to 70.0 min), 90% (70.0 to 75.0 min), 10% (75.1 to 85.0 min), Column temp.: 40 degree C, Flow rate=0.5mL/min, PDA: 200-650 nm (2 nm step). FT-ICR-MS conditions: Ionization Mode: ESI (Electro spray ionization) with spray voltage at 4.0 kV, and capillary temperature at 300C. Detection Mode: Negative-ion mode. Nitrogen sheath gas and auxiliary gas were set at 40 and 15 arbitrary units, respectively. Scan Event Details: Full mass scan was performed in the mass range 100-1500 (m/z) or 200-1800 (m/z) at resolution 100,000 (at m/z 400). MS/MS and MS/MS/MS fragmentation was carried out at normalized collision energy 35.0% and isolation width 4.0 (m/z). IS Used for Mass Offset Correction: Mixture of internal calibration standards dissolved in 50% (v/v) acetonitlile was introduced by a post-column method at a flow rate of 20 ul/min. The concentration of each standards in the mixture was as follows; 11.2 uM 2,4-dichlorophenoxyacetic acid (m/z: 218.9615753 [M-H]-), 3.1 uM ampicillin (m/z: 348.1018030 [M-H]-), 0.25 uM 3-[(3-Cholamidopropyl)dimethylammonio]propanesulfonate (CHAPS, m/z: 659.3941299 [M+HCOO]-), 1.0 uM tetra-N-acetylchitotetraose (m/z: 875.3257160 [M+HCOO]-), 0.6 uM aureobasidin A (m/z: 1145.686214 [M+HCOO]-). Rejected mass=174.9500, 180.9700, 198.9200, 211.0000, 218.9600, 220.9500, 222.7600, 225.0600, 235.9200, 242.9400, 248.9600, 254.9900, 258.9100, 264.9600, 265.9100, 266.9600, 286.9400, 288.9400, 298.9800, 310.9300, 340.9600, 341.9600, 348.9200, 349.1000, 354.9300, 394.1000, 409.9574, 410.9579, 416.0900, 659.3961, 660.3995, 727.3833, 875.3283, 943.3158, 1145.6918, 1146.6950, 1147.6980, 1165.9921, 1265.9890, 1365.9812

Data Analysis Information

ID D01
Title PowerGet data analysis for KomicMarket
Data Analysis Details ID DS1
Recommended decimal places of m/z 6|ITMS 2
Comment Peaks of M01 to M02 were merged as aligned peaks. M101 was assigned to make a metadata ID of D01. [KomicMarket ID] 4

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The annotation data and quantitative data of the metabolite peaks in this sample are available at KomicMarket.

Data Analysis Details Information

Title PowerGet analysis
Description 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.
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