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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 S08
Title Solanum lycopersicum Micro-Tom RF
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. Flesh of fruit at the stage of red (approx. 45-48 days after anthesis) is harvested as sample "RF".
Sample Preparation Details ID
Comment [KomicMarket ID] 8

Analytical Method Information

ID M02
Title LC-FTICR-MS, ESI Negative analysis
Method Details ID MS2
Sample Amount 3.3-5.3 mg
Comment [MassBase ID] MDLC1_04399

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The raw (binary) and near-raw (text) files of this analysis are available at MassBase.

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
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