SE15:/S03/M02/D02

Sample Set Information

ID	SE15
Title	Comparison of fruit metabolites among developmental stages of Jatropha curcas
Description	Investigation of Jatropha curcas fruit metabolites. 4 developmental stages and 3 replicates data are examined.
Authors	Ryosuke Sano 1, Takeshi Ara 1, Nayumi Akimoto 1, Yoshihiko Morishita 1, Mitsuo Enomoto 1, Nozomu Sakurai 1, Hideyuki Suzuki 1, Yasunori Fukuzawa 2, Yoshinobu Kawamitsu 2, Masami Ueno 2, Daisuke Shibata 1, 1: Kazusa DNA Research Institute, 2: Faculty of Agriculture, University of the Ryukyus
Reference	Sano R. et al. (2012) Plant Biotechnology 29: 175-178
Comment	version 5

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

http://pgdbj.jp/plantdb/plantinfo.html?ln=en&cmd=entry&ppid=t180498

The original paper is available at Plant Biotechnology

Sample Information

ID	S03
Title	Jatropha curcas Fruit stage 3
Organism - Scientific Name	Jatropha curcas
Organism - ID	NCBI taxonomy:180498
Compound - ID
Compound - Source
Preparation	Jatropha curcas are grown in an open experimental　field at the University of the Ryukyus (Okinawa island, Okinawa, Japan), located in a subtropical area.
Sample Preparation Details ID
Comment	[KomicMarket ID] KSBA_5

Analytical Method Information

ID	M02
Title	LC-Orbitrap-MS, ESI Positive analysis
Method Details ID	MS1
Sample Amount	3.4mg
Comment	[MassBase ID] MDLC1_25027

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

Analytical Method Details Information

ID	MS1
Title	LC-Orbitrap-MS ESI positive method 1
Instrument	Agilent1100 HPLC (Agilent), LTQ-Orbitrap (Thermo Fisher Scientific)
Instrument Type	LC-Orbitrap-MS
Ionization	ESI
Ion Mode	Positive
Description	Harvested sample is frozen by liquid N2 and ground to powder by a homogenizer, Shake Master (Biomedical Science, Tokyo, Japan). The powdered sample (100mg) are solved in 300uL 80% methanol solution. 10uL sample is injected into HPLC after 0.2um membrane filter treatment. HPLC conditions: Agilent 1100 series (Agilent), Column: TSKgel ODS-100V (4.6 x 250 mm, 5 micrometer; TOSOH), Solvent: A; 0.1% formic acid aq. B; ACN (addition 0.1% formic acid fc.), Gradient: (B);3 to 97% (0.0 to 45.0 min), 97% (45.1 to 50.0 min), 3% (50.1 to 57.0 min), Column temp.: 40 degree C, Flow rate=0.5mL/min, PDA: 200-650 nm (2 nm step). Orbitrap-MS conditions: Filter 1: FTMS + c norm !corona !pi res=60000 o(100.0-1500.0); 2: ITMS + c norm !corona !pi Dep MS/MS Most intense ion from (1); 3: ITMS + c norm !corona !pi Dep MS/MS 2nd most intense ion from (1); 4: ITMS + c norm !corona !pi Dep MS/MS 3rd most intense ion from (1); 5: ITMS + c norm !corona !pi Dep MS/MS 4th most intense ion from (1); 6: ITMS + c norm !corona !pi Dep MS/MS 5th most intense ion from (1)., Rejected mass=102.09000, 102.13000, 103.11000, 116.14000, 121.12000, 130.16000, 158.00000, 171.15000, 202.13000, 235.18000, 249.21000, 252.22000, 294.26000, 308.00000, 376.04000, 379.04000, 380.03000, 540.61000, 540.95000, 609.28000, 810.41000, 1101.70000, 1123.68000, 1146.75000, 1147.76000.
Comment_of_details

Data Analysis Information

ID	D02
Title	PowerGet data analysis for KomicMarket2
Data Analysis Details ID	DS2
Recommended decimal places of m/z	6|ITMS 2
Comment

The peak data files written in TogoMD format are downloadable at the KomicMarket2 temporary web site.

Data Analysis Details Information

ID	DS2
Title	PowerGet analysis for detection of all peaks (B5)
Description	Raw data files are converted to text file by MSGet software without cut off value and peaks are extracted from the text files by PowerFT with parameters (intensity cut off in peak detection=30000, margin of ion grouping in peak detection=5, peak selection filter is default). The replicates data are aligned by PowerMatch with blank data. The alignment is manually edited. Assigned peaks observed in multiple replicate samples are selected for annotation process.
Comment_of_details