SE20:/S01/M01/D01

From Metabolonote

jump-to-nav Jump to: navigation, search

Sample Set Information

ID	SE20
Title	Arabidopsis thaliana leaf metabolite analysis for a software test
Description	Investigation of Arabidopsis thaliana leaf metabolites. The raw data file obtained from M01 was used one of the data files that were investigated to optimize the parameters of PowerGet software for better metabolite annotation in high-throughput metabolome analyses. The analysis data of D01 was annotated manually and was used as a reference to annotate peak data from different parameters. The analysis data of D01 was registered in KomicMarket.
Authors	Takeshi Ara, Ryosuke Sasaki, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute
Reference	Direct Submittion
Comment	version 1

ID	S01
Title	Arabidopsis wt leaf
Organism - Scientific Name	Arabidopsis thaliana
Organism - ID	NCBI taxonomy:3702
Compound - ID
Compound - Source
Preparation	Arabidopsis thaliana Col-0 seeds are sown on pots filled by vemiculite and are grown in an incubator with 18h Light/6h Dark and 22 degree C condition. After 2 months later, all leafs are harvested.
Sample Preparation Details ID
Comment	[KomicMarket ID] KSBA_7

ID	M01
Title	LC-FTICR-MS, ESI Positive analysis
Method Details ID	MS1
Sample Amount	6.7 mg
Comment	[MassBase ID] MDLC1_13296

ID	MS1
Title	LC-FT-ICR-MS ESI positive method 1
Instrument	Agilent1100 HPLC (Agilent), LTQ-FT (Thermo Fisher Scientific)
Instrument Type	LC-FTICR-MS
Ionization	ESI
Ion Mode	Positive
Description	Harvested sample is frozen by liquid N2 and resulting powder (100mg) are solved in 300uL 80% methanol solution. 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 (addition 0.1% formic acid fc.), Gradient: (B);3 to 50% (0.0 to 20.0 min), 50 to 90% (20.0 to 40.0 min), 90% (40.0 to 45.0 min), 90 to 95% (45.1 to 50.0 min), 95% (50.1 to 55.0 min), 95% to 97% (55.1 to 60.0 min), 97% ((60.1 to 62.0 min) Column temp.: 40 degree C, Flow rate=0.5mL/min, PDA: 200-650 nm (2 nm step). FT-ICR-MS conditions: Filter 1: FTMS + c norm !corona !pi res=100000 o(100.0-1500.0); 2: ITMS + c norm !corona !pi Dep MS/MS Most intense ion from (1)., Rejected mass=235.1800, 376.0400, 609.2800, 810.4100, 1123.6800.
Comment_of_details

ID	D01
Title	PowerGet data analysis for KomicMarket
Data Analysis Details ID	DS1
Recommended decimal places of m/z	6\|ITMS 2
Comment	[KomicMarket ID] KSBA_7

ID	DS1
Title	PowerGet analysis for detection of all peaks (C1)
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=10000, peak selection filter is default, peak shape is manually checked).
Comment_of_details	At first, all peak shapes were manually selected by eye at both peak selection step and peak assignment step to make a reference data set. The data set was manually annotated after database search process. Then data sets made by different values (cut off intesity=0, 1000, 5000, 10000, 50000, 100000 in peak detection step) without manual check at peak selection step were manually annotated after database search process. The selected value (5000) showed >90% coverage of metabolite annotation of the reference data set.