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Sample Set Information

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

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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).

Sample Information

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

Analytical Method Information

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

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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 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.

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 [KomicMarket ID] KSBA_7

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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 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.
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