From Metabolonote
jump-to-nav Jump to: navigation, search

Sample Set Information

Title Arabidopsis thaliana leaf metabolite analysis
Description Investigation of Arabidopsis thaliana leaf metabolites. 6 replicates data are examined for each sample.
Authors Takeshi Ara, Ryosuke Sasaki, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute
Reference Direct Submittion
Comment version 6

Link icon database.png Link icon pgdbj.png

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 leaves are harvested.
Sample Preparation Details ID
Comment [KomicMarket ID] KSBA_11

Link icon database.png Komicmarket logo.png

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

Analytical Method Information

ID M02
Title LC-FTICR-MS, ESI Positive analysis
Method Details ID MS1
Sample Amount 6.7 mg
Comment [MassBase ID] MDLC1_05712

Link icon database.png Link icon massbase.png

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 30% (0.0 to 25.0 min), 30 to 90% (25.0 to 40.0 min), 90% (40.0 to 45.0 min), 95% (45.1 to 50.0 min), 3% (50.1 to 57.0 min), Column temp.: 30 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(200.0-1500.0); 2: ITMS + c norm !corona !pi Dep MS/MS Most intense ion from (1)., Rejected mass=256.2000;266.0000;284.2000;300.2000;328.2000;344.2000;372.2000;388.2000;416.3000;432.3000;460.0000.
Comment_of_details [column] TSKgel-100V (4.6 x 250 mm, 5 micrometer; TOSOH)

[gradient] Solvent: A; 0.1% formic acid aq. B; ACN (addition 0.1% formic acid fc.), Gradient: (B);3 to 30% (0.0 to 25.0 min), 30 to 90% (25.0 to 40.0 min), 90% (40.0 to 45.0 min), 95% (45.1 to 50.0 min), 3% (50.1 to 57.0 min) [total separation time] 60 min

Data Analysis Information

ID D01
Title PowerGet data analysis for Bio-MassBank
Data Analysis Details ID DS1
Recommended decimal places of m/z 6|ITMS 2

Link icon database2.png Link icon biomassbank.png

The mass spectrum data are available at Bio-MassBank.

Data Analysis Details Information

Title PowerGet analysis for annotation of peaks with MS/MS (A2)
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=5000, peak selection filter is default, peak shape is manually checked for peaks with intensity < 1000). 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. Assigned peaks with clear MS2 data are manually selected for the registration of Bio-MassBank.
Personal tools
View and Edit Metadata