SE1:/S01/M01/D01
From Metabolonote
Sample Set Information
| ID | SE1 |
|---|---|
| Title | Arabidopsis thaliana leaf metabolite analysis |
| Description | Investigation of Arabidopsis thaliana leaf metabolites. 6 replicates (for extraction) 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 7 |
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 |
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_05711 |
The raw (binary) and near-raw (text) files of this analysis are available at MassBase.
Analytical Method Details Information
| 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 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 |
| Comment |
The mass spectrum data are available at Bio-MassBank.
The peak data files written in TogoMD format are downloadable at the KomicMarket2 temporary web site.
Data Analysis Details Information
| ID | DS1 |
|---|---|
| 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. |
| Comment_of_details |
