SE6:/S01/M02/D02
From Metabolonote
Sample Set Information
| ID | SE6 |
|---|---|
| Title | Synechocystis sp. metabolite analysis |
| Description | Investigation of Synechocystis sp. PCC6803 metabolites. 3 replicates data are examined. |
| Authors | Takeshi Ara, Norimoto Shimada, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute |
| Reference | Direct Submittion |
| Comment | version 1 |
Sample Information
| ID | S01 |
|---|---|
| Title | Synechocystis sp. PCC6803 |
| Organism - Scientific Name | Synechocystis sp. PCC6803 |
| Organism - ID | NCBI taxonomy:1148 |
| Compound - ID | |
| Compound - Source | |
| Preparation | Synechocystis sp. PCC6803 are grown in the BG11 culture medium in an incubator with Light at all times condition (32 degree C, 150rpm). |
| Sample Preparation Details ID | |
| Comment | [KomicMarket ID] KSBA_27 |
Analytical Method Information
| ID | M02 |
|---|---|
| Title | LC-Orbitrap-MS, ESI Positive analysis |
| Method Details ID | MS1 |
| Sample Amount | 6.7mg |
| Comment | [MassBase ID] MDLC1_18904 |
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 resulting powder (100mg) are solved in 500uL 80% methanol solution. Cells are homogenized by TissueLyser (QUIAGEN) and centrifuged (15000rpm, 10min, 4 degree C). 20uL of the supernatant (300uL) is injected into HPLC after 0.2um membrane filter treatment. HPLC conditions: Agilent 1100 series (Agilent), Column: TSKgel Amide-80 (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);80 to 45% (0.0 to 30.0 min), 45 to 35% (30.0 to 30.1 min), 35% (30.1 to 35.0 min), 35% to 80% (35.0 to 35.1 min), 80% (35.1 to 42.0 min), Column temp.: 40 degree C, Flow rate=0.8mL/min, PDA: 200-600 nm (2 nm step). Orbitrap-MS conditions: Filter 1: FTMS + c norm !corona !pi res=60000 o(150.0-2000.0); 2: FTMS + c norm !corona !pi res=7500 Dep MS/MS Most intense ion from (1); 3: FTMS + c norm !corona !pi res=7500 Dep MS/MS 2nd most intense ion from (1). |
| 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 (B4) |
| 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=20000, margin of ion grouping in peak detection=5, peak selection filter is default, intensity cut off in peak assignment=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. |
| Comment_of_details |
