SE229:/S289/M91/D9
Sample Set Information
| ID | SE229 |
|---|---|
| Title | LC-MS based untargeted metabolome analysis of Oryza |
| Description | Compounds in the Oryza species were analyzed using liquid chromatography-mass spectrometry (LC-MS) in a untargeted manner. The same analytical conditions are applied to all samples. Therefore, the compound peaks can be compared to each other by the mass values, the retention time of the LC, and the CID mass spectrum. |
| Authors | Yutaka Sato (National Institute of Genetics), Nozomu Sakurai (National Institute of Genetics, Kazusa DNA Research Institute, email: sakurai (at) kazusa.or.jp) |
| Reference | |
| Comment |
Sample Information
| ID | S289 |
|---|---|
| Title | Rice seed, O. sativa, JRC47 (No.238-1) |
| Organism - Scientific Name | Oryza sativa |
| Organism - ID | NCBI taxonomy: 4530 |
| Compound - ID | |
| Compound - Source | |
| Preparation | The sample was provided by the Oryzabase sponsored by NBRP. |
| Sample Preparation Details ID | SS1 |
| Comment |
Sample Preparation Details Information
| ID | SS1 |
|---|---|
| Title | Sample preparation |
| Description | The harvested sample was stored at low temperature. The sample was ground to a fine powder using a homogenizer Multi-beads shocker MB3200(S) (Yasui Kikai Corp., Osaka, Japan) with 3,000 rpm for 15 min and stored at -80 degree C until use. |
| Comment_of_details |
Analytical Method Information
| ID | M91 |
|---|---|
| Title | PSEUDO: Negative, A set of analyses for valid peak selection. |
| Method Details ID | |
| Sample Amount | |
| Comment | This metadata represents a set of data obtained below for the convenience of the subsequent data analysis, including peak alignment between the data.
SE229_S289_M11 (http://metabolonote.kazusa.or.jp/SE229:/S289/M11) SE229_S901_M11 (http://metabolonote.kazusa.or.jp/SE229:/S901/M11) SE229_S901_M12 (http://metabolonote.kazusa.or.jp/SE229:/S901/M12) |
Data Analysis Information
| ID | D9 |
|---|---|
| Title | Valid peak detection and characterization |
| Data Analysis Details ID | DS1 |
| Recommended decimal places of m/z | default |
| Comment |
Data Analysis Details Information
| ID | DS1 |
|---|---|
| Title | Peak detection, alignment and characterization using PowerGetBatch |
| Description | Mass values were calibrated using the signals of sodium formate detected at 16-17 min using Compass DataAnalysis software (ver. 4.2, Bruker Daltonik, GmbH). The calibrated mass chromatogram was converted to an mzXML-formatted file using the MSConvert function of the ProteoWizard software (ver. 3.0, http://proteowizard.sourceforge.net/, Kessner et al., Bioinformatics 24: 2534-2536, 2008).
The compound peaks were detected and characterized using the mzXML files and PowerGetBatch software (ver. 0.5.4, http://www.kazusa.or.jp/komics/software/PowerGetBatch, Sakurai and Shibata, Carotenoid Science 22: 16-22, 2017). Three different sets (Setting 1-3) of peak detection parameters were applied for each sample and a single set of parameters was used for the mock sample. The parameters were available at the Things Metabolome Repository website (http://metabolites.in/oryza/data/PGB_params.zip). The peaks detected with all three parameters for a sample and not detected in two mock samples obtained in the same measurement batch were selected as valid peaks. The peaks with a retention time less than 1.5 min or greater than 15 min were omitted. The most intense and major pattern of the MS/MS spectrum was selected among the alignment results for each peak. Compound database search and prediction of flavonoid aglycones were performed as described in AM1 (http://metabolonote.kazusa.or.jp/SE229:/AM1). |
| Comment_of_details |
