SE231:/S159/M91/D9
Sample Set Information
| ID | S231 |
|---|---|
| Title | LC-MS based untargeted metabolome analysis of soybean |
| Description | Untargeted metabolome analysis in leaves of 79 accessions of soybean provided by the World Soybean Core Collection (The Research Center of Genetic Resources, National Agriculture and Food Research Organization, NARO) was conducted using liquid chromatography-mass spectrometry (LC-MS). |
| Authors | Nozomu Sakurai (National Institute of Genetics, Kazusa DNA Research Institute, Sakura Scientific, email: sakurai (at) kazusa.or.jp) |
| Reference | |
| Comment |
Sample Information
| ID | S159 |
|---|---|
| Title | Soybean (GmWMC151, JAVA 7, JP 30213) / Leaf / Indonesia (Landrace) / ダイズ (GmWMC151, JAVA 7, JP 30213) / 葉 / インドネシア (在来) |
| Organism - Scientific Name | Glycine max |
| Organism - ID | NCBI taxonomy: 3847 |
| Compound - ID | |
| Compound - Source | |
| Preparation | The sample was harvested outdoors (July or August, 2021, Japan). |
| Sample Preparation Details ID | SS1 |
| Comment |
Sample Preparation Details Information
| ID | SS1 |
|---|---|
| Title | Homogenated and stored at -80 C |
| Description | After harvesting, the leaves were dried using a ventilation dryer (TTM-435S, TOHMEI Tech Co., Ltd., Osaka, Japan) at 60 ºC for 4 hours. The dried leaves were ground into a fine powder using a mortar and pestle at room temperature, weighed, and stored at 4C 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.
SE231_S159_M11 (https://metabolonote.jp/SE231:/S159/M11) SE231_S901_M11 (https://metabolonote.jp/SE231:/S901/M11) SE231_S901_M12 (https://metabolonote.jp/SE231:/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 39-40 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/things/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 3 min or greater than 32 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/SE230:/AM1). The results were available at the Things Metabolome Repository website (http://metabolites.in/things). |
| Comment_of_details |
