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Sample Set Information

ID SE225
Title LC-MS based untargeted metabolome analysis of various samples
Description Compounds in various samples were analyzed using liquid chromatography-mass spectrometry (LC-MS). 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. The data were obtained for the construction of the “Thing Metabolome Repository” website (
Authors Nozomu Sakurai (National Institute of Genetics, Kazusa DNA Research Institute, email: sakurai (at)
Reference The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites. Sakurai N, Yamazaki S, Suda K, Hosoki A, Akimoto N, Takahashi H, Shibata D and Aoki Y, Nucleic Acids Research Database Issue) 51 (D1): D660-D677 (2023), DOI: 10.1093/nar/gkac1058

Sample Information

ID S112
Title Pokeweed, Fruit (immature) / ヨウシュヤマゴボウ, 果実(未熟)
Organism - Scientific Name Phytolacca americana
Organism - ID NCBI taxonomy: 3527
Compound - ID
Compound - Source
Preparation The sample was harvested outdoors (June 5, 2021, Japan).
Sample Preparation Details ID SS1

Sample Preparation Details Information

Title Homogenated and stored at -80 C
Description After harvesting, the sample was immediately frozen in liquid nitrogen and stored at -80 degree C. The sample was ground to a fine powder under liquid nitrogen using mortar and pestle and stored at -80 degree C until use.

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 comvenience of the subsequent data analysis which includes peak alignment between the data.

SE225_S112_M11 (

SE225_S902_M105 (

SE225_S902_M106 (

Data Analysis Information

Title Valid peak detection and characterization
Data Analysis Details ID DS1
Recommended decimal places of m/z default

Data Analysis Details Information

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,, 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,, 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 (

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 ( The results were available at the Things Metabolome Repository website (

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