{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001095","ANALYSIS_ID":"AN001781","VERSION":"1","CREATED_ON":"November 15, 2018, 1:10 pm"}, "PROJECT":{"PROJECT_TITLE":"Computational metabolomics to characterize metabolites in stable isotope-labelled organisms.","PROJECT_SUMMARY":"We developed a computational metabolomics workflow to characterize metabolite structures by using the set of fully 13C-labelled and non-labelled LC-MS/MS data. The platform was applied to structure elucidations for 31 tissues of 12 plant species, resulting in the assignments of 1,092 structures and 344 formulas to 3,604 carbon-determined metabolite ions. We also applied the methodology to find the trait-metabolite associations in natural accessions of Arabidopsis thaliana.","INSTITUTE":"RIKEN","DEPARTMENT":"Center for Sustainable Resource Science","LABORATORY":"Metabolome Informatics Research Team","LAST_NAME":"Tsugawa","FIRST_NAME":"Hiroshi","ADDRESS":"1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan","EMAIL":"hiroshi.tsugawa@riken.jp","PHONE":"+81-45-503-9618"}, "STUDY":{"STUDY_TITLE":"Data resource for fully 13C labelled and non-labelled plant tissues (part-I)","STUDY_SUMMARY":"LC-MS/MS data files of fully 13C labelled and 12C plant tissues, which were utilized to determine the carbon element number for metabolite characterizations.","INSTITUTE":"RIKEN","DEPARTMENT":"Center for Sustainable Resource Science","LABORATORY":"Metabolome Informatics Research Team","LAST_NAME":"Tsugawa","FIRST_NAME":"Hiroshi","ADDRESS":"1-7-22 Suehiro-cho, Tsurumi-ku","EMAIL":"hiroshi.tsugawa@riken.jp","PHONE":"+81-45-503-9618"}, "SUBJECT":{"SUBJECT_TYPE":"Plant","SUBJECT_SPECIES":"Allium cepa;Arabidopsis thaliana;Glycine max;Glycyrrhiza glabra Allium cepa;Arabidopsis thaliana;Glycine max;Glycyrrhiza glabra pumila / Oryza sativa / Solanum lycopersicum / Solanum tuberosum / Zea mays"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"13C-AT-LeafAndStem", "Factors":{"Label":"U-13C","Species":"Arabidopsis thaliana","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"13C-AT-Root", "Factors":{"Label":"U-13C","Species":"Arabidopsis thaliana","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-AT-LeafAndStem", "Factors":{"Label":"Non-labelled","Species":"Arabidopsis thaliana","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"12C-AT-Root", "Factors":{"Label":"Non-labelled","Species":"Arabidopsis thaliana","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"13C-GM-LeafAndStem", "Factors":{"Label":"U-13C","Species":"Glycine max","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"13C-GM-Root", "Factors":{"Label":"U-13C","Species":"Glycine max","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-GM-LeafAndStem", "Factors":{"Label":"Non-labelled","Species":"Glycine max","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"12C-GM-Root", "Factors":{"Label":"Non-labelled","Species":"Glycine max","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"13C-GG-LeafAndStem", "Factors":{"Label":"U-13C","Species":"Glycyrrhiza glabra","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"13C-GG-Root", "Factors":{"Label":"U-13C","Species":"Glycyrrhiza glabra","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-GG-LeafAndStem", "Factors":{"Label":"Non-labelled","Species":"Glycyrrhiza glabra","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"12C-GG-Root", "Factors":{"Label":"Non-labelled","Species":"Glycyrrhiza glabra","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"13C-GU-LeafAndStem", "Factors":{"Label":"U-13C","Species":"Glycyrrhiza uralensis","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"13C-GU-Root", "Factors":{"Label":"U-13C","Species":"Glycyrrhiza uralensis","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-GU-LeafAndStem", "Factors":{"Label":"Non-labelled","Species":"Glycyrrhiza uralensis","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"12C-GU-Root", "Factors":{"Label":"Non-labelled","Species":"Glycyrrhiza uralensis","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"13C-ST-LeafAndStem", "Factors":{"Label":"U-13C","Species":"Solanum tuberosum","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"13C-ST-Root", "Factors":{"Label":"U-13C","Species":"Solanum tuberosum","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"13C-ST-Tuber", "Factors":{"Label":"U-13C","Species":"Solanum tuberosum","SampleSource":"tuber"} }, { "Subject ID":"-", "Sample ID":"12C-ST-LeafAndStem", "Factors":{"Label":"Non-labelled","Species":"Solanum tuberosum","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"12C-ST-Root", "Factors":{"Label":"Non-labelled","Species":"Solanum tuberosum","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-ST-Tuber", "Factors":{"Label":"Non-labelled","Species":"Solanum tuberosum","SampleSource":"tuber"} }, { "Subject ID":"-", "Sample ID":"13C-MT-LeafAndStem", "Factors":{"Label":"U-13C","Species":"Medicago truncatula","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"13C-MT-Flower", "Factors":{"Label":"U-13C","Species":"Medicago truncatula","SampleSource":"flower"} }, { "Subject ID":"-", "Sample ID":"13C-MT-RipePod", "Factors":{"Label":"U-13C","Species":"Medicago truncatula","SampleSource":"ripe pod"} }, { "Subject ID":"-", "Sample ID":"13C-MT-Seed", "Factors":{"Label":"U-13C","Species":"Medicago truncatula","SampleSource":"seed"} }, { "Subject ID":"-", "Sample ID":"13C-MT-Root", "Factors":{"Label":"U-13C","Species":"Medicago truncatula","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-MT-LeafAndStem", "Factors":{"Label":"Non-labelled","Species":"Medicago truncatula","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"12C-MT-Flower", "Factors":{"Label":"Non-labelled","Species":"Medicago truncatula","SampleSource":"flower"} }, { "Subject ID":"-", "Sample ID":"12C-MT-RipePod", "Factors":{"Label":"Non-labelled","Species":"Medicago truncatula","SampleSource":"ripe pod"} }, { "Subject ID":"-", "Sample ID":"12C-MT-Seed", "Factors":{"Label":"Non-labelled","Species":"Medicago truncatula","SampleSource":"seed"} }, { "Subject ID":"-", "Sample ID":"12C-MT-Root", "Factors":{"Label":"Non-labelled","Species":"Medicago truncatula","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"13C-OS-LeafAndStem", "Factors":{"Label":"U-13C","Species":"Oryza sativa","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"13C-OS-Root", "Factors":{"Label":"U-13C","Species":"Oryza sativa","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-OS-LeafAndStem", "Factors":{"Label":"Non-labelled","Species":"Oryza sativa","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"12C-OS-Root", "Factors":{"Label":"Non-labelled","Species":"Oryza sativa","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"13C-SL-LeafAndSLem", "Factors":{"Label":"U-13C","Species":"Solanum lycopersicum","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"13C-SL-FruitGreen", "Factors":{"Label":"U-13C","Species":"Solanum lycopersicum","SampleSource":"fruit green"} }, { "Subject ID":"-", "Sample ID":"13C-SL-Ripe", "Factors":{"Label":"U-13C","Species":"Solanum lycopersicum","SampleSource":"ripe"} }, { "Subject ID":"-", "Sample ID":"12C-SL-LeafAndSLem", "Factors":{"Label":"Non-labelled","Species":"Solanum lycopersicum","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"12C-SL-FruitGreen", "Factors":{"Label":"Non-labelled","Species":"Solanum lycopersicum","SampleSource":"fruit green"} }, { "Subject ID":"-", "Sample ID":"12C-SL-Ripe", "Factors":{"Label":"Non-labelled","Species":"Solanum lycopersicum","SampleSource":"ripe"} }, { "Subject ID":"-", "Sample ID":"13C-ZM-Leaf", "Factors":{"Label":"U-13C","Species":"Zea mays","SampleSource":"leaf"} }, { "Subject ID":"-", "Sample ID":"13C-ZM-Stem", "Factors":{"Label":"U-13C","Species":"Zea mays","SampleSource":"stem"} }, { "Subject ID":"-", "Sample ID":"13C-ZM-Seed", "Factors":{"Label":"U-13C","Species":"Zea mays","SampleSource":"seed"} }, { "Subject ID":"-", "Sample ID":"13C-ZM-Root", "Factors":{"Label":"U-13C","Species":"Zea mays","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-ZM-Leaf", "Factors":{"Label":"Non-labelled","Species":"Zea mays","SampleSource":"leaf"} }, { "Subject ID":"-", "Sample ID":"12C-ZM-Stem", "Factors":{"Label":"Non-labelled","Species":"Zea mays","SampleSource":"stem"} }, { "Subject ID":"-", "Sample ID":"12C-ZM-Seed", "Factors":{"Label":"Non-labelled","Species":"Zea mays","SampleSource":"seed"} }, { "Subject ID":"-", "Sample ID":"12C-ZM-Root", "Factors":{"Label":"Non-labelled","Species":"Zea mays","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"13C-AC-Leaf", "Factors":{"Label":"U-13C","Species":"Allium cepa","SampleSource":"leaf"} }, { "Subject ID":"-", "Sample ID":"13C-AC-Bulb", "Factors":{"Label":"U-13C","Species":"Allium cepa","SampleSource":"bulb"} }, { "Subject ID":"-", "Sample ID":"13C-AC-Root", "Factors":{"Label":"U-13C","Species":"Allium cepa","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-AC-Leaf", "Factors":{"Label":"Non-labelled","Species":"Allium cepa","SampleSource":"leaf"} }, { "Subject ID":"-", "Sample ID":"12C-AC-Bulb", "Factors":{"Label":"Non-labelled","Species":"Allium cepa","SampleSource":"bulb"} }, { "Subject ID":"-", "Sample ID":"12C-AC-Root", "Factors":{"Label":"Non-labelled","Species":"Allium cepa","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"13C-NT-LeafAndStem", "Factors":{"Label":"U-13C","Species":"Nicotiana tabacum","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"13C-NT-Root", "Factors":{"Label":"U-13C","Species":"Nicotiana tabacum","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-NT-LeafAndStem", "Factors":{"Label":"Non-labelled","Species":"Nicotiana tabacum","SampleSource":"leaf&stem"} }, { "Subject ID":"-", "Sample ID":"12C-NT-Root", "Factors":{"Label":"Non-labelled","Species":"Nicotiana tabacum","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"13C-OP-Root", "Factors":{"Label":"U-13C","Species":"Ophiorrhiza pumila","SampleSource":"root"} }, { "Subject ID":"-", "Sample ID":"12C-OP-Root", "Factors":{"Label":"Non-labelled","Species":"Ophiorrhiza pumila","SampleSource":"root"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Leaf/stem and root tissues of Arabidopsis thaliana, Nicotiana tabacum, Glycine max, Glycyrrhiza glabra, Glycyrrhiza urahensis, and Oryza sativa, bulb, leaf, and root tissues of Allium cepa, flower, leaf/stem, seed pod, seed, and root tissues of Medicago truncatula, green and ripe fruit-, and leaf/stem tissues of Solanum lycopersicum, leaf/stem, root, and tuber tissues of Solanum tuberosum, and leaf, stem, seed, and root tissues of Zea mays were purchased from IsoLife Co. (Wageningen UR, Netherlands). The hairy root of Ophiorrhiza pumila was grown as follows. O. pumila hairy roots were derived and maintained, except for the carbon source. We supplied 1.5% D-glucose instead of 1.5% sucrose. We obtained 4-week-old O. pumila hairy roots and sub-cultured them in 1.5% D-glucose (U-13C6, 99%) (Cambridge Isotope Laboratories, Inc.) for two generations for complete isotope labeling of the metabolome. Hairy roots from the same batch used for isotope-labeling were sub-cultured for two subcultures in 1.5% D-glucose (Nacalai Tesque, Inc); they served as the control. Hairy roots from the second sub-culture of sub-cultured tissues growing in 1.5% isotope-labelled or un-labelled 1.5% D-glucose were harvested, wiped with paper towels and snap-frozen in liquid-N2.","SAMPLE_TYPE":"Plant"}, "TREATMENT":{"TREATMENT_SUMMARY":"NA"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Samples (3 mg) of dried plant tissues were weighted in a 2.0-ml microtube (Sarstedt). Their metabolites were extracted with 150 µl of 80% MeOH containing 2.5 µM lidocaine and 10-camphour sulfonic acid per mg of dry weight using a mixer-mill with zirconia beads [7 min at 18 Hz and 4 degree C (MM300; Retsch)]. After 10-min centrifugation at 17,800 g the supernatant was filtered using an HLB µElution plate (Waters)."}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity BEH C18 (100 x 2.1mm, 1.7um)","FLOW_GRADIENT":"99.5% solvent A/0.5% solvent B at 0 min, 99.5%A/0.5%B at 0.1 min, 20%A/80%B at 10 min, 0.5%A/99.5%B at 10.1 min, 0.5%A/99.5%B at 12.0 min, 99.5%A/0.5%B at 12.1 min and 99.5%A/0.5%B at 15.0 min","FLOW_RATE":"0.3 ml/min at 0 min, 0.3 ml/min at 10 min, 0.4 ml/min at 10.1 min, 0.4 ml/min at 14.4 min, and 0.3 ml/min at 14.5 min","COLUMN_TEMPERATURE":"40","SOLVENT_A":"water including 0.1% formic acid","SOLVENT_B":"acetonitrile including 0.1% formic acid"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS","DATA_FORMAT":".raw"}, "MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Waters Synapt G2 S QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","CAPILLARY_VOLTAGE":"+3.00 kV","COLLISION_ENERGY":"6 V","SOURCE_TEMPERATURE":"120","DESOLVATION_GAS_FLOW":"800 l/hr","DESOLVATION_TEMPERATURE":"450 degree C","SCAN_RANGE_MOVERZ":"50 - 1500","MS_RESULTS_FILE":"ST001095_AN001781_Results.txt UNITS:Peak intensity Has m/z:Yes Has RT:Yes RT units:Minutes"} }