#METABOLOMICS WORKBENCH Mikikot_20181108_212853_mwtab.txt DATATRACK_ID:1567 STUDY_ID:ST001095 ANALYSIS_ID:AN001781 PROJECT_ID:PR000733 VERSION 1 CREATED_ON November 15, 2018, 1:10 pm #PROJECT PR:PROJECT_TITLE Computational metabolomics to characterize metabolites in stable PR:PROJECT_TITLE isotope-labelled organisms. PR:PROJECT_SUMMARY We developed a computational metabolomics workflow to characterize metabolite PR:PROJECT_SUMMARY structures by using the set of fully 13C-labelled and non-labelled LC-MS/MS PR:PROJECT_SUMMARY data. The platform was applied to structure elucidations for 31 tissues of 12 PR:PROJECT_SUMMARY plant species, resulting in the assignments of 1,092 structures and 344 formulas PR:PROJECT_SUMMARY to 3,604 carbon-determined metabolite ions. We also applied the methodology to PR:PROJECT_SUMMARY find the trait-metabolite associations in natural accessions of Arabidopsis PR:PROJECT_SUMMARY thaliana. PR:INSTITUTE RIKEN PR:DEPARTMENT Center for Sustainable Resource Science PR:LABORATORY Metabolome Informatics Research Team PR:LAST_NAME Tsugawa PR:FIRST_NAME Hiroshi PR:ADDRESS 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan PR:EMAIL hiroshi.tsugawa@riken.jp PR:PHONE +81-45-503-9618 #STUDY ST:STUDY_TITLE Data resource for fully 13C labelled and non-labelled plant tissues (part-I) ST:STUDY_SUMMARY LC-MS/MS data files of fully 13C labelled and 12C plant tissues, which were ST:STUDY_SUMMARY utilized to determine the carbon element number for metabolite ST:STUDY_SUMMARY characterizations. ST:INSTITUTE RIKEN ST:DEPARTMENT Center for Sustainable Resource Science ST:LABORATORY Metabolome Informatics Research Team ST:LAST_NAME Tsugawa ST:FIRST_NAME Hiroshi ST:ADDRESS 1-7-22 Suehiro-cho, Tsurumi-ku ST:EMAIL hiroshi.tsugawa@riken.jp ST:PHONE +81-45-503-9618 #SUBJECT SU:SUBJECT_TYPE Plant SU:SUBJECT_SPECIES Allium cepa;Arabidopsis thaliana;Glycine max;Glycyrrhiza glabra SU:SUBJECT_SPECIES Allium cepa;Arabidopsis thaliana;Glycine max;Glycyrrhiza glabra SU:SUBJECT_SPECIES pumila / Oryza sativa / Solanum lycopersicum / Solanum tuberosum / Zea mays #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - 13C-AT-LeafAndStem Label:U-13C | Species:Arabidopsis thaliana | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 13C-AT-Root Label:U-13C | Species:Arabidopsis thaliana | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-AT-LeafAndStem Label:Non-labelled | Species:Arabidopsis thaliana | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 12C-AT-Root Label:Non-labelled | Species:Arabidopsis thaliana | SampleSource:root SUBJECT_SAMPLE_FACTORS - 13C-GM-LeafAndStem Label:U-13C | Species:Glycine max | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 13C-GM-Root Label:U-13C | Species:Glycine max | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-GM-LeafAndStem Label:Non-labelled | Species:Glycine max | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 12C-GM-Root Label:Non-labelled | Species:Glycine max | SampleSource:root SUBJECT_SAMPLE_FACTORS - 13C-GG-LeafAndStem Label:U-13C | Species:Glycyrrhiza glabra | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 13C-GG-Root Label:U-13C | Species:Glycyrrhiza glabra | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-GG-LeafAndStem Label:Non-labelled | Species:Glycyrrhiza glabra | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 12C-GG-Root Label:Non-labelled | Species:Glycyrrhiza glabra | SampleSource:root SUBJECT_SAMPLE_FACTORS - 13C-GU-LeafAndStem Label:U-13C | Species:Glycyrrhiza uralensis | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 13C-GU-Root Label:U-13C | Species:Glycyrrhiza uralensis | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-GU-LeafAndStem Label:Non-labelled | Species:Glycyrrhiza uralensis | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 12C-GU-Root Label:Non-labelled | Species:Glycyrrhiza uralensis | SampleSource:root SUBJECT_SAMPLE_FACTORS - 13C-ST-LeafAndStem Label:U-13C | Species:Solanum tuberosum | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 13C-ST-Root Label:U-13C | Species:Solanum tuberosum | SampleSource:root SUBJECT_SAMPLE_FACTORS - 13C-ST-Tuber Label:U-13C | Species:Solanum tuberosum | SampleSource:tuber SUBJECT_SAMPLE_FACTORS - 12C-ST-LeafAndStem Label:Non-labelled | Species:Solanum tuberosum | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 12C-ST-Root Label:Non-labelled | Species:Solanum tuberosum | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-ST-Tuber Label:Non-labelled | Species:Solanum tuberosum | SampleSource:tuber SUBJECT_SAMPLE_FACTORS - 13C-MT-LeafAndStem Label:U-13C | Species:Medicago truncatula | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 13C-MT-Flower Label:U-13C | Species:Medicago truncatula | SampleSource:flower SUBJECT_SAMPLE_FACTORS - 13C-MT-RipePod Label:U-13C | Species:Medicago truncatula | SampleSource:ripe pod SUBJECT_SAMPLE_FACTORS - 13C-MT-Seed Label:U-13C | Species:Medicago truncatula | SampleSource:seed SUBJECT_SAMPLE_FACTORS - 13C-MT-Root Label:U-13C | Species:Medicago truncatula | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-MT-LeafAndStem Label:Non-labelled | Species:Medicago truncatula | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 12C-MT-Flower Label:Non-labelled | Species:Medicago truncatula | SampleSource:flower SUBJECT_SAMPLE_FACTORS - 12C-MT-RipePod Label:Non-labelled | Species:Medicago truncatula | SampleSource:ripe pod SUBJECT_SAMPLE_FACTORS - 12C-MT-Seed Label:Non-labelled | Species:Medicago truncatula | SampleSource:seed SUBJECT_SAMPLE_FACTORS - 12C-MT-Root Label:Non-labelled | Species:Medicago truncatula | SampleSource:root SUBJECT_SAMPLE_FACTORS - 13C-OS-LeafAndStem Label:U-13C | Species:Oryza sativa | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 13C-OS-Root Label:U-13C | Species:Oryza sativa | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-OS-LeafAndStem Label:Non-labelled | Species:Oryza sativa | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 12C-OS-Root Label:Non-labelled | Species:Oryza sativa | SampleSource:root SUBJECT_SAMPLE_FACTORS - 13C-SL-LeafAndSLem Label:U-13C | Species:Solanum lycopersicum | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 13C-SL-FruitGreen Label:U-13C | Species:Solanum lycopersicum | SampleSource:fruit green SUBJECT_SAMPLE_FACTORS - 13C-SL-Ripe Label:U-13C | Species:Solanum lycopersicum | SampleSource:ripe SUBJECT_SAMPLE_FACTORS - 12C-SL-LeafAndSLem Label:Non-labelled | Species:Solanum lycopersicum | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 12C-SL-FruitGreen Label:Non-labelled | Species:Solanum lycopersicum | SampleSource:fruit green SUBJECT_SAMPLE_FACTORS - 12C-SL-Ripe Label:Non-labelled | Species:Solanum lycopersicum | SampleSource:ripe SUBJECT_SAMPLE_FACTORS - 13C-ZM-Leaf Label:U-13C | Species:Zea mays | SampleSource:leaf SUBJECT_SAMPLE_FACTORS - 13C-ZM-Stem Label:U-13C | Species:Zea mays | SampleSource:stem SUBJECT_SAMPLE_FACTORS - 13C-ZM-Seed Label:U-13C | Species:Zea mays | SampleSource:seed SUBJECT_SAMPLE_FACTORS - 13C-ZM-Root Label:U-13C | Species:Zea mays | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-ZM-Leaf Label:Non-labelled | Species:Zea mays | SampleSource:leaf SUBJECT_SAMPLE_FACTORS - 12C-ZM-Stem Label:Non-labelled | Species:Zea mays | SampleSource:stem SUBJECT_SAMPLE_FACTORS - 12C-ZM-Seed Label:Non-labelled | Species:Zea mays | SampleSource:seed SUBJECT_SAMPLE_FACTORS - 12C-ZM-Root Label:Non-labelled | Species:Zea mays | SampleSource:root SUBJECT_SAMPLE_FACTORS - 13C-AC-Leaf Label:U-13C | Species:Allium cepa | SampleSource:leaf SUBJECT_SAMPLE_FACTORS - 13C-AC-Bulb Label:U-13C | Species:Allium cepa | SampleSource:bulb SUBJECT_SAMPLE_FACTORS - 13C-AC-Root Label:U-13C | Species:Allium cepa | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-AC-Leaf Label:Non-labelled | Species:Allium cepa | SampleSource:leaf SUBJECT_SAMPLE_FACTORS - 12C-AC-Bulb Label:Non-labelled | Species:Allium cepa | SampleSource:bulb SUBJECT_SAMPLE_FACTORS - 12C-AC-Root Label:Non-labelled | Species:Allium cepa | SampleSource:root SUBJECT_SAMPLE_FACTORS - 13C-NT-LeafAndStem Label:U-13C | Species:Nicotiana tabacum | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 13C-NT-Root Label:U-13C | Species:Nicotiana tabacum | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-NT-LeafAndStem Label:Non-labelled | Species:Nicotiana tabacum | SampleSource:leaf&stem SUBJECT_SAMPLE_FACTORS - 12C-NT-Root Label:Non-labelled | Species:Nicotiana tabacum | SampleSource:root SUBJECT_SAMPLE_FACTORS - 13C-OP-Root Label:U-13C | Species:Ophiorrhiza pumila | SampleSource:root SUBJECT_SAMPLE_FACTORS - 12C-OP-Root Label:Non-labelled | Species:Ophiorrhiza pumila | SampleSource:root #COLLECTION CO:COLLECTION_SUMMARY Leaf/stem and root tissues of Arabidopsis thaliana, Nicotiana tabacum, Glycine CO:COLLECTION_SUMMARY max, Glycyrrhiza glabra, Glycyrrhiza urahensis, and Oryza sativa, bulb, leaf, CO:COLLECTION_SUMMARY and root tissues of Allium cepa, flower, leaf/stem, seed pod, seed, and root CO:COLLECTION_SUMMARY tissues of Medicago truncatula, green and ripe fruit-, and leaf/stem tissues of CO:COLLECTION_SUMMARY Solanum lycopersicum, leaf/stem, root, and tuber tissues of Solanum tuberosum, CO:COLLECTION_SUMMARY and leaf, stem, seed, and root tissues of Zea mays were purchased from IsoLife CO:COLLECTION_SUMMARY Co. (Wageningen UR, Netherlands). The hairy root of Ophiorrhiza pumila was grown CO:COLLECTION_SUMMARY as follows. O. pumila hairy roots were derived and maintained, except for the CO:COLLECTION_SUMMARY carbon source. We supplied 1.5% D-glucose instead of 1.5% sucrose. We obtained CO:COLLECTION_SUMMARY 4-week-old O. pumila hairy roots and sub-cultured them in 1.5% D-glucose CO:COLLECTION_SUMMARY (U-13C6, 99%) (Cambridge Isotope Laboratories, Inc.) for two generations for CO:COLLECTION_SUMMARY complete isotope labeling of the metabolome. Hairy roots from the same batch CO:COLLECTION_SUMMARY used for isotope-labeling were sub-cultured for two subcultures in 1.5% CO:COLLECTION_SUMMARY D-glucose (Nacalai Tesque, Inc); they served as the control. Hairy roots from CO:COLLECTION_SUMMARY the second sub-culture of sub-cultured tissues growing in 1.5% isotope-labelled CO:COLLECTION_SUMMARY or un-labelled 1.5% D-glucose were harvested, wiped with paper towels and CO:COLLECTION_SUMMARY snap-frozen in liquid-N2. CO:SAMPLE_TYPE Plant #TREATMENT TR:TREATMENT_SUMMARY NA #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Samples (3 mg) of dried plant tissues were weighted in a 2.0-ml microtube SP:SAMPLEPREP_SUMMARY (Sarstedt). Their metabolites were extracted with 150 µl of 80% MeOH containing SP:SAMPLEPREP_SUMMARY 2.5 µM lidocaine and 10-camphour sulfonic acid per mg of dry weight using a SP:SAMPLEPREP_SUMMARY mixer-mill with zirconia beads [7 min at 18 Hz and 4 degree C (MM300; Retsch)]. SP:SAMPLEPREP_SUMMARY After 10-min centrifugation at 17,800 g the supernatant was filtered using an SP:SAMPLEPREP_SUMMARY HLB µElution plate (Waters). #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Waters Acquity CH:COLUMN_NAME Waters Acquity BEH C18 (100 x 2.1mm, 1.7um) CH: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 CH:FLOW_GRADIENT 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 CH:FLOW_GRADIENT min and 99.5%A/0.5%B at 15.0 min CH: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 CH:FLOW_RATE 14.4 min, and 0.3 ml/min at 14.5 min CH:COLUMN_TEMPERATURE 40 CH:SOLVENT_A water including 0.1% formic acid CH:SOLVENT_B acetonitrile including 0.1% formic acid #ANALYSIS AN:ANALYSIS_TYPE MS AN:DATA_FORMAT .raw #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Waters Synapt G2 S QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:CAPILLARY_VOLTAGE +3.00 kV MS:COLLISION_ENERGY 6 V MS:SOURCE_TEMPERATURE 120 MS:DESOLVATION_GAS_FLOW 800 l/hr MS:DESOLVATION_TEMPERATURE 450 degree C MS:SCAN_RANGE_MOVERZ 50 - 1500 MS:MS_RESULTS_FILE ST001095_AN001781_Results.txt UNITS:Peak intensity Has m/z:Yes Has RT:Yes RT units:Minutes #END