#METABOLOMICS WORKBENCH Mikikot_20181114_173233_mwtab.txt DATATRACK_ID:1569 STUDY_ID:ST001096 ANALYSIS_ID:AN001784 PROJECT_ID:PR000733 VERSION 1 CREATED_ON November 20, 2018, 10:08 am #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 Arabidopsis thaliana 25 accessions ST:STUDY_SUMMARY Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis ST:STUDY_SUMMARY thaliana accessions. 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 Arabidopsis thaliana SU:TAXONOMY_ID 3702 SU:GENOTYPE_STRAIN Col-0/Cvi-0/Bur-0/MIB-22/Shahdara/Fei-0/Bor-4/Ts-1/Tsu-0/RRS-7/Est-1/Ler-1/C24/RRS-10/Bla-1/Br-0/Got-7/Kas-2/Lov-5/Mr-0/Pna-17/T540/Tamm-2/UKNW06-460/Ty-0 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - S00_1 ecotype:Col-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S00_2 ecotype:Col-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S00_3 ecotype:Col-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S01_1 ecotype:Cvi-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S01_2 ecotype:Cvi-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S01_3 ecotype:Cvi-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S02_1 ecotype:Bur-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S02_2 ecotype:Bur-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S02_3 ecotype:Bur-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S03_1 ecotype:MIB-22 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S03_2 ecotype:MIB-22 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S03_3 ecotype:MIB-22 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S04_1 ecotype:Shahdara | tissue:shoot SUBJECT_SAMPLE_FACTORS - S04_2 ecotype:Shahdara | tissue:shoot SUBJECT_SAMPLE_FACTORS - S04_3 ecotype:Shahdara | tissue:shoot SUBJECT_SAMPLE_FACTORS - S05_1 ecotype:Fei-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S05_2 ecotype:Fei-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S05_3 ecotype:Fei-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S06_1 ecotype:Bor-4 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S06_2 ecotype:Bor-4 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S06_3 ecotype:Bor-4 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S07_1 ecotype:Ts-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S07_2 ecotype:Ts-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S07_3 ecotype:Ts-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S08_1 ecotype:Tsu-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S08_2 ecotype:Tsu-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S08_3 ecotype:Tsu-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S09_1 ecotype:RRS-7 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S09_2 ecotype:RRS-7 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S09_3 ecotype:RRS-7 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S10_1 ecotype:Est-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S10_2 ecotype:Est-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S10_3 ecotype:Est-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S11_1 ecotype:Ler-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S11_2 ecotype:Ler-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S11_3 ecotype:Ler-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S12_1 ecotype:C24 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S12_2 ecotype:C24 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S12_3 ecotype:C24 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S13_1 ecotype:RRS-10 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S13_2 ecotype:RRS-10 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S13_3 ecotype:RRS-10 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S14_1 ecotype:Bla-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S14_2 ecotype:Bla-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S14_3 ecotype:Bla-1 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S15_1 ecotype:Br-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S15_2 ecotype:Br-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S15_3 ecotype:Br-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S16_1 ecotype:Got-7 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S16_2 ecotype:Got-7 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S16_3 ecotype:Got-7 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S17_1 ecotype:Kas-2 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S17_2 ecotype:Kas-2 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S17_3 ecotype:Kas-2 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S18_1 ecotype:Lov-5 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S18_2 ecotype:Lov-5 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S18_3 ecotype:Lov-5 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S19_1 ecotype:Mr-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S19_2 ecotype:Mr-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S19_3 ecotype:Mr-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S20_1 ecotype:Pna-17 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S20_2 ecotype:Pna-17 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S20_3 ecotype:Pna-17 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S21_1 ecotype:T540 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S21_2 ecotype:T540 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S21_3 ecotype:T540 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S22_1 ecotype:Tamm-2 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S22_2 ecotype:Tamm-2 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S22_3 ecotype:Tamm-2 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S23_1 ecotype:UKNW06-460 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S23_2 ecotype:UKNW06-460 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S23_3 ecotype:UKNW06-460 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S24_1 ecotype:Ty-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S24_2 ecotype:Ty-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - S24_3 ecotype:Ty-0 | tissue:shoot SUBJECT_SAMPLE_FACTORS - R00_1 ecotype:Col-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R00_2 ecotype:Col-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R00_3 ecotype:Col-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R01_1 ecotype:Cvi-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R01_2 ecotype:Cvi-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R01_3 ecotype:Cvi-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R02_1 ecotype:Bur-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R02_2 ecotype:Bur-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R02_3 ecotype:Bur-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R03_1 ecotype:MIB-22 | tissue:root SUBJECT_SAMPLE_FACTORS - R03_2 ecotype:MIB-22 | tissue:root SUBJECT_SAMPLE_FACTORS - R03_3 ecotype:MIB-22 | tissue:root SUBJECT_SAMPLE_FACTORS - R04_1 ecotype:Shahdara | tissue:root SUBJECT_SAMPLE_FACTORS - R04_2 ecotype:Shahdara | tissue:root SUBJECT_SAMPLE_FACTORS - R04_3 ecotype:Shahdara | tissue:root SUBJECT_SAMPLE_FACTORS - R05_1 ecotype:Fei-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R05_2 ecotype:Fei-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R05_3 ecotype:Fei-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R06_1 ecotype:Bor-4 | tissue:root SUBJECT_SAMPLE_FACTORS - R06_2 ecotype:Bor-4 | tissue:root SUBJECT_SAMPLE_FACTORS - R06_3 ecotype:Bor-4 | tissue:root SUBJECT_SAMPLE_FACTORS - R07_1 ecotype:Ts-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R07_2 ecotype:Ts-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R07_3 ecotype:Ts-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R08_1 ecotype:Tsu-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R08_2 ecotype:Tsu-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R08_3 ecotype:Tsu-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R09_1 ecotype:RRS-7 | tissue:root SUBJECT_SAMPLE_FACTORS - R09_2 ecotype:RRS-7 | tissue:root SUBJECT_SAMPLE_FACTORS - R09_3 ecotype:RRS-7 | tissue:root SUBJECT_SAMPLE_FACTORS - R10_1 ecotype:Est-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R10_2 ecotype:Est-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R10_3 ecotype:Est-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R11_1 ecotype:Ler-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R11_2 ecotype:Ler-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R11_3 ecotype:Ler-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R12_1 ecotype:C24 | tissue:root SUBJECT_SAMPLE_FACTORS - R12_2 ecotype:C24 | tissue:root SUBJECT_SAMPLE_FACTORS - R12_3 ecotype:C24 | tissue:root SUBJECT_SAMPLE_FACTORS - R13_1 ecotype:RRS-10 | tissue:root SUBJECT_SAMPLE_FACTORS - R13_2 ecotype:RRS-10 | tissue:root SUBJECT_SAMPLE_FACTORS - R13_3 ecotype:RRS-10 | tissue:root SUBJECT_SAMPLE_FACTORS - R14_1 ecotype:Bla-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R14_2 ecotype:Bla-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R14_3 ecotype:Bla-1 | tissue:root SUBJECT_SAMPLE_FACTORS - R15_1 ecotype:Br-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R15_2 ecotype:Br-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R15_3 ecotype:Br-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R16_1 ecotype:Got-7 | tissue:root SUBJECT_SAMPLE_FACTORS - R16_2 ecotype:Got-7 | tissue:root SUBJECT_SAMPLE_FACTORS - R16_3 ecotype:Got-7 | tissue:root SUBJECT_SAMPLE_FACTORS - R17_1 ecotype:Kas-2 | tissue:root SUBJECT_SAMPLE_FACTORS - R17_2 ecotype:Kas-2 | tissue:root SUBJECT_SAMPLE_FACTORS - R17_3 ecotype:Kas-2 | tissue:root SUBJECT_SAMPLE_FACTORS - R18_1 ecotype:Lov-5 | tissue:root SUBJECT_SAMPLE_FACTORS - R18_2 ecotype:Lov-5 | tissue:root SUBJECT_SAMPLE_FACTORS - R18_3 ecotype:Lov-5 | tissue:root SUBJECT_SAMPLE_FACTORS - R19_1 ecotype:Mr-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R19_2 ecotype:Mr-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R19_3 ecotype:Mr-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R20_1 ecotype:Pna-17 | tissue:root SUBJECT_SAMPLE_FACTORS - R20_2 ecotype:Pna-17 | tissue:root SUBJECT_SAMPLE_FACTORS - R20_3 ecotype:Pna-17 | tissue:root SUBJECT_SAMPLE_FACTORS - R21_1 ecotype:T540 | tissue:root SUBJECT_SAMPLE_FACTORS - R21_2 ecotype:T540 | tissue:root SUBJECT_SAMPLE_FACTORS - R21_3 ecotype:T540 | tissue:root SUBJECT_SAMPLE_FACTORS - R22_1 ecotype:Tamm-2 | tissue:root SUBJECT_SAMPLE_FACTORS - R22_2 ecotype:Tamm-2 | tissue:root SUBJECT_SAMPLE_FACTORS - R22_3 ecotype:Tamm-2 | tissue:root SUBJECT_SAMPLE_FACTORS - R23_1 ecotype:UKNW06-460 | tissue:root SUBJECT_SAMPLE_FACTORS - R23_2 ecotype:UKNW06-460 | tissue:root SUBJECT_SAMPLE_FACTORS - R23_3 ecotype:UKNW06-460 | tissue:root SUBJECT_SAMPLE_FACTORS - R24_1 ecotype:Ty-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R24_2 ecotype:Ty-0 | tissue:root SUBJECT_SAMPLE_FACTORS - R24_3 ecotype:Ty-0 | tissue:root #COLLECTION CO:COLLECTION_SUMMARY The ABRC stock IDs are stored in the uploaded data folder. Sterilized seeds were CO:COLLECTION_SUMMARY kept for 2 days at 4 degreeC in the dark, and then sown on Murashige and Skoog CO:COLLECTION_SUMMARY (MS) medium agar containing 1% sucrose. All plates were placed in a growth CO:COLLECTION_SUMMARY chamber at 22 degreeC under a 16-hr light (approximately 40 micro mol/(sec CO:COLLECTION_SUMMARY m^2)/8-hr dark cycle. After 3-week cultivation the plants were harvested and CO:COLLECTION_SUMMARY shoot and root parts were immediately frozen in liquid nitrogen and lyophilized CO:COLLECTION_SUMMARY at -55 degreeC. Lyophilized samples were stored at -80 degreeC until use. Three CO:COLLECTION_SUMMARY technical replicates for each strain were prepared from quenched samples. 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 NEGATIVE MS:CAPILLARY_VOLTAGE -2.75 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 ST001096_AN001784_Results.txt UNITS:Peak intensity Has m/z:Yes Has RT:Yes RT units:Minutes #END