{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002841","ANALYSIS_ID":"AN004650","VERSION":"1","CREATED_ON":"August 30, 2023, 10:03 am"},

"PROJECT":{"PROJECT_TITLE":"Collaborative role of YqgC and superoxide dismutase (MnSOD) in manganese intoxication","PROJECT_TYPE":"LC-MS targettged analysis","PROJECT_SUMMARY":"Bacterial metal ion homeostasis is strongly regulated by various metalloregulators. This project is focused on the role of yqgC-soda operon of B. subtilis in Manganese (Mn) ion metal homeostasis and the dependencies of these genes to maintain bacterial survival in the excess of Mn.","INSTITUTE":"Weill Cornell Medicine","DEPARTMENT":"Medicine","LABORATORY":"Rhee Lab","LAST_NAME":"Soni","FIRST_NAME":"Vijay","ADDRESS":"413 E 69TH STREET, Belfer Research Building, New York, New York, 10021, USA","EMAIL":"vis2032@med.cornell.edu","PHONE":"9175391105","FUNDING_SOURCE":"R35GM122461, NIAID:R25 AI140472","PROJECT_COMMENTS":"NA","PUBLICATIONS":"NA","CONTRIBUTORS":"Ankita J. Sachla, Vijay Soni, Yuanchan Luo, Kyu Y. Rhee, John D. Helmann"},

"STUDY":{"STUDY_TITLE":"Collaborative role of YqgC and superoxide dismutase (MnSOD) in manganese intoxication: Replicate Experiment 2","STUDY_TYPE":"Targeted MS Analysis","STUDY_SUMMARY":"In this study, we are validating the mutual impact of yqgC and superoxide dismutase (MnSOD) deletion (YS strain) and resultant hypersensitivity to Manganese (Mn). Our genetic and physiological studies show that Mn intoxication is a result of distinct enzymatic vulnerabilities via alleviated expression of Mg-dependent, chorismate-utilizing enzymes of the menaquinone, siderophore, and tryptophan (MST) family (due to mismetalation).","INSTITUTE":"Cornell University","DEPARTMENT":"Medicine","LABORATORY":"Rhee Lab","LAST_NAME":"Soni","FIRST_NAME":"Vijay","ADDRESS":"Weill Cornell Medical College, 413 E 69th St","EMAIL":"vis2032@med.cornell.edu","PHONE":"9175391105","NUM_GROUPS":"10","TOTAL_SUBJECTS":"60","STUDY_COMMENTS":"NA","PUBLICATIONS":"NA"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Bacillus subtilis","TAXONOMY_ID":"1423","GENOTYPE_STRAIN":"168","AGE_OR_AGE_RANGE":"NA","WEIGHT_OR_WEIGHT_RANGE":"NA","HEIGHT_OR_HEIGHT_RANGE":"NA","GENDER":"Not applicable","CELL_BIOSOURCE_OR_SUPPLIER":"NA","CELL_STRAIN_DETAILS":"NA","SUBJECT_COMMENTS":"NA","CELL_PRIMARY_IMMORTALIZED":"NA","CELL_PASSAGE_NUMBER":"NA","CELL_COUNTS":"NA","SPECIES_GROUP":"NA"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"WTd_UT_Lys2",
"Factors":{"Genotype":"WTCU1065_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"WTd_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"WTe_UT_Lys2",
"Factors":{"Genotype":"WTCU1065_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"WTe_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"WTf_UT_Lys2",
"Factors":{"Genotype":"WTCU1065_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"WTf_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Sd_UT_Lys2",
"Factors":{"Genotype":"sodA_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"Sd_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Se_UT_Lys2",
"Factors":{"Genotype":"sodA_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"Se_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Sf_UT_Lys2",
"Factors":{"Genotype":"sodA_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"Sf_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Yd_UT_Lys2",
"Factors":{"Genotype":"yqgC_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"Yd_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Ye_UT_Lys2",
"Factors":{"Genotype":"yqgC_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"Ye_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Yf_UT_Lys2",
"Factors":{"Genotype":"yqgC_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"Yf_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"YSd_UT_Lys2",
"Factors":{"Genotype":"yqgC-sodA_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"YSd_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"YSe_UT_Lys2",
"Factors":{"Genotype":"yqgC-sodA_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"YSe_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"YSf_UT_Lys2",
"Factors":{"Genotype":"yqgC-sodA_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"YSf_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"PSd_UT_Lys2",
"Factors":{"Genotype":"mnePmneS_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"PSd_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"PSe_UT_Lys2",
"Factors":{"Genotype":"mnePmneS_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"PSe_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"PSf_UT_Lys2",
"Factors":{"Genotype":"mnePmneS_untreated"},
"Additional sample data":{"Treatment":"Control","RAW_FILE_NAME":"PSf_UT_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"WTd_Mn_Lys2",
"Factors":{"Genotype":"WTCU1065_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"WTd_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"WTe_Mn_Lys2",
"Factors":{"Genotype":"WTCU1065_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"WTe_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"WTf_Mn_Lys2",
"Factors":{"Genotype":"WTCU1065_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"WTf_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Sd_Mn_Lys2",
"Factors":{"Genotype":"sodA_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"Sd_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Se_Mn_Lys2",
"Factors":{"Genotype":"sodA_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"Se_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Sf_Mn_Lys2",
"Factors":{"Genotype":"sodA_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"Sf_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Yd_Mn_Lys2",
"Factors":{"Genotype":"yqgC_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"Yd_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Ye_Mn_Lys2",
"Factors":{"Genotype":"yqgC_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"Ye_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"Yf_Mn_Lys2",
"Factors":{"Genotype":"yqgC_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"Yf_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"YSd_Mn_Lys2",
"Factors":{"Genotype":"yqgC-sodA_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"YSd_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"YSe_Mn_Lys2",
"Factors":{"Genotype":"yqgC-sodA_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"YSe_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"YSf_Mn_Lys2",
"Factors":{"Genotype":"yqgC-sodA_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"YSf_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"PSd_Mn_Lys2",
"Factors":{"Genotype":"mnePmneS_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"PSd_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"PSe_Mn_Lys2",
"Factors":{"Genotype":"mnePmneS_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"PSe_Mn_Lys2"}
},
{
"Subject ID":"-",
"Sample ID":"PSf_Mn_Lys2",
"Factors":{"Genotype":"mnePmneS_Mn_treated"},
"Additional sample data":{"Treatment":"Mn Treated","RAW_FILE_NAME":"PSf_Mn_Lys2"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"All strains were grown in LB at 37 ˚C until 0.4 OD600 followed by 60 min treatment with or without 0.15 mM MnCl2 37 ˚C. Cells were pelleted and quenched by resuspending in chilled 0.6 ml of mixtures of acetonitrile:methanol:water (40:40:20).","COLLECTION_PROTOCOL_ID":"NA","COLLECTION_PROTOCOL_FILENAME":"NA","COLLECTION_PROTOCOL_COMMENTS":"NA","SAMPLE_TYPE":"Bacterial cells","COLLECTION_METHOD":"NA","COLLECTION_LOCATION":"NA","COLLECTION_FREQUENCY":"NA","COLLECTION_DURATION":"NA","VOLUMEORAMOUNT_COLLECTED":"NA","STORAGE_CONDITIONS":"-80℃","COLLECTION_VIALS":"Bead beating tubes","STORAGE_VIALS":"NA","ADDITIVES":"NA","TISSUE_CELL_IDENTIFICATION":"NA","TISSUE_CELL_QUANTITY_TAKEN":"NA"},

"TREATMENT":{"TREATMENT_SUMMARY":"All strains were treated without (control group) or with (treated group) 0.15 mM of MnCl2 for 60 min at 37 ˚C.","TREATMENT_PROTOCOL_ID":"NA","TREATMENT_PROTOCOL_FILENAME":"NA","TREATMENT_PROTOCOL_COMMENTS":"NA","TREATMENT":"NA","TREATMENT_COMPOUND":"MnCl2 salt","TREATMENT_ROUTE":"Direct in bacterial culture","TREATMENT_DOSE":"0.15 mM","TREATMENT_DOSEVOLUME":"NA","TREATMENT_DOSEDURATION":"NA","TREATMENT_VEHICLE":"Water","CELL_STORAGE":"-80","CELL_GROWTH_CONTAINER":"Flask","CELL_GROWTH_CONFIG":"200 rpm","CELL_GROWTH_RATE":"40-60 min","CELL_INOC_PROC":"NA","CELL_MEDIA":"LB Media","CELL_ENVIR_COND":"NA","CELL_HARVESTING":"acetonitrile:methanol:water (40:40:20)","CELL_PCT_CONFLUENCE":"0.4 OD600","CELL_MEDIA_LASTCHANGED":"NA"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Samples were lysed using 0.1 mm Zirconia beads in a Precellys homogenizer. Lysed suspensions were centrifuged at 12,000 rpm for 8 min at 37 ˚C. Supernatants were passed through 0.22 um SpinX tube filter and flowthrough was collected for the LC-MS run.","SAMPLEPREP_PROTOCOL_ID":"NA","SAMPLEPREP_PROTOCOL_FILENAME":"NA","SAMPLEPREP_PROTOCOL_COMMENTS":"NA","PROCESSING_METHOD":"NA","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACTION_METHOD":"Beat beating","EXTRACT_ENRICHMENT":"NA","EXTRACT_CLEANUP":"NA","EXTRACT_STORAGE":"4℃","SAMPLE_RESUSPENSION":"NA","SAMPLE_DERIVATIZATION":"NA","SAMPLE_SPIKING":"NA","SUBCELLULAR_LOCATION":"NA"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Liquid chromatography (Agilent 1290 Infinity II) was used for the formic acid method.","CHROMATOGRAPHY_TYPE":"Normal phase","INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"Microsolv Diamond hydride (150 x 2.1mm,4um)","SOLVENT_A":"Milli Q H2O + 0.2% Formic Acid","SOLVENT_B":"Acetonitrile + 0.2% Formic Acid","SOLVENT_C":"NA","FLOW_GRADIENT":"0–2 min, 85% B; 3–5 min, 80% B; 6–7 min, 75%; 8–9 min, 70% B; 10–11 min, 50% B; 11–14 min 20% B; 14–24 min 5% B followed by a 10 min re-equilibration period at 85% B","FLOW_RATE":"0.4","COLUMN_TEMPERATURE":"25"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Rhee lab","OPERATOR_NAME":"Vijay Soni","SOFTWARE_VERSION":"Profinder B.08.00"},

"MS":{"INSTRUMENT_NAME":"Agilent 6220 TOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Profinder B.08.00 Was used for the data analysis"},

"MS_METABOLITE_DATA":{
"Units":"Area under the curve",

"Data":[{"Metabolite":"2,6-Diaminopimelic Acid","WTd_UT_Lys2":"1389127.63","WTe_UT_Lys2":"1939540.352","WTf_UT_Lys2":"2159591.01","Sd_UT_Lys2":"3272603.489","Se_UT_Lys2":"3225506.272","Sf_UT_Lys2":"3229631.369","Yd_UT_Lys2":"3707825.132","Ye_UT_Lys2":"3557487.316","Yf_UT_Lys2":"3579650.89","YSd_UT_Lys2":"2217343.603","YSe_UT_Lys2":"2357565.275","YSf_UT_Lys2":"2150389.975","PSd_UT_Lys2":"2276621.017","PSe_UT_Lys2":"2129560.484","PSf_UT_Lys2":"2448523.118","WTd_Mn_Lys2":"2185028.943","WTe_Mn_Lys2":"2289631.302","WTf_Mn_Lys2":"2063129.216","Sd_Mn_Lys2":"2877567.166","Se_Mn_Lys2":"2775349.099","Sf_Mn_Lys2":"3180614.191","Yd_Mn_Lys2":"2682179.566","Ye_Mn_Lys2":"2624021.751","Yf_Mn_Lys2":"2530168.865","YSd_Mn_Lys2":"4611917.757","YSe_Mn_Lys2":"3787342.936","YSf_Mn_Lys2":"3176265.843","PSd_Mn_Lys2":"3602041.913","PSe_Mn_Lys2":"3296502.55","PSf_Mn_Lys2":"3340758.55"},{"Metabolite":"5-Methylthioadenosine","WTd_UT_Lys2":"32023.01652","WTe_UT_Lys2":"38174.85481","WTf_UT_Lys2":"37131.69137","Sd_UT_Lys2":"59608.30874","Se_UT_Lys2":"61161.61643","Sf_UT_Lys2":"66499.50401","Yd_UT_Lys2":"145401.3443","Ye_UT_Lys2":"158976.9418","Yf_UT_Lys2":"159405.9771","YSd_UT_Lys2":"48195.45719","YSe_UT_Lys2":"63862.96316","YSf_UT_Lys2":"65911.18304","PSd_UT_Lys2":"50582.60801","PSe_UT_Lys2":"48371.70664","PSf_UT_Lys2":"57313.71681","WTd_Mn_Lys2":"37552.50138","WTe_Mn_Lys2":"37147.03013","WTf_Mn_Lys2":"38437.63856","Sd_Mn_Lys2":"47387.37377","Se_Mn_Lys2":"40914.5966","Sf_Mn_Lys2":"43135.78622","Yd_Mn_Lys2":"46720.65852","Ye_Mn_Lys2":"46706.37042","Yf_Mn_Lys2":"53358.08467","YSd_Mn_Lys2":"79261.01043","YSe_Mn_Lys2":"81385.37489","YSf_Mn_Lys2":"76044.70966","PSd_Mn_Lys2":"100038.6168","PSe_Mn_Lys2":"104253.5229","PSf_Mn_Lys2":"107275.5505"},{"Metabolite":"Acetylhomoserine","WTd_UT_Lys2":"2422204.544","WTe_UT_Lys2":"1987688.473","WTf_UT_Lys2":"1903300.225","Sd_UT_Lys2":"4725780.662","Se_UT_Lys2":"4380918.754","Sf_UT_Lys2":"4142836.138","Yd_UT_Lys2":"2323522.097","Ye_UT_Lys2":"2259932.714","Yf_UT_Lys2":"2251995.401","YSd_UT_Lys2":"1875152.398","YSe_UT_Lys2":"1783875.035","YSf_UT_Lys2":"1739862.753","PSd_UT_Lys2":"1425375.218","PSe_UT_Lys2":"1436252.803","PSf_UT_Lys2":"1262502.585","WTd_Mn_Lys2":"1155724.4","WTe_Mn_Lys2":"1069663.668","WTf_Mn_Lys2":"1049240.307","Sd_Mn_Lys2":"1099497.241","Se_Mn_Lys2":"1062538.048","Sf_Mn_Lys2":"1054687.29","Yd_Mn_Lys2":"656388.1653","Ye_Mn_Lys2":"624847.0248","Yf_Mn_Lys2":"651084.3797","YSd_Mn_Lys2":"426665.6153","YSe_Mn_Lys2":"557702.9284","YSf_Mn_Lys2":"760621.9751","PSd_Mn_Lys2":"515273.958","PSe_Mn_Lys2":"535848.4827","PSf_Mn_Lys2":"618700.5726"},{"Metabolite":"Acetyl-L-glutamate 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