{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002547","ANALYSIS_ID":"AN004194","VERSION":"1","CREATED_ON":"April 7, 2023, 10:51 am"},

"PROJECT":{"PROJECT_TITLE":"LCMS analysis of WT mice treated with PBS or bleomycin","PROJECT_SUMMARY":"C57bl/6 mice were treated with either PBS or bleomycin and waited for 21 days to develop fibrosis. Mouse lungs were resected following by LC-QTOF analysis.","INSTITUTE":"University of Florida","LAST_NAME":"Sun","FIRST_NAME":"Ramon","ADDRESS":"1200 Newell Drive, ARB, Gainesville, FL, 32610, USA","EMAIL":"ramonsun@ufl.edu","PHONE":"8594733233"},

"STUDY":{"STUDY_TITLE":"C57bl/6 mice subjected to either PBS or bleomycin treatment to develop fibrosis","STUDY_SUMMARY":"C57bl/6 mice subjected to either PBS or bleomycin treatment. By day 21, lung fibrosis will develop. We resected the lung and performed LC-QTOF analysis on small molecule metabolites between the two groups.","INSTITUTE":"University of Florida","LAST_NAME":"Sun","FIRST_NAME":"Ramon","ADDRESS":"1200 Newell Drive, ARB, Gainesville, FL, 32610, USA","EMAIL":"ramonsun@ufl.edu","PHONE":"8594733233"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"WT_Bleo_1",
"Factors":{"Treatment":"Bleomycin"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME":"WT_Bleo_1.d"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Bleo_2",
"Factors":{"Treatment":"Bleomycin"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME":"WT_Bleo_2.d"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Bleo_3",
"Factors":{"Treatment":"Bleomycin"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME":"WT_Bleo_3.d"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Bleo_4",
"Factors":{"Treatment":"Bleomycin"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME":"WT_Bleo_4.d"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Bleo_5",
"Factors":{"Treatment":"Bleomycin"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME":"WT_Bleo_5.d"}
},
{
"Subject ID":"-",
"Sample ID":"WT_PBS_1",
"Factors":{"Treatment":"PBS"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME":"WT_PBS_1.d"}
},
{
"Subject ID":"-",
"Sample ID":"WT_PBS_2",
"Factors":{"Treatment":"PBS"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME":"WT_PBS_2.d"}
},
{
"Subject ID":"-",
"Sample ID":"WT_PBS_3",
"Factors":{"Treatment":"PBS"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME":"WT_PBS_3.d"}
},
{
"Subject ID":"-",
"Sample ID":"WT_PBS_4",
"Factors":{"Treatment":"PBS"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME":"WT_PBS_4.d"}
},
{
"Subject ID":"-",
"Sample ID":"WT_PBS_5",
"Factors":{"Treatment":"PBS"},
"Additional sample data":{"Genotype":"Wild-type","RAW_FILE_NAME":"WT_PBS_5.d"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Approximately 20mg of pulverized, frozen tissue was extracted in 3ml ice-cold 60% acetonitrile by extensively vortexing. Next, 1ml chloroform was added to each sample and samples were mixed by manual shaking followed by centrifuging at 3,200g for 20 minutes at 4°C. The aqueous layer was moved to a new tube and lyophilized. The middle layer containing protein and insoluble material was transferred to a new tube, washed twice with 50% methanol, once with 100% methanol, and briefly dried in a speed-vac. After drying, the insoluble material was hydrolyzed by heating samples in 3N HCl at 95°C for 2 hours. 100% methanol was added to hydrolysate to achieve a final concentration of 50% methanol, samples mixed, centrifuged at 18,000g for 10 min at 4°C, then supernatant dried on a speed vac.","SAMPLE_TYPE":"Lung","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"mice were treated with either PBS or bleomycin."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Approximately 20mg of pulverized, frozen tissue was extracted in 3ml ice-cold 60% acetonitrile by extensively vortexing. Next, 1ml chloroform was added to each sample and samples were mixed by manual shaking followed by centrifuging at 3,200g for 20 minutes at 4°C. The aqueous layer was moved to a new tube and lyophilized. The middle layer containing protein and insoluble material was transferred to a new tube, washed twice with 50% methanol, once with 100% methanol, and briefly dried in a speed-vac. After drying, the insoluble material was hydrolyzed by heating samples in 3N HCl at 95°C for 2 hours. 100% methanol was added to hydrolysate to achieve a final concentration of 50% methanol, samples mixed, centrifuged at 18,000g for 10 min at 4°C, then supernatant dried on a speed vac.","PROCESSING_STORAGE_CONDITIONS":"-80℃","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Agilent InfinityLab Poroshell 120 EC-C8 (150 x 2.1mm,2.7um)","SOLVENT_A":"100% water; 10mM ammonium acetate","SOLVENT_B":"100% acetonitrile","FLOW_GRADIENT":"0-15 min linear ramp 90%B to 30%B, 15-18 min isocratic flow of 30%B, 18-19 min linear ramp from 30%B to 90%B, and 19-27 min column regeneration with isocratic flow of 90%B","FLOW_RATE":"0.25ml/min","COLUMN_TEMPERATURE":"40"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Agilent 6545 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Metabolites were measured using an Agilent 6545 quadrapole-time of flight mass spectrometer (MS) coupled to an Agilent 1290 Infinity II UHPLC. Individual samples and standards were acquired with full scan MS in negative mode. Peaks for the deprotonated [M-H]¬- ions were extracted and integrated using Agilent Qualitative Analysis software."},

"MS_METABOLITE_DATA":{
"Units":"normalized abundance",

"Data":[{"Metabolite":"Glycogen","WT_PBS_1":"0.605233062","WT_PBS_2":"0.31144096","WT_PBS_3":"0.408441054","WT_PBS_4":"0.358180007","WT_PBS_5":"0.239911497","WT_Bleo_1":"0.321150661","WT_Bleo_2":"0.385355064","WT_Bleo_3":"0.505263955","WT_Bleo_4":"0.30419289","WT_Bleo_5":"0.35147671"},{"Metabolite":"alanine","WT_PBS_1":"0.0009349","WT_PBS_2":"0.00082358","WT_PBS_3":"0.00844705","WT_PBS_4":"0.00849274","WT_PBS_5":"0.00415192","WT_Bleo_1":"0.00406858","WT_Bleo_2":"0.00482769","WT_Bleo_3":"0.00393863","WT_Bleo_4":"0.00440866","WT_Bleo_5":"0.00486184"},{"Metabolite":"lactate","WT_PBS_1":"0.005574986","WT_PBS_2":"0.004054798","WT_PBS_3":"0.024797797","WT_PBS_4":"0.041267525","WT_PBS_5":"0.014373707","WT_Bleo_1":"0.020187162","WT_Bleo_2":"0.025968448","WT_Bleo_3":"0.035710483","WT_Bleo_4":"0.01480433","WT_Bleo_5":"0.015376958"},{"Metabolite":"serine","WT_PBS_1":"0.000250325","WT_PBS_2":"3.15117E-05","WT_PBS_3":"0.000664789","WT_PBS_4":"0.000601507","WT_PBS_5":"0.00037111","WT_Bleo_1":"0.001117206","WT_Bleo_2":"0.001397057","WT_Bleo_3":"0.001039627","WT_Bleo_4":"0.000729278","WT_Bleo_5":"0.001113888"},{"Metabolite":"norvaline","WT_PBS_1":"0.045042633","WT_PBS_2":"0.058210915","WT_PBS_3":"0.227861799","WT_PBS_4":"0.292377359","WT_PBS_5":"0.157563905","WT_Bleo_1":"0.126897566","WT_Bleo_2":"0.078398261","WT_Bleo_3":"0.057810656","WT_Bleo_4":"0.063060562","WT_Bleo_5":"0.09888369"},{"Metabolite":"succinate","WT_PBS_1":"0.000525258","WT_PBS_2":"0.000628969","WT_PBS_3":"0.002459071","WT_PBS_4":"0.002818623","WT_PBS_5":"0.001306143","WT_Bleo_1":"0.001601458","WT_Bleo_2":"0.002131449","WT_Bleo_3":"0.001211851","WT_Bleo_4":"0.001660998","WT_Bleo_5":"0.001352133"},{"Metabolite":"aspartic acid","WT_PBS_1":"0.011231498","WT_PBS_2":"0.012304176","WT_PBS_3":"0.165664304","WT_PBS_4":"0.135874554","WT_PBS_5":"0.061565885","WT_Bleo_1":"0.041541047","WT_Bleo_2":"0.042458234","WT_Bleo_3":"0.020919815","WT_Bleo_4":"0.025091175","WT_Bleo_5":"0.04376086"},{"Metabolite":"malate","WT_PBS_1":"0.0924343","WT_PBS_2":"0.12598456","WT_PBS_3":"0.07552393","WT_PBS_4":"0.05182775","WT_PBS_5":"0.0712876","WT_Bleo_1":"0.03615668","WT_Bleo_2":"0.03126342","WT_Bleo_3":"0.01576377","WT_Bleo_4":"0.02056699","WT_Bleo_5":"0.03757182"},{"Metabolite":"glutamine","WT_PBS_1":"0.0018315","WT_PBS_2":"0.00140017","WT_PBS_3":"0.0202885","WT_PBS_4":"0.01642977","WT_PBS_5":"0.00763188","WT_Bleo_1":"0.01037753","WT_Bleo_2":"0.01037281","WT_Bleo_3":"0.00688208","WT_Bleo_4":"0.00753524","WT_Bleo_5":"0.01216027"},{"Metabolite":"glutamic acid","WT_PBS_1":"0.00698358","WT_PBS_2":"0.00592375","WT_PBS_3":"0.05106516","WT_PBS_4":"0.03499098","WT_PBS_5":"0.02483869","WT_Bleo_1":"0.02209001","WT_Bleo_2":"0.02617074","WT_Bleo_3":"0.01658751","WT_Bleo_4":"0.01764384","WT_Bleo_5":"0.02492585"},{"Metabolite":"DHAP/G3P","WT_PBS_1":"0","WT_PBS_2":"0","WT_PBS_3":"0","WT_PBS_4":"0.003724501","WT_PBS_5":"0","WT_Bleo_1":"0","WT_Bleo_2":"0","WT_Bleo_3":"0","WT_Bleo_4":"0","WT_Bleo_5":"0"},{"Metabolite":"N-acetyl-aspartate","WT_PBS_1":"0.005449591","WT_PBS_2":"0.007195353","WT_PBS_3":"0.051519539","WT_PBS_4":"0.058412113","WT_PBS_5":"0.030823235","WT_Bleo_1":"0.016414528","WT_Bleo_2":"0.021026921","WT_Bleo_3":"0.009244828","WT_Bleo_4":"0.012466844","WT_Bleo_5":"0.01875474"},{"Metabolite":"glucose","WT_PBS_1":"0.001148272","WT_PBS_2":"0.000700262","WT_PBS_3":"0.020883774","WT_PBS_4":"0.026216931","WT_PBS_5":"0.005215696","WT_Bleo_1":"0.007498452","WT_Bleo_2":"0.005029069","WT_Bleo_3":"0.005162432","WT_Bleo_4":"0.003272864","WT_Bleo_5":"0.002507878"},{"Metabolite":"3PG","WT_PBS_1":"8.89886E-05","WT_PBS_2":"0.000135371","WT_PBS_3":"0.002588599","WT_PBS_4":"0.00066524","WT_PBS_5":"0.00194306","WT_Bleo_1":"0.001378302","WT_Bleo_2":"0.001021196","WT_Bleo_3":"0.000482722","WT_Bleo_4":"0.000716047","WT_Bleo_5":"0.00060653"},{"Metabolite":"citrate","WT_PBS_1":"0.1664217","WT_PBS_2":"0.12069924","WT_PBS_3":"0.16293699","WT_PBS_4":"0.119533742","WT_PBS_5":"0.13933751","WT_Bleo_1":"0.0758937","WT_Bleo_2":"0.04403494","WT_Bleo_3":"0.03607964","WT_Bleo_4":"0.03125702","WT_Bleo_5":"0.05354841"},{"Metabolite":"palmitate","WT_PBS_1":"0.059327672","WT_PBS_2":"0.083714388","WT_PBS_3":"0.270704231","WT_PBS_4":"0.307199134","WT_PBS_5":"0.169930792","WT_Bleo_1":"0.148506738","WT_Bleo_2":"0.091935611","WT_Bleo_3":"0.059359117","WT_Bleo_4":"0.058633895","WT_Bleo_5":"0.092315412"},{"Metabolite":"G6P","WT_PBS_1":"0.028119","WT_PBS_2":"0.029534","WT_PBS_3":"0.02716506","WT_PBS_4":"0.023143","WT_PBS_5":"0.025144","WT_Bleo_1":"0.00404964","WT_Bleo_2":"0.00232608","WT_Bleo_3":"0.0032266","WT_Bleo_4":"0.00127998","WT_Bleo_5":"0.0017998"},{"Metabolite":"F6P","WT_PBS_1":"0.0081192","WT_PBS_2":"0.029534","WT_PBS_3":"0.00708718","WT_PBS_4":"0.01221656","WT_PBS_5":"0.050005","WT_Bleo_1":"0.00393262","WT_Bleo_2":"0.00533279","WT_Bleo_3":"0.00226718","WT_Bleo_4":"0.0026718","WT_Bleo_5":"0.00497691"},{"Metabolite":"AMP","WT_PBS_1":"0.003138001","WT_PBS_2":"0.002901206","WT_PBS_3":"0.020115707","WT_PBS_4":"0.031979618","WT_PBS_5":"0.017307319","WT_Bleo_1":"0.013097816","WT_Bleo_2":"0.015601454","WT_Bleo_3":"0.007321662","WT_Bleo_4":"0.012195186","WT_Bleo_5":"0.011795218"},{"Metabolite":"ADP","WT_PBS_1":"0.00453305","WT_PBS_2":"0.001861918","WT_PBS_3":"0.00677537","WT_PBS_4":"0.006663577","WT_PBS_5":"0.03776343","WT_Bleo_1":"0.01431559","WT_Bleo_2":"0.009719385","WT_Bleo_3":"0.002629915","WT_Bleo_4":"0.006627242","WT_Bleo_5":"0.004576713"},{"Metabolite":"ATP","WT_PBS_1":"0.001935485","WT_PBS_2":"0.000452254","WT_PBS_3":"0.001213456","WT_PBS_4":"0.000458244","WT_PBS_5":"0.016483115","WT_Bleo_1":"0.008772914","WT_Bleo_2":"0.003547585","WT_Bleo_3":"0.000870076","WT_Bleo_4":"0.001561953","WT_Bleo_5":"0.001145418"},{"Metabolite":"UDP-glucose","WT_PBS_1":"0.0070561","WT_PBS_2":"0.0025035","WT_PBS_3":"0.0030113","WT_PBS_4":"0.00209043","WT_PBS_5":"0.0025613","WT_Bleo_1":"0.00024078","WT_Bleo_2":"0.000052898","WT_Bleo_3":"0.000036436","WT_Bleo_4":"0.00059006","WT_Bleo_5":"0.000048164"},{"Metabolite":"UDP-GlcNAc","WT_PBS_1":"0.000128967","WT_PBS_2":"0.000120085","WT_PBS_3":"0.004558006","WT_PBS_4":"0.005419704","WT_PBS_5":"0.001053744","WT_Bleo_1":"0.000734131","WT_Bleo_2":"0.000256377","WT_Bleo_3":"0.000314107","WT_Bleo_4":"0.000330884","WT_Bleo_5":"0.000341633"}],

"Metabolites":[{"Metabolite":"Glycogen","PubChem":"439177","KEGG":"C00182"},{"Metabolite":"alanine","PubChem":"5950","KEGG":"C00041"},{"Metabolite":"lactate","PubChem":"61503","KEGG":"C00186"},{"Metabolite":"serine","PubChem":"5951","KEGG":"C00716"},{"Metabolite":"norvaline","PubChem":"439575","KEGG":"C01799"},{"Metabolite":"succinate","PubChem":"1110","KEGG":"C00042"},{"Metabolite":"aspartic acid","PubChem":"5960","KEGG":"C00049"},{"Metabolite":"malate","PubChem":"222656","KEGG":"C00149"},{"Metabolite":"glutamine","PubChem":"5961","KEGG":"C00064"},{"Metabolite":"glutamic acid","PubChem":"33032","KEGG":"C00025"},{"Metabolite":"DHAP/G3P","PubChem":"668","KEGG":"C00111"},{"Metabolite":"N-acetyl-aspartate","PubChem":"65065","KEGG":"C01042"},{"Metabolite":"glucose","PubChem":"5793","KEGG":"C00221"},{"Metabolite":"3PG","PubChem":"724","KEGG":"C00597"},{"Metabolite":"citrate","PubChem":"311","KEGG":"C00158"},{"Metabolite":"palmitate","PubChem":"985","KEGG":"C00249"},{"Metabolite":"G6P","PubChem":"5958","KEGG":"C00092"},{"Metabolite":"F6P","PubChem":"69507","KEGG":"C00085"},{"Metabolite":"AMP","PubChem":"6083","KEGG":"C00020"},{"Metabolite":"ADP","PubChem":"6022","KEGG":"C00008"},{"Metabolite":"ATP","PubChem":"5957","KEGG":"C00002"},{"Metabolite":"UDP-glucose","PubChem":"53477679","KEGG":"C00029"},{"Metabolite":"UDP-GlcNAc","PubChem":"9547196","KEGG":"C00043"}]
}

}