{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003253","ANALYSIS_ID":"AN005331","PROJECT_ID":"PR002019","VERSION":"1","CREATED_ON":"June 11, 2024, 12:41 pm"},

"PROJECT":{"PROJECT_TITLE":"4-diet multi-organ and multi-omic crosstalk","PROJECT_TYPE":"Targeted MS quantitative analysis","PROJECT_SUMMARY":"Presently, dietary patterns have undergone significant shifts, and understanding the intricate interplay between diet, particularly high fat and high sucrose diets, the gut microbiome, and cardiometabolic health has become paramount. These dietary patterns have been consistently associated with heightened cardiometabolic risk factors including obesity, insulin resistance, dyslipidemia, and hypertension. High-fat diets, in particular, contribute to increased adiposity and ectopic fat deposition, exacerbating systemic inflammation and oxidative stress, thereby promoting the development of metabolic dysfunction. Similarly, high sucrose diets have been implicated in the dysregulation of glucose homeostasis, leading to insulin resistance and hyperglycemia, key hallmarks of cardiometabolic diseases such as type 2 diabetes mellitus. Amidst this, the exploration of multi-omic profiles alongside the gut microbial landscape has emerged as a pivotal avenue for unraveling the complexities of cardiometabolic health dynamics affected by the effects of high-fat and high-sucrose diets. The approach of using a multi-omic comparison between organs offers a comprehensive lens through which the intricate molecular signatures underlying the impact of dietary compositions, particularly high fat and high sucrose, on metabolic health, can be examined.","INSTITUTE":"University of Sydney","DEPARTMENT":"School of Medical Sciences","LABORATORY":"Cardiometabolic Disease","LAST_NAME":"Liu","FIRST_NAME":"Renping","ADDRESS":"The Hub, Charles Perkins Centre, D17, The University of Sydney, NSW, 2006","EMAIL":"renping.liu@sydney.edu.au","PHONE":"+61432953638"},

"STUDY":{"STUDY_TITLE":"Metabolomics studies on mouse liver samples on a Western diet","STUDY_SUMMARY":"Targeted metabolomics was performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS).to measure polar metabolites in both positive and negative ionization mode on cardiac mice tissue acquired after a 30 week dietary intervention.","INSTITUTE":"University of Sydney","DEPARTMENT":"School of Medical Sciences","LABORATORY":"Cardiometabolic Disease","LAST_NAME":"Liu","FIRST_NAME":"Renping","ADDRESS":"Charles Perkins Centre","EMAIL":"renping.liu@sydney.edu.au","PHONE":"+61432953638","NUM_GROUPS":"4","TOTAL_SUBJECTS":"35","NUM_MALES":"35"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6J","AGE_OR_AGE_RANGE":"6 weeks old","GENDER":"Male","ANIMAL_ANIMAL_SUPPLIER":"Australian Resource Centre","ANIMAL_HOUSING":"3 per cage","ANIMAL_LIGHT_CYCLE":"12-hour light-dark cycle"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"C59.1",
"Factors":{"Sample source":"liver tissue","Diet":"chow"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"C59.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"C59.2",
"Factors":{"Sample source":"liver tissue","Diet":"chow"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"C59.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"C61.1",
"Factors":{"Sample source":"liver tissue","Diet":"chow"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"C61.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"C61.2",
"Factors":{"Sample source":"liver tissue","Diet":"chow"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"C61.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"C61.3",
"Factors":{"Sample source":"liver tissue","Diet":"chow"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"C61.3_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"C62.1",
"Factors":{"Sample source":"liver tissue","Diet":"chow"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"C62.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"C62.2",
"Factors":{"Sample source":"liver tissue","Diet":"chow"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"C62.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"C62.3",
"Factors":{"Sample source":"liver tissue","Diet":"chow"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"C62.3_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HF58.1",
"Factors":{"Sample source":"liver tissue","Diet":"hfd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HF58.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HF58.2",
"Factors":{"Sample source":"liver tissue","Diet":"hfd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HF58.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HF65.1",
"Factors":{"Sample source":"liver tissue","Diet":"hfd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HF65.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HF65.2",
"Factors":{"Sample source":"liver tissue","Diet":"hfd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HF65.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HF65.3",
"Factors":{"Sample source":"liver tissue","Diet":"hfd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HF65.3_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HF67.1",
"Factors":{"Sample source":"liver tissue","Diet":"hfd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HF67.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HF67.2",
"Factors":{"Sample source":"liver tissue","Diet":"hfd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HF67.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HF67.3",
"Factors":{"Sample source":"liver tissue","Diet":"hfd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HF67.3_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HFHS56.1",
"Factors":{"Sample source":"liver tissue","Diet":"hfhsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HFHS56.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HFHS56.2",
"Factors":{"Sample source":"liver tissue","Diet":"hfhsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HFHS56.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HFHS57.1",
"Factors":{"Sample source":"liver tissue","Diet":"hfhsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HFHS57.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HFHS57.3",
"Factors":{"Sample source":"liver tissue","Diet":"hfhsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HFHS57.3_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HFHS66.1",
"Factors":{"Sample source":"liver tissue","Diet":"hfhsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HFHS66.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HFHS66.2",
"Factors":{"Sample source":"liver tissue","Diet":"hfhsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HFHS66.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HFHS66.3",
"Factors":{"Sample source":"liver tissue","Diet":"hfhsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HFHS66.3_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HS60.1",
"Factors":{"Sample source":"liver tissue","Diet":"hsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HS60.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HS60.2",
"Factors":{"Sample source":"liver tissue","Diet":"hsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HS60.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HS63.1",
"Factors":{"Sample source":"liver tissue","Diet":"hsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HS63.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HS63.2",
"Factors":{"Sample source":"liver tissue","Diet":"hsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HS63.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HS63.3",
"Factors":{"Sample source":"liver tissue","Diet":"hsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HS63.3_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HS64.1",
"Factors":{"Sample source":"liver tissue","Diet":"hsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HS64.1_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HS64.2",
"Factors":{"Sample source":"liver tissue","Diet":"hsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HS64.2_liver.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"HS64.3",
"Factors":{"Sample source":"liver tissue","Diet":"hsd"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"HS64.3_liver.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mouse liver samples were collected at the end of the experimental design (after 30-weeks on the diet) during the cull. These samples were immediately clamped with metal clamps and snap-frozen in liquid nitrogen and stored in -80 degrees Celsius until further analysis. This process was approved by the University of Sydney’s Ethics Committee (USYD # 2017/1294).","SAMPLE_TYPE":"Liver","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"36 male C57BL/6J mice were allocated to four different diets (n = 7-8) consisting of a control diet (Chow), a high-sucrose diet (HSD), a high-fat diet (HFD), and a high-fat high-sucrose (western) diet (HFHSD) at 8 weeks of age. Mice had ad libitum access to their food and autoclaved water. One mouse was euthanised prior to the expected experimental endpoint due to the loss of body condition and was excluded from this study. 4 samples were not collected after euthanisation making the groups (n = 7-8)","TREATMENT":"Chow, HFD, HSD, HFHSD"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Approximately 50 mg of ground liver tissue was weighed into 2 mL Eppendorf tube and subjected to a two-phase extraction protocol involving tissue, ice-cold extraction medium (methanol:water, and chloroform). Samples were then centrifuged at 14 000 x g at 4 °C for 25 min. The aqueous layer was transferred into a new microfuge tube and reconstituted in the acetonitrile/methanol/formic acid (75:25:0.2; v/v/v, HPLC grade; Thermo Fisher Scientific) for the HILIC analysis, and acetonitrile/methanol (25:25; v/v/v, HPLC grade) for the AMIDE and NAD analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Chromatographic method to detect analytes such as amino acids, endocannabinoids, fatty acid β-oxidation intermediates, gut-derived metabolites, nucleotides, neurotransmitters, cofactors and vitamins.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1260","COLUMN_NAME":"Waters XBridge BEH Amide (100 x 2.1mm,2.5um)","SOLVENT_A":"95% acetonitrile/5% water; 20mM ammonium acetate; 20mM ammonium hydroxide (pH 9.0)","SOLVENT_B":"100% acetonitrile","FLOW_GRADIENT":"The LC gradient program is initialized with an initial mobile phase composition of 15% solvent A and 85% solvent B at a flow rate of 0.25 mL/min. Over the course of 8 minutes, the mobile phase composition undergoes a transition to 65% solvent A and 35% solvent B. Subsequently, at 8 minutes, the composition shifts to 98% solvent A and 2% solvent B, maintained for 1 minute. The mobile phase reverts back to the initial composition of 15% solvent A and 85% solvent B at 10 minutes. At 12.5 minutes, the flow rate is increased to 0.4 mL/min, while maintaining a constant mobile phase composition of 15% solvent A and 85% solvent B for a period of 2.5 minutes. Finally, at 15 minutes, the flow rate is reduced back to 0.25 mL/min. To ensure system stability, the final condition is maintained for 1 minute prior to subsequent analyses.","FLOW_RATE":"0.250 – 0.400 mL/min","COLUMN_TEMPERATURE":"40"},

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

"MS":{"INSTRUMENT_NAME":"ABI Sciex 6500 QTrap","INSTRUMENT_TYPE":"QTRAP","MS_TYPE":"API","ION_MODE":"NEGATIVE","MS_COMMENTS":"Targeted metabolite profiling was performed using MS multiple reaction-monitoring transitions. Multiple Reaction Monitoring (MRM) Q1/Q3 peak integration of the raw data files (Analyst software, v.1.6.2; ABSciex) was performed using software MultiQuant 3.0 (ABSciex)."},

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

"Data":[{"Metabolite":"2H2MB","C59.1":"2828567.239","C59.2":"2689992.596","C61.1":"2666402.095","C61.2":"3001184.18","C61.3":"2904923.788","C62.1":"2729970.7","C62.2":"2511056.697","C62.3":"2755326.479","HF58.1":"2361224.218","HF58.2":"2554778.319","HF65.1":"2305537.153","HF65.2":"2580072.602","HF65.3":"2640553.304","HF67.1":"2719616.261","HF67.2":"2757687.173","HF67.3":"2663476.454","HFHS56.1":"2281829.333","HFHS56.2":"2810260.687","HFHS57.1":"2633798.365","HFHS57.3":"2620447.233","HFHS66.1":"3969640.896","HFHS66.2":"2823696.367","HFHS66.3":"2866752.776","HS60.1":"2915081.539","HS60.2":"2561834.257","HS63.1":"2667983.2","HS63.2":"2789823.5","HS63.3":"2771135.82","HS64.1":"2924689.465","HS64.2":"2744315.072","HS64.3":"2862073.831"},{"Metabolite":"2-HG","C59.1":"196530.207","C59.2":"140265.329","C61.1":"153151.3225","C61.2":"206255.095","C61.3":"136268.9185","C62.1":"177419.363","C62.2":"131495.3635","C62.3":"242636.7205","HF58.1":"303217.1785","HF58.2":"322450.356","HF65.1":"230757.867","HF65.2":"175684.972","HF65.3":"225606.244","HF67.1":"203505.296","HF67.2":"198907.139","HF67.3":"324084.2235","HFHS56.1":"255196.1455","HFHS56.2":"282007.0805","HFHS57.1":"231520.191","HFHS57.3":"363848.247","HFHS66.1":"245261.4495","HFHS66.2":"414469.572","HFHS66.3":"353630.032","HS60.1":"207916.8775","HS60.2":"122380.753","HS63.1":"104426.028","HS63.2":"327529.3575","HS63.3":"369440.8915","HS64.1":"175026.66","HS64.2":"86191.0425","HS64.3":"211422.157"},{"Metabolite":"2-IPM","C59.1":"954788.5836","C59.2":"825102.982","C61.1":"870339.6278","C61.2":"1053987.341","C61.3":"972854.476","C62.1":"804421.164","C62.2":"910229.8412","C62.3":"1198366.364","HF58.1":"1414536.398","HF58.2":"1738554.302","HF65.1":"1199458.612","HF65.2":"976104.5138","HF65.3":"1260453.621","HF67.1":"931462.6949","HF67.2":"1030600.454","HF67.3":"1681723.525","HFHS56.1":"1190436.704","HFHS56.2":"1763036.971","HFHS57.1":"1317528.172","HFHS57.3":"1724206.605","HFHS66.1":"1227545.989","HFHS66.2":"1703867.279","HFHS66.3":"1777745.979","HS60.1":"1269184.594","HS60.2":"690732.9874","HS63.1":"675839.003","HS63.2":"1487626.299","HS63.3":"1913008.548","HS64.1":"942714.525","HS64.2":"618959.4212","HS64.3":"890973.625"},{"Metabolite":"2-KH","C59.1":"32786002.95","C59.2":"21911791.3","C61.1":"30205816.6","C61.2":"18847500.2","C61.3":"23276714.12","C62.1":"29998143.51","C62.2":"17347317.66","C62.3":"32801132.08","HF58.1":"30530303.63","HF58.2":"34740414.4","HF65.1":"30246139.59","HF65.2":"34362880.91","HF65.3":"29303600.92","HF67.1":"32166178.29","HF67.2":"15407771","HF67.3":"27228118.72","HFHS56.1":"32306397","HFHS56.2":"30984734.86","HFHS57.1":"34298556.3","HFHS57.3":"37604173.49","HFHS66.1":"33343592.47","HFHS66.2":"44569095.93","HFHS66.3":"34214318.84","HS60.1":"29364591.02","HS60.2":"22771843.54","HS63.1":"37246337.6","HS63.2":"25953643.94","HS63.3":"36601071.05","HS64.1":"21032078.65","HS64.2":"32409245.01","HS64.3":"22409982.29"},{"Metabolite":"2-MAA","C59.1":"25806.798","C59.2":"13006.5435","C61.1":"18799.295","C61.2":"18227.696","C61.3":"19720.3195","C62.1":"23934.3375","C62.2":"18189.088","C62.3":"25486.408","HF58.1":"28993.9495","HF58.2":"31461.666","HF65.1":"24547.3225","HF65.2":"18933.7475","HF65.3":"19854.951","HF67.1":"21095.178","HF67.2":"15914.1045","HF67.3":"26676.5785","HFHS56.1":"23940.73","HFHS56.2":"27106.8025","HFHS57.1":"23369.071","HFHS57.3":"28373.571","HFHS66.1":"20665.116","HFHS66.2":"27754.929","HFHS66.3":"28573.225","HS60.1":"28174.992","HS60.2":"12224.0515","HS63.1":"9578.023","HS63.2":"26613.649","HS63.3":"33222.9075","HS64.1":"20481.4785","HS64.2":"13589.2525","HS64.3":"16542.8385"},{"Metabolite":"2-OB","C59.1":"7513.6","C59.2":"7136.8645","C61.1":"3887.333","C61.2":"6905.405139","C61.3":"7308.617","C62.1":"11624.6425","C62.2":"14079.742","C62.3":"3846.4365","HF58.1":"6495.0815","HF58.2":"6583.409285","HF65.1":"9572.7115","HF65.2":"7524.906884","HF65.3":"13337.299","HF67.1":"7154.3675","HF67.2":"10209.31","HF67.3":"18154.6535","HFHS56.1":"15103.00784","HFHS56.2":"4932.44","HFHS57.1":"9188.7265","HFHS57.3":"17412.929","HFHS66.1":"6580.698259","HFHS66.2":"6805.9885","HFHS66.3":"6167.479413","HS60.1":"15580.043","HS60.2":"4986.004","HS63.1":"2943.426","HS63.2":"3960.963","HS63.3":"12894.652","HS64.1":"15151.9245","HS64.2":"13525.877","HS64.3":"2081.984"},{"Metabolite":"3M2OB","C59.1":"83978.884","C59.2":"125913.732","C61.1":"42631.84125","C61.2":"42310.946","C61.3":"86480.31674","C62.1":"89242.91581","C62.2":"38093.14373","C62.3":"56166.05162","HF58.1":"85309.882","HF58.2":"86698.764","HF65.1":"59090.266","HF65.2":"75168.556","HF65.3":"84698.264","HF67.1":"49879.48","HF67.2":"96190.298","HF67.3":"73221.308","HFHS56.1":"35665.24","HFHS56.2":"24382.446","HFHS57.1":"172245.132","HFHS57.3":"51118.886","HFHS66.1":"18881.296","HFHS66.2":"38056.152","HFHS66.3":"63696.308","HS60.1":"38224.71","HS60.2":"46242.182","HS63.1":"48301.618","HS63.2":"49395.50956","HS63.3":"70462.884","HS64.1":"55625.996","HS64.2":"67811.08","HS64.3":"37734.056"},{"Metabo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}

}