{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000222","ANALYSIS_ID":"AN000331","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"Metabolomic analysis of the small intestinal content of malnourished mice","PROJECT_SUMMARY":"-","INSTITUTE":"University of British Columbia","DEPARTMENT":"Microbiology and Immunology","LABORATORY":"Dr. B. Brett Finlay","LAST_NAME":"Finlay","FIRST_NAME":"Brett","ADDRESS":"2185 East Mall, Vancouver, BC, Canada V6T 1Z4","EMAIL":"bfinlay@msl.ubc.ca","PHONE":"-","FUNDING_SOURCE":"Canadian Institutes for Health Research"},

"STUDY":{"STUDY_TITLE":"Bile acid targeted metabolomics of the small intestine in malnourished and mice","STUDY_TYPE":"Targeted metabolomics","STUDY_SUMMARY":"A total of 8 samples from 6 week old, female C57BL/6 mice, treated for 3 weeks a malnourished diet or a control-fed isocaloric diet. Samples were taken from small intestinal fecal content at the terminus of the ileum for targeted bile analysis.","INSTITUTE":"University of Victoria","DEPARTMENT":"The Uvic Proteomics and Metabolomics Innovation Centre","LAST_NAME":"Borchers","FIRST_NAME":"Christoph","ADDRESS":"#3101-4464 Markham St Victoria, BC Canada, V8Z 7X8","EMAIL":"christoph@proteincentre.com","PHONE":"-","NUM_GROUPS":"2","TOTAL_SUBJECTS":"8*","STUDY_COMMENTS":"*One sample failed quality control in the malnourished group, thus was not in the study"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6","AGE_OR_AGE_RANGE":"6 weeks at collection","GENDER":"Female","ANIMAL_ANIMAL_SUPPLIER":"Jackson Labs","ANIMAL_HOUSING":"Conventional","ANIMAL_FEED":"Low Protein, Low Fat Malnourished Diet/Isocaloric Control Diet","CELL_PRIMARY_IMMORTALIZED":"Malnourished/Control"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Control_SI_1",
"Sample ID":"CON1",
"Factors":{"Diet":"control"}
},
{
"Subject ID":"Control_SI_2",
"Sample ID":"CON2",
"Factors":{"Diet":"control"}
},
{
"Subject ID":"Control_SI_3",
"Sample ID":"CON3",
"Factors":{"Diet":"control"}
},
{
"Subject ID":"Control_SI_4",
"Sample ID":"CON4",
"Factors":{"Diet":"control"}
},
{
"Subject ID":"Malnourished_SI_1",
"Sample ID":"MAL1",
"Factors":{"Diet":"malnourished"}
},
{
"Subject ID":"Malnourished_SI_2",
"Sample ID":"MAL2",
"Factors":{"Diet":"malnourished"}
},
{
"Subject ID":"Malnourished_SI_3",
"Sample ID":"MAL3",
"Factors":{"Diet":"malnourished"}
},
{
"Subject ID":"Malnourished_SI_4",
"Sample ID":"MAL4",
"Factors":{"Diet":"malnourished"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"Small intestinal fecal contents","COLLECTION_TIME":"6 weeks of age","STORAGE_CONDITIONS":"-80 degrees","TISSUE_CELL_QUANTITY_TAKEN":"15-40mg"},

"TREATMENT":{"TREATMENT_SUMMARY":"4 mice were given a malnourished diet and 4 mice were untreated, fed a control"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Bile-acid targeted metabolomics. Each sample was homogenized in LC-MS grade at a ratio of 150 ?L per 10 mg raw material and with the aid of 5-mm stainless metal balls. Bile acids were extracted by addition of acetonitrile at a ratio 350 ?L per 10 mg raw material followed by vortexing and sonication (1 min) in ice-water ultrasonic bath. The samples were centrifuged. 20 ?L of the were precisely taken out and mixed with a predefined mix of 14 bile acids as the internal standards. The mixtures were subjected to solid-phase extraction according to a validated protocol for sample cleanup and acid enrichment62. The flow-through fractions were collected and then dried a gentle nitrogen flow. The dried residues were dissolved in 200 ?L of 50% 10 ?L were injected for quantitation by UPLC-MRM/MS. A Dionex UPLC system was to an AB Sciex 4000 QTRAP mass spectrometer which was operated in the negative multiple-reaction monitoring (MRM) mode and with electrospray ionization. UPLC was carried out on a 15 cm long C-18 UPLC column with water-acetonitrile-formic as the mobile phase for binary gradient elution using a developed and validated for comprehensive analysis of bile acids in biological samples (Han, etc. submitted to Analytical Chemistry). The column temperature was 45 oC and the rate was 0.35 mL/min. 45 bile acids (including the 19 targeted bile acids) were in the quantitation by UPLC/scheduled MRM/MS. Concentrations of the detected acids were calculated with internal standard calibration from the linearly standard calibration curves of individual bile acids. The lower limits of were 0.08 nmoles/mg for all the bile acids."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"-","INSTRUMENT_NAME":"-","COLUMN_NAME":"-"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"ABI Sciex API 4000 QTrap","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"nM/mg",

"Data":[{"Metabolite":"12-Ketochenodeoxycholic acid","CON1":"108.7730","CON2":"1.3820","CON3":"7.8860","CON4":"7.2030","MAL1":"12.4300","MAL2":"4.6520","MAL3":"0.0000","MAL4":"0.8890"},{"Metabolite":"3-Oxocholic acid","CON1":"6.8920","CON2":"0.1110","CON3":"1.0330","CON4":"0.8540","MAL1":"0.7920","MAL2":"0.4250","MAL3":"0.0000","MAL4":"1.1570"},{"Metabolite":"7-12-Ketolithocholic acid","CON1":"2.1870","CON2":"0.0000","CON3":"0.3590","CON4":"0.1960","MAL1":"0.8320","MAL2":"0.2250","MAL3":"0.0000","MAL4":"0.5700"},{"Metabolite":"7-Ketodeoxycholic acid","CON1":"3.0704","CON2":"0.7200","CON3":"6.6340","CON4":"4.9730","MAL1":"16.0190","MAL2":"4.7440","MAL3":"0.0000","MAL4":"11.8960"},{"Metabolite":"7-Ketolithocholic acid","CON1":"1.7674","CON2":"0.1590","CON3":"1.4570","CON4":"1.6570","MAL1":"1.5330","MAL2":"1.2340","MAL3":"0.0000","MAL4":"0.0850"},{"Metabolite":"Allocholic acid","CON1":"1.4670","CON2":"0.0180","CON3":"0.1140","CON4":"0.0900","MAL1":"0.2640","MAL2":"0.0870","MAL3":"0.0000","MAL4":"0.0550"},{"Metabolite":"a-Muricholic acid","CON1":"7.8133","CON2":"4.5970","CON3":"0.2560","CON4":"15.7920","MAL1":"37.2710","MAL2":"11.5280","MAL3":"0.3440","MAL4":"3.2230"},{"Metabolite":"b-Muricholic acid","CON1":"72.0297","CON2":"18.6790","CON3":"124.0930","CON4":"83.3740","MAL1":"634.4700","MAL2":"186.3680","MAL3":"2.0130","MAL4":"83.3590"},{"Metabolite":"Chenodeoxycholic acid","CON1":"6.3277","CON2":"1.0050","CON3":"6.7610","CON4":"4.1130","MAL1":"9.1510","MAL2":"8.3550","MAL3":"0.1200","MAL4":"1.0680"},{"Metabolite":"Cholic acid","CON1":"1960.5300","CON2":"47.6040","CON3":"357.6140","CON4":"223.0970","MAL1":"856.6850","MAL2":"299.6020","MAL3":"1.4750","MAL4":"164.7670"},{"Metabolite":"Dehydrolithocholic acid","CON1":"0.0000","CON2":"0.0000","CON3":"0.0000","CON4":"0.0000","MAL1":"0.0000","MAL2":"0.0000","MAL3":"0.0000","MAL4":"0.0000"},{"Metabolite":"Deoxycholic acid","CON1":"6.4202","CON2":"0.9840","CON3":"12.1270","CON4":"6.0950","MAL1":"38.2260","MAL2":"14.0890","MAL3":"0.2460","MAL4":"18.0430"},{"Metabolite":"Dioxolithocholic acid","CON1":"0.0000","CON2":"0.0000","CON3":"0.0000","CON4":"0.0000","MAL1":"0.0000","MAL2":"0.0000","MAL3":"0.0000","MAL4":"0.0000"},{"Metabolite":"Glycochenodeoxycholic acid","CON1":"0.0000","CON2":"0.0000","CON3":"0.1010","CON4":"0.0000","MAL1":"0.0000","MAL2":"0.1080","MAL3":"0.0000","MAL4":"0.0000"},{"Metabolite":"Glycocholic acid","CON1":"1.4330","CON2":"2.1090","CON3":"5.3160","CON4":"3.4020","MAL1":"2.4370","MAL2":"3.5920","MAL3":"0.0000","MAL4":"0.4310"},{"Metabolite":"Hyodeoxycholic acid","CON1":"4.0018","CON2":"0.3030","CON3":"2.8260","CON4":"1.3760","MAL1":"2.4980","MAL2":"0.2660","MAL3":"0.0230","MAL4":"1.3350"},{"Metabolite":"Isolithocholic acid","CON1":"0.0000","CON2":"0.0000","CON3":"0.0000","CON4":"0.0000","MAL1":"0.0000","MAL2":"0.0000","MAL3":"0.0000","MAL4":"0.0000"},{"Metabolite":"lam-MCA hyocholic acid","CON1":"4.0300","CON2":"0.0000","CON3":"0.3440","CON4":"0.3060","MAL1":"0.4480","MAL2":"0.2650","MAL3":"0.0000","MAL4":"0.1110"},{"Metabolite":"Lithocholic acid","CON1":"0.6050","CON2":"0.0520","CON3":"0.1020","CON4":"0.0730","MAL1":"0.0910","MAL2":"0.0860","MAL3":"0.0380","MAL4":"0.0580"},{"Metabolite":"Murocholic acid","CON1":"0.1995","CON2":"0.1240","CON3":"1.2120","CON4":"0.6630","MAL1":"4.0050","MAL2":"1.1300","MAL3":"0.0000","MAL4":"0.8530"},{"Metabolite":"Tauro-a-muricholic acid","CON1":"90.8230","CON2":"153.7910","CON3":"272.9110","CON4":"294.7870","MAL1":"191.3270","MAL2":"99.0960","MAL3":"1.0090","MAL4":"22.6630"},{"Metabolite":"Tauro-b-muricholic acid","CON1":"679.5520","CON2":"775.2880","CON3":"1643.5810","CON4":"573.3680","MAL1":"1284.4940","MAL2":"650.6100","MAL3":"7.6530","MAL4":"379.7440"},{"Metabolite":"Taurochenodexycholic acid","CON1":"29.6820","CON2":"35.0870","CON3":"61.6400","CON4":"72.7730","MAL1":"21.2490","MAL2":"20.1210","MAL3":"0.0940","MAL4":"2.5490"},{"Metabolite":"Taurocholic acid","CON1":"193.7090","CON2":"690.7660","CON3":"1546.0760","CON4":"1219.1530","MAL1":"1020.8630","MAL2":"504.3730","MAL3":"5.8910","MAL4":"174.9120"},{"Metabolite":"Taurodeoxycholic acid","CON1":"23.6950","CON2":"25.2320","CON3":"76.8910","CON4":"49.1540","MAL1":"58.3880","MAL2":"23.5710","MAL3":"0.1770","MAL4":"28.7400"},{"Metabolite":"Taurohyocholic acid (tauro-?-MCA)","CON1":"0.3360","CON2":"0.6690","CON3":"0.7420","CON4":"0.7120","MAL1":"0.6280","MAL2":"0.2930","MAL3":"0.0000","MAL4":"0.2790"},{"Metabolite":"Taurohyodeoxycholic acid","CON1":"63.5980","CON2":"45.9080","CON3":"108.4530","CON4":"89.4540","MAL1":"36.3660","MAL2":"17.7530","MAL3":"0.1610","MAL4":"10.7030"},{"Metabolite":"Taurolithocholic acid","CON1":"1.5680","CON2":"0.4370","CON3":"1.0410","CON4":"0.9630","MAL1":"0.5470","MAL2":"0.2340","MAL3":"0.0000","MAL4":""},{"Metabolite":"Tauroursodexycholic acid","CON1":"63.6590","CON2":"46.8690","CON3":"114.4200","CON4":"97.8610","MAL1":"36.2920","MAL2":"18.6230","MAL3":"0.2460","MAL4":"11.0130"},{"Metabolite":"Tauro-w-muricholic acid","CON1":"96.6590","CON2":"163.4190","CON3":"232.1770","CON4":"224.7020","MAL1":"91.0140","MAL2":"34.8140","MAL3":"0.4930","MAL4":"84.7320"},{"Metabolite":"Ursocholic acid","CON1":"1.1780","CON2":"0.0120","CON3":"0.5250","CON4":"0.3480","MAL1":"2.5870","MAL2":"1.3010","MAL3":"0.0000","MAL4":"0.5180"},{"Metabolite":"Ursodeoxycholic acid","CON1":"6.1289","CON2":"0.4410","CON3":"5.2620","CON4":"3.2880","MAL1":"27.0110","MAL2":"21.1920","MAL3":"0.0000","MAL4":"2.7360"},{"Metabolite":"w-Muricholic acid","CON1":"4.2596","CON2":"1.4930","CON3":"5.4190","CON4":"4.4960","MAL1":"7.2730","MAL2":"2.7010","MAL3":"0.0000","MAL4":"7.9960"}],

"Metabolites":[{"Metabolite":"12-Ketochenodeoxycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"3-Oxocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"7-12-Ketolithocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"7-Ketodeoxycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"7-Ketolithocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Allocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"a-Muricholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"b-Muricholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Chenodeoxycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Cholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Dehydrolithocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Deoxycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Dioxolithocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Glycochenodeoxycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Glycocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Hyodeoxycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Isolithocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"lam-MCA hyocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Lithocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Murocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Tauro-a-muricholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Tauro-b-muricholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Taurochenodexycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Taurocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Taurodeoxycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Taurohyocholic acid (tauro-?-MCA)","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Taurohyodeoxycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Taurolithocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Tauroursodexycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Tauro-w-muricholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Ursocholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Ursodeoxycholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"w-Muricholic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"}]
}

}