{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000224","ANALYSIS_ID":"AN000334","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":"Vitamin 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 of vitamin concentrations.","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"},

"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":"Vitamin-targeted metabolomics. The samples were analyzed by UPLC-MRM/MS on a UltiMate 3400 RSLC system coupled to an AB Sciex 4000 QTRAP triple-quadrupole spectrometer equipped with an electrospray ionization source. The standard of vitamin A (retinal, retinol, retinoic acid), B1 (thiamine), B2 (riboflavin), (niacinamide), B6 (pydidoximine, pyridoxine, pyridoxal, B7 (biotin), B9 (folic acid), D2, D3, E (?-tocopherol, ?-tocopherol, and K1 and K2, were purchased either from Sigma-Aldrich or from Cayman Chemicals The MRM transitions of individual analytes were optimized by direct infusion of standard solution of each compound into the MS instrument. Each sample was with a methanolic BHT (2 mg/mL) solution at a ratio of 15 ?L per mg of the intestine digestate. Vitamins were extracted by homogenizing the samples at a frequency of 30 Hz for 1 min twice using a Retsch MM400 mixer mill and with the of two 3-mm stainless steel metal balls, followed by 5-min sonication in an icy bath. The samples were then centrifuged in a micro-centrifuge at 12,500 rpm and for 10 min. A 300-?L aliquot of the supernatant was transferred into a 3-mL glass test tube and mixed with 300 ?L of water and 900 ?L of hexane. After 1 vortex mixing, the tubes were centrifuged at 4000 rpm and 10 oC in a Beckman centrifuge to separate the supernatant organic phase from the lower aqueous The supernatants were carefully pipetted out to another sets of 3-mL test The fat-soluble vitamins were further extracted from the aqueous phase with 900 of hexane two more times. After liquid-liquid extraction, the pooled organic for each sample was dried down in a speed-vacuum concentrator at room The dried residue was reconstituted in 100 ?L of ethanol. A 20-?L aliquot was for quantitation of the fat-soluble vitamins by LC-(+)ESI-MRM/MS on Waters BEH (2.1 x 50 mm, 1.7 ?m) UPLC column and with 0.1% formic acid in water and as the mobile phase for binary solvent gradient elution. An efficient elution was 50% to 100% B in 10 min. The column temperature was 50oC and the flow rate 300 ?L/min. The aqueous phases were loaded onto reversed-phase polymeric HLB (60 mg/1mL, Waters Inc.), which have been activated with 1 mL of methanol and with 1 mL of 50% methanol before use. Under a 5-inch Hg vaccum, the flow-throw were collected and the resins were washed with 1 mL of 50% methanol with the fractions collected. The pooled flow-through fractions were dried in a nitrogen at 30 oC. The residue from each sample was reconstituted in 100 ?L of 2% A 20-?L aliquot was injected for quantitation of the water-soluble vitamins by with (+) or (-) ESI and on a Waters BEH C18 (2.1 x 150 mm, 1.7 ?m) UPLC column using 0.01% formic acid in water and methanol as the mobile phase for binary gradient elution. The efficient elution gradient was 2% B for 0.5 min and 2% to B in 8 min. The column temperature was 30 oC and the flow rate was 250 ?L/min. concentrations of all the detected vitamins were calculated from the standard curves of individual vitamins, which were prepared with the use of their compounds."},

"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":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"nmol/g",

"Data":[{"Metabolite":"Vitamin A_Retinal","CON1":"0.0075","CON2":"0.0082","CON3":"0.0074","CON4":"0.0079","MAL1":"0.0007","MAL2":"0.0008","MAL3":"0.0009","MAL4":"0.0009"},{"Metabolite":"Vitamin A_Retinoic acid","CON1":"","CON2":"","CON3":"","CON4":"","MAL1":"","MAL2":"","MAL3":"","MAL4":""},{"Metabolite":"Vitamin A_Retinol","CON1":"0.3736","CON2":"0.3488","CON3":"0.2424","CON4":"0.3145","MAL1":"0.1774","MAL2":"0.1114","MAL3":"0.1457","MAL4":"0.1798"},{"Metabolite":"Vitamin D2","CON1":"0.1831","CON2":"0.1545","CON3":"0.1709","CON4":"0.1407","MAL1":"0.0854","MAL2":"0.1058","MAL3":"0.1002","MAL4":"0.0703"},{"Metabolite":"Vitamin D3","CON1":"0.5489","CON2":"0.5749","CON3":"0.4471","CON4":"0.6929","MAL1":"1.5762","MAL2":"3.0405","MAL3":"1.5821","MAL4":"1.0678"},{"Metabolite":"Vitamin E_a-tocopherol","CON1":"13.2240","CON2":"9.4649","CON3":"7.1510","CON4":"12.1395","MAL1":"1.8691","MAL2":"3.5904","MAL3":"2.6829","MAL4":"1.1860"},{"Metabolite":"Vitamin E_d-tocopherol","CON1":"0.0524","CON2":"0.0421","CON3":"0.0398","CON4":"0.0592","MAL1":"0.0057","MAL2":"0.0297","MAL3":"0.0090","MAL4":"0.0033"},{"Metabolite":"Vitamin E_d-tocotrienol","CON1":"0.2240","CON2":"0.2170","CON3":"0.2200","CON4":"0.2820","MAL1":"0.0640","MAL2":"0.1610","MAL3":"0.0900","MAL4":"0.0600"},{"Metabolite":"Vitamin K1","CON1":"","CON2":"","CON3":"","CON4":"","MAL1":"","MAL2":"","MAL3":"","MAL4":""},{"Metabolite":"Vitamin K2","CON1":"0.0036","CON2":"0.0043","CON3":"0.0034","CON4":"0.0035","MAL1":"0.0051","MAL2":"0.0036","MAL3":"0.0034","MAL4":"0.0035"}],

"Metabolites":[{"Metabolite":"Vitamin A_Retinal","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Vitamin A_Retinoic acid","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Vitamin A_Retinol","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Vitamin D2","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Vitamin D3","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Vitamin E_a-tocopherol","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Vitamin E_d-tocopherol","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Vitamin E_d-tocotrienol","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Vitamin K1","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"},{"Metabolite":"Vitamin K2","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"Uvictoria_ID"}]
}

}