{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001249","ANALYSIS_ID":"AN002073","VERSION":"1","CREATED_ON":"September 13, 2019, 1:09 pm"},

"PROJECT":{"PROJECT_TITLE":"Untargeted metabolomics after biliary diversion surgery","PROJECT_SUMMARY":"Obesity and diabetes are worldwide problems, and treatment and control are proving more difficult and expensive. Bariatric surgery is the primary method for treating these disorders. An alternative procedure, bile diversion, dysregulates the circulation of bile acids in order to minimize fatty acid absorption. It is recognized that bile acids are involved in multiple signaling cascades, however the downstream effects of their malabsorption are yet unknown. In order to investigate the effects this will have on the metabolome, an untargeted liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) method was developed and optimized. We describe a fecal metabolite extraction method for separating species in multiple dimensions, comparing relative abundances across groups, and annotating compounds when possible. Utilizing our untargeted metabolomic pipeline, we were able to detect molecules with perturbed abundance values, including secondary bile acids, which contribute to differences between the experimental metabolomic profiles.","INSTITUTE":"Vanderbilt University","LABORATORY":"John A. McLean Research Group","LAST_NAME":"Poland","FIRST_NAME":"James","ADDRESS":"2301 Vanderbilt Place","EMAIL":"j.c.poland@vanderbilt.edu","PHONE":"6153434564"},

"STUDY":{"STUDY_TITLE":"Biliary diversion fecal extractions","STUDY_SUMMARY":"Stool samples are acquired from mice models after biliary diversion surgery. Metabolite extractions are then performed on the stool samples and run through an optimized RPLC-IM-MS method.","INSTITUTE":"Vanderbilt University","DEPARTMENT":"Chemistry","LABORATORY":"John A. McLean Research Group","LAST_NAME":"Poland","FIRST_NAME":"James","ADDRESS":"2301 Vanderbilt Place","EMAIL":"j.c.poland@vanderbilt.edu","PHONE":"6153434564","NUM_GROUPS":"3","TOTAL_SUBJECTS":"15"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
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"Subject ID":"-",
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"Additional sample data":{"Treatment":"GB-ILdist","Mode":"Negative"}
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"Sample ID":"20151115_jcp_iso_dilu_con_1_1",
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"Sample ID":"20151115_jcp_iso_dilu_con_1_2",
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"Subject ID":"-",
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"Additional sample data":{"Treatment":"GB-ILdist","Mode":"positive"}
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"Subject ID":"-",
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"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL4_4_2",
"Factors":{"Group":"GB-IL4"},
"Additional sample data":{"Treatment":"GB-ILdist","Mode":"positive"}
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{
"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL4_5_1",
"Factors":{"Group":"GB-IL4"},
"Additional sample data":{"Treatment":"GB-ILdist","Mode":"positive"}
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{
"Subject ID":"-",
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"Additional sample data":{"Treatment":"GB-ILdist","Mode":"positive"}
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"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL10_1_1",
"Factors":{"Group":"GB-IL10"},
"Additional sample data":{"Treatment":"GB-ILprox","Mode":"positive"}
},
{
"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL10_1_2",
"Factors":{"Group":"GB-IL10"},
"Additional sample data":{"Treatment":"GB-ILprox","Mode":"positive"}
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{
"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL10_2_1",
"Factors":{"Group":"GB-IL10"},
"Additional sample data":{"Treatment":"GB-ILprox","Mode":"positive"}
},
{
"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL10_2_2",
"Factors":{"Group":"GB-IL10"},
"Additional sample data":{"Treatment":"GB-ILprox","Mode":"positive"}
},
{
"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL10_3_1",
"Factors":{"Group":"GB-IL10"},
"Additional sample data":{"Treatment":"GB-ILprox","Mode":"positive"}
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{
"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL10_3_2",
"Factors":{"Group":"GB-IL10"},
"Additional sample data":{"Treatment":"GB-ILprox","Mode":"positive"}
},
{
"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL10_4_1",
"Factors":{"Group":"GB-IL10"},
"Additional sample data":{"Treatment":"GB-ILprox","Mode":"positive"}
},
{
"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL10_4_2",
"Factors":{"Group":"GB-IL10"},
"Additional sample data":{"Treatment":"GB-ILprox","Mode":"positive"}
},
{
"Subject ID":"-",
"Sample ID":"20151115_jcp_iso_dilu_IL10_5_1",
"Factors":{"Group":"GB-IL10"},
"Additional sample data":{"Treatment":"GB-ILprox","Mode":"positive"}
},
{
"Subject ID":"-",
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}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mouse feces are collected and stored at -80 until processed.","SAMPLE_TYPE":"Feces","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Male C57BL/6J mice were housed at 23°C on a 07:00-19:00 light cycle and were fed a high fat diet starting at six weeks of age for 12 weeks prior to being randomly allocated to a surgical group. Biliary diversion surgeries are performed the next week."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Fecal pellets are thawed on ice prior to extraction. 25mg of fecal material is extracted with 1 ml of 75:25 ACN:H2O.","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"RPLC-IM-MS chromatography method (positive mode)","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters NanoAcquity","COLUMN_NAME":"Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)","FLOW_GRADIENT":"linear","FLOW_RATE":"75 uL/min","COLUMN_TEMPERATURE":"40 C","SOLVENT_A":"80:20 (v:v) H2O:ACN","SOLVENT_B":"80:20 (v:v) ACN:H2O","RETENTION_TIME":"30 min","CAPILLARY_VOLTAGE":"3.0 kV"},

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

"MS":{"INSTRUMENT_NAME":"Waters Synapt G2 S QTOF","INSTRUMENT_TYPE":"RPLC-IM-MS","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Progenesis QI software version 2.3 is used for data processing.","MS_RESULTS_FILE":"ST001249_AN002073_Results.txt UNITS:Intensity Has m/z:Yes Has RT:Yes RT units:Seconds"}

}