#METABOLOMICS WORKBENCH Jcpoland06_20190910_114115 DATATRACK_ID:1815 STUDY_ID:ST001249 ANALYSIS_ID:AN002074 PROJECT_ID:PR000836 VERSION 1 CREATED_ON September 13, 2019, 1:09 pm #PROJECT PR:PROJECT_TITLE Untargeted metabolomics after biliary diversion surgery PR:PROJECT_SUMMARY Obesity and diabetes are worldwide problems, and treatment and control are PR:PROJECT_SUMMARY proving more difficult and expensive. Bariatric surgery is the primary method PR:PROJECT_SUMMARY for treating these disorders. An alternative procedure, bile diversion, PR:PROJECT_SUMMARY dysregulates the circulation of bile acids in order to minimize fatty acid PR:PROJECT_SUMMARY absorption. It is recognized that bile acids are involved in multiple signaling PR:PROJECT_SUMMARY cascades, however the downstream effects of their malabsorption are yet unknown. PR:PROJECT_SUMMARY In order to investigate the effects this will have on the metabolome, an PR:PROJECT_SUMMARY untargeted liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) PR:PROJECT_SUMMARY method was developed and optimized. We describe a fecal metabolite extraction PR:PROJECT_SUMMARY method for separating species in multiple dimensions, comparing relative PR:PROJECT_SUMMARY abundances across groups, and annotating compounds when possible. Utilizing our PR:PROJECT_SUMMARY untargeted metabolomic pipeline, we were able to detect molecules with perturbed PR:PROJECT_SUMMARY abundance values, including secondary bile acids, which contribute to PR:PROJECT_SUMMARY differences between the experimental metabolomic profiles. PR:INSTITUTE Vanderbilt University PR:LABORATORY John A. McLean Research Group PR:LAST_NAME Poland PR:FIRST_NAME James PR:ADDRESS 2301 Vanderbilt Place PR:EMAIL j.c.poland@vanderbilt.edu PR:PHONE 6153434564 #STUDY ST:STUDY_TITLE Biliary diversion fecal extractions ST:STUDY_SUMMARY Stool samples are acquired from mice models after biliary diversion surgery. ST:STUDY_SUMMARY Metabolite extractions are then performed on the stool samples and run through ST:STUDY_SUMMARY an optimized RPLC-IM-MS method. ST:INSTITUTE Vanderbilt University ST:DEPARTMENT Chemistry ST:LABORATORY John A. McLean Research Group ST:LAST_NAME Poland ST:FIRST_NAME James ST:ADDRESS 2301 Vanderbilt Place ST:EMAIL j.c.poland@vanderbilt.edu ST:PHONE 6153434564 ST:NUM_GROUPS 3 ST:TOTAL_SUBJECTS 15 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #FACTORS #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_con_1_1 Group:Control Treatment=Sham; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_con_1_2 Group:Control Treatment=Sham; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_con_2_1 Group:Control Treatment=Sham; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_con_2_2 Group:Control Treatment=Sham; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_con_3_1 Group:Control Treatment=Sham; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_con_3_2 Group:Control Treatment=Sham; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_con_4_1 Group:Control Treatment=Sham; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_con_4_2 Group:Control Treatment=Sham; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_con_5_1 Group:Control Treatment=Sham; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_con_5_2 Group:Control Treatment=Sham; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL10_1_1 Group:GB-IL10 Treatment=GB-ILprox; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL10_1_2 Group:GB-IL10 Treatment=GB-ILprox; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL10_2_1 Group:GB-IL10 Treatment=GB-ILprox; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL10_2_2 Group:GB-IL10 Treatment=GB-ILprox; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL10_3_1 Group:GB-IL10 Treatment=GB-ILprox; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL10_3_2 Group:GB-IL10 Treatment=GB-ILprox; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL10_4_1 Group:GB-IL10 Treatment=GB-ILprox; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL10_4_2 Group:GB-IL10 Treatment=GB-ILprox; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL10_5_1 Group:GB-IL10 Treatment=GB-ILprox; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL10_5_2 Group:GB-IL10 Treatment=GB-ILprox; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL4_1_1 Group:GB-IL4 Treatment=GB-ILdist; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL4_1_2 Group:GB-IL4 Treatment=GB-ILdist; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL4_2_1 Group:GB-IL4 Treatment=GB-ILdist; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL4_2_2 Group:GB-IL4 Treatment=GB-ILdist; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL4_3_1 Group:GB-IL4 Treatment=GB-ILdist; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL4_3_2 Group:GB-IL4 Treatment=GB-ILdist; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL4_4_1 Group:GB-IL4 Treatment=GB-ILdist; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL4_4_2 Group:GB-IL4 Treatment=GB-ILdist; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL4_5_1 Group:GB-IL4 Treatment=GB-ILdist; Mode=Negative SUBJECT_SAMPLE_FACTORS - jcp_20160831_BD_rerun_neg_IL4_5_2 Group:GB-IL4 Treatment=GB-ILdist; Mode=Negative SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_con_1_1 Group:Control Treatment=Sham; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_con_1_2 Group:Control Treatment=Sham; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_con_2_1 Group:Control Treatment=Sham; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_con_2_2 Group:Control Treatment=Sham; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_con_3_1 Group:Control Treatment=Sham; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_con_3_2 Group:Control Treatment=Sham; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_con_4_1 Group:Control Treatment=Sham; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_con_4_2 Group:Control Treatment=Sham; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_con_5_1 Group:Control Treatment=Sham; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_con_5_2 Group:Control Treatment=Sham; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL4_1_1 Group:GB-IL4 Treatment=GB-ILdist; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL4_1_2 Group:GB-IL4 Treatment=GB-ILdist; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL4_2_1 Group:GB-IL4 Treatment=GB-ILdist; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL4_2_2 Group:GB-IL4 Treatment=GB-ILdist; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL4_3_1 Group:GB-IL4 Treatment=GB-ILdist; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL4_3_2 Group:GB-IL4 Treatment=GB-ILdist; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL4_4_1 Group:GB-IL4 Treatment=GB-ILdist; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL4_4_2 Group:GB-IL4 Treatment=GB-ILdist; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL4_5_1 Group:GB-IL4 Treatment=GB-ILdist; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL4_5_2 Group:GB-IL4 Treatment=GB-ILdist; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL10_1_1 Group:GB-IL10 Treatment=GB-ILprox; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL10_1_2 Group:GB-IL10 Treatment=GB-ILprox; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL10_2_1 Group:GB-IL10 Treatment=GB-ILprox; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL10_2_2 Group:GB-IL10 Treatment=GB-ILprox; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL10_3_1 Group:GB-IL10 Treatment=GB-ILprox; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL10_3_2 Group:GB-IL10 Treatment=GB-ILprox; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL10_4_1 Group:GB-IL10 Treatment=GB-ILprox; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL10_4_2 Group:GB-IL10 Treatment=GB-ILprox; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL10_5_1 Group:GB-IL10 Treatment=GB-ILprox; Mode=positive SUBJECT_SAMPLE_FACTORS - 20151115_jcp_iso_dilu_IL10_5_2 Group:GB-IL10 Treatment=GB-ILprox; Mode=positive #COLLECTION CO:COLLECTION_SUMMARY Mouse feces are collected and stored at -80 until processed. CO:SAMPLE_TYPE Feces CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY Male C57BL/6J mice were housed at 23°C on a 07:00-19:00 light cycle and were TR:TREATMENT_SUMMARY fed a high fat diet starting at six weeks of age for 12 weeks prior to being TR:TREATMENT_SUMMARY randomly allocated to a surgical group. Biliary diversion surgeries are TR:TREATMENT_SUMMARY performed the next week. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Fecal pellets are thawed on ice prior to extraction. 25mg of fecal material is SP:SAMPLEPREP_SUMMARY extracted with 1 ml of 75:25 ACN:H2O. SP:PROCESSING_STORAGE_CONDITIONS On ice SP:EXTRACT_STORAGE -80℃ #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY RPLC-IM-MS chromatography method (negative mode) CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Waters NanoAcquity CH:COLUMN_NAME Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um) CH:FLOW_GRADIENT linear CH:FLOW_RATE 75 uL/min CH:COLUMN_TEMPERATURE 40 C CH:SOLVENT_A 80:20 (v:v) H2O:ACN CH:SOLVENT_B 80:20 (v:v) ACN:H2O CH:RETENTION_TIME 30 min CH:CAPILLARY_VOLTAGE -2.2 kV #ANALYSIS AN:ANALYSIS_TYPE MS AN:DATA_FORMAT continuum #MS MS:INSTRUMENT_NAME Waters Synapt G2 QTOF MS:INSTRUMENT_TYPE RPLC-IM-MS MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS Progenesis QI software version 2.3 is used for data processing. MS:MS_RESULTS_FILE ST001249_AN002074_Results.txt UNITS:Intensity Has m/z:Yes Has RT:Yes RT units:Seconds #END