Summary of Study ST001249

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000836. The data can be accessed directly via it's Project DOI: 10.21228/M8MQ2G This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001249
Study TitleBiliary diversion fecal extractions
Study SummaryStool 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
DepartmentChemistry
LaboratoryJohn A. McLean Research Group
Last NamePoland
First NameJames
Address2301 Vanderbilt Place
Emailj.c.poland@vanderbilt.edu
Phone6153434564
Submit Date2019-09-10
Num Groups3
Total Subjects15
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2019-10-11
Release Version1
James Poland James Poland
https://dx.doi.org/10.21228/M8MQ2G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000836
Project DOI:doi: 10.21228/M8MQ2G
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

Subject:

Subject ID:SU001317
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Group
SA09094620151115_jcp_iso_dilu_con_3_1Control
SA09094720151115_jcp_iso_dilu_con_2_2Control
SA09094820151115_jcp_iso_dilu_con_1_2Control
SA09094920151115_jcp_iso_dilu_con_3_2Control
SA09095020151115_jcp_iso_dilu_con_2_1Control
SA09095120151115_jcp_iso_dilu_con_4_1Control
SA09095220151115_jcp_iso_dilu_con_5_2Control
SA09095320151115_jcp_iso_dilu_con_5_1Control
SA09095420151115_jcp_iso_dilu_con_4_2Control
SA090955jcp_20160831_BD_rerun_neg_con_1_1Control
SA09095620151115_jcp_iso_dilu_con_1_1Control
SA090957jcp_20160831_BD_rerun_neg_con_4_1Control
SA090958jcp_20160831_BD_rerun_neg_con_4_2Control
SA090959jcp_20160831_BD_rerun_neg_con_5_1Control
SA090960jcp_20160831_BD_rerun_neg_con_3_1Control
SA090961jcp_20160831_BD_rerun_neg_con_2_2Control
SA090962jcp_20160831_BD_rerun_neg_con_1_2Control
SA090963jcp_20160831_BD_rerun_neg_con_2_1Control
SA090964jcp_20160831_BD_rerun_neg_con_5_2Control
SA090965jcp_20160831_BD_rerun_neg_con_3_2Control
SA090966jcp_20160831_BD_rerun_neg_IL10_2_1GB-IL10
SA090967jcp_20160831_BD_rerun_neg_IL10_4_2GB-IL10
SA090968jcp_20160831_BD_rerun_neg_IL10_5_1GB-IL10
SA090969jcp_20160831_BD_rerun_neg_IL10_5_2GB-IL10
SA090970jcp_20160831_BD_rerun_neg_IL10_4_1GB-IL10
SA090971jcp_20160831_BD_rerun_neg_IL10_3_2GB-IL10
SA09097220151115_jcp_iso_dilu_IL10_1_1GB-IL10
SA09097320151115_jcp_iso_dilu_IL10_1_2GB-IL10
SA090974jcp_20160831_BD_rerun_neg_IL10_3_1GB-IL10
SA090975jcp_20160831_BD_rerun_neg_IL10_1_1GB-IL10
SA09097620151115_jcp_iso_dilu_IL10_2_1GB-IL10
SA09097720151115_jcp_iso_dilu_IL10_5_1GB-IL10
SA09097820151115_jcp_iso_dilu_IL10_5_2GB-IL10
SA090979jcp_20160831_BD_rerun_neg_IL10_2_2GB-IL10
SA09098020151115_jcp_iso_dilu_IL10_4_1GB-IL10
SA09098120151115_jcp_iso_dilu_IL10_4_2GB-IL10
SA090982jcp_20160831_BD_rerun_neg_IL10_1_2GB-IL10
SA09098320151115_jcp_iso_dilu_IL10_3_2GB-IL10
SA09098420151115_jcp_iso_dilu_IL10_2_2GB-IL10
SA09098520151115_jcp_iso_dilu_IL10_3_1GB-IL10
SA09098620151115_jcp_iso_dilu_IL4_4_2GB-IL4
SA09098720151115_jcp_iso_dilu_IL4_5_1GB-IL4
SA09098820151115_jcp_iso_dilu_IL4_5_2GB-IL4
SA09098920151115_jcp_iso_dilu_IL4_4_1GB-IL4
SA09099020151115_jcp_iso_dilu_IL4_1_1GB-IL4
SA090991jcp_20160831_BD_rerun_neg_IL4_4_1GB-IL4
SA090992jcp_20160831_BD_rerun_neg_IL4_4_2GB-IL4
SA090993jcp_20160831_BD_rerun_neg_IL4_3_2GB-IL4
SA090994jcp_20160831_BD_rerun_neg_IL4_3_1GB-IL4
SA090995jcp_20160831_BD_rerun_neg_IL4_2_1GB-IL4
SA090996jcp_20160831_BD_rerun_neg_IL4_2_2GB-IL4
SA090997jcp_20160831_BD_rerun_neg_IL4_5_1GB-IL4
SA090998jcp_20160831_BD_rerun_neg_IL4_5_2GB-IL4
SA09099920151115_jcp_iso_dilu_IL4_2_2GB-IL4
SA09100020151115_jcp_iso_dilu_IL4_3_1GB-IL4
SA09100120151115_jcp_iso_dilu_IL4_2_1GB-IL4
SA09100220151115_jcp_iso_dilu_IL4_1_2GB-IL4
SA091003jcp_20160831_BD_rerun_neg_IL4_1_1GB-IL4
SA091004jcp_20160831_BD_rerun_neg_IL4_1_2GB-IL4
SA09100520151115_jcp_iso_dilu_IL4_3_2GB-IL4
Showing results 1 to 60 of 60

Collection:

Collection ID:CO001311
Collection Summary:Mouse feces are collected and stored at -80 until processed.
Sample Type:Feces
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001332
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.

Sample Preparation:

Sampleprep ID:SP001325
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℃

Combined analysis:

Analysis ID AN002073 AN002074
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters NanoAcquity Waters NanoAcquity
Column Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type QTOF RPLC-IM-MS
MS instrument name Waters Synapt G2 Waters Synapt G2
Ion Mode POSITIVE NEGATIVE
Units Intensity Intensity

Chromatography:

Chromatography ID:CH001510
Chromatography Summary:RPLC-IM-MS chromatography method (positive mode)
Instrument Name:Waters NanoAcquity
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:40 C
Flow Gradient:linear
Flow Rate:75 uL/min
Retention Time:30 min
Solvent A:80% water/20% acetonitrile
Solvent B:80% acetonitrile/20% water
Capillary Voltage:3.0 kV
Chromatography Type:Reversed phase
  
Chromatography ID:CH001511
Chromatography Summary:RPLC-IM-MS chromatography method (negative mode)
Instrument Name:Waters NanoAcquity
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:40 C
Flow Gradient:linear
Flow Rate:75 uL/min
Retention Time:30 min
Solvent A:80% water/20% acetonitrile
Solvent B:80% acetonitrile/20% water
Capillary Voltage:-2.2 kV
Chromatography Type:Reversed phase

MS:

MS ID:MS001924
Analysis ID:AN002073
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
MS Comments:Progenesis QI software version 2.3 is used for data processing.
Ion Mode:POSITIVE
  
MS ID:MS001925
Analysis ID:AN002074
Instrument Name:Waters Synapt G2
Instrument Type:RPLC-IM-MS
MS Type:ESI
MS Comments:Progenesis QI software version 2.3 is used for data processing.
Ion Mode:NEGATIVE
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