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.
| Study ID | ST001249 |
| 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 |
| j.c.poland@vanderbilt.edu | |
| Phone | 6153434564 |
| Submit Date | 2019-09-10 |
| Num Groups | 3 |
| Total Subjects | 15 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Waters) |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-10-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Group |
|---|---|---|
| SA090946 | 20151115_jcp_iso_dilu_con_3_1 | Control |
| SA090947 | 20151115_jcp_iso_dilu_con_2_2 | Control |
| SA090948 | 20151115_jcp_iso_dilu_con_1_2 | Control |
| SA090949 | 20151115_jcp_iso_dilu_con_3_2 | Control |
| SA090950 | 20151115_jcp_iso_dilu_con_2_1 | Control |
| SA090951 | 20151115_jcp_iso_dilu_con_4_1 | Control |
| SA090952 | 20151115_jcp_iso_dilu_con_5_2 | Control |
| SA090953 | 20151115_jcp_iso_dilu_con_5_1 | Control |
| SA090954 | 20151115_jcp_iso_dilu_con_4_2 | Control |
| SA090955 | jcp_20160831_BD_rerun_neg_con_1_1 | Control |
| SA090956 | 20151115_jcp_iso_dilu_con_1_1 | Control |
| SA090957 | jcp_20160831_BD_rerun_neg_con_4_1 | Control |
| SA090958 | jcp_20160831_BD_rerun_neg_con_4_2 | Control |
| SA090959 | jcp_20160831_BD_rerun_neg_con_5_1 | Control |
| SA090960 | jcp_20160831_BD_rerun_neg_con_3_1 | Control |
| SA090961 | jcp_20160831_BD_rerun_neg_con_2_2 | Control |
| SA090962 | jcp_20160831_BD_rerun_neg_con_1_2 | Control |
| SA090963 | jcp_20160831_BD_rerun_neg_con_2_1 | Control |
| SA090964 | jcp_20160831_BD_rerun_neg_con_5_2 | Control |
| SA090965 | jcp_20160831_BD_rerun_neg_con_3_2 | Control |
| SA090966 | jcp_20160831_BD_rerun_neg_IL10_2_1 | GB-IL10 |
| SA090967 | jcp_20160831_BD_rerun_neg_IL10_4_2 | GB-IL10 |
| SA090968 | jcp_20160831_BD_rerun_neg_IL10_5_1 | GB-IL10 |
| SA090969 | jcp_20160831_BD_rerun_neg_IL10_5_2 | GB-IL10 |
| SA090970 | jcp_20160831_BD_rerun_neg_IL10_4_1 | GB-IL10 |
| SA090971 | jcp_20160831_BD_rerun_neg_IL10_3_2 | GB-IL10 |
| SA090972 | 20151115_jcp_iso_dilu_IL10_1_1 | GB-IL10 |
| SA090973 | 20151115_jcp_iso_dilu_IL10_1_2 | GB-IL10 |
| SA090974 | jcp_20160831_BD_rerun_neg_IL10_3_1 | GB-IL10 |
| SA090975 | jcp_20160831_BD_rerun_neg_IL10_1_1 | GB-IL10 |
| SA090976 | 20151115_jcp_iso_dilu_IL10_2_1 | GB-IL10 |
| SA090977 | 20151115_jcp_iso_dilu_IL10_5_1 | GB-IL10 |
| SA090978 | 20151115_jcp_iso_dilu_IL10_5_2 | GB-IL10 |
| SA090979 | jcp_20160831_BD_rerun_neg_IL10_2_2 | GB-IL10 |
| SA090980 | 20151115_jcp_iso_dilu_IL10_4_1 | GB-IL10 |
| SA090981 | 20151115_jcp_iso_dilu_IL10_4_2 | GB-IL10 |
| SA090982 | jcp_20160831_BD_rerun_neg_IL10_1_2 | GB-IL10 |
| SA090983 | 20151115_jcp_iso_dilu_IL10_3_2 | GB-IL10 |
| SA090984 | 20151115_jcp_iso_dilu_IL10_2_2 | GB-IL10 |
| SA090985 | 20151115_jcp_iso_dilu_IL10_3_1 | GB-IL10 |
| SA090986 | 20151115_jcp_iso_dilu_IL4_4_2 | GB-IL4 |
| SA090987 | 20151115_jcp_iso_dilu_IL4_5_1 | GB-IL4 |
| SA090988 | 20151115_jcp_iso_dilu_IL4_5_2 | GB-IL4 |
| SA090989 | 20151115_jcp_iso_dilu_IL4_4_1 | GB-IL4 |
| SA090990 | 20151115_jcp_iso_dilu_IL4_1_1 | GB-IL4 |
| SA090991 | jcp_20160831_BD_rerun_neg_IL4_4_1 | GB-IL4 |
| SA090992 | jcp_20160831_BD_rerun_neg_IL4_4_2 | GB-IL4 |
| SA090993 | jcp_20160831_BD_rerun_neg_IL4_3_2 | GB-IL4 |
| SA090994 | jcp_20160831_BD_rerun_neg_IL4_3_1 | GB-IL4 |
| SA090995 | jcp_20160831_BD_rerun_neg_IL4_2_1 | GB-IL4 |
| SA090996 | jcp_20160831_BD_rerun_neg_IL4_2_2 | GB-IL4 |
| SA090997 | jcp_20160831_BD_rerun_neg_IL4_5_1 | GB-IL4 |
| SA090998 | jcp_20160831_BD_rerun_neg_IL4_5_2 | GB-IL4 |
| SA090999 | 20151115_jcp_iso_dilu_IL4_2_2 | GB-IL4 |
| SA091000 | 20151115_jcp_iso_dilu_IL4_3_1 | GB-IL4 |
| SA091001 | 20151115_jcp_iso_dilu_IL4_2_1 | GB-IL4 |
| SA091002 | 20151115_jcp_iso_dilu_IL4_1_2 | GB-IL4 |
| SA091003 | jcp_20160831_BD_rerun_neg_IL4_1_1 | GB-IL4 |
| SA091004 | jcp_20160831_BD_rerun_neg_IL4_1_2 | GB-IL4 |
| SA091005 | 20151115_jcp_iso_dilu_IL4_3_2 | GB-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 |
