Summary of Study ST000222

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000182. The data can be accessed directly via it's Project DOI: 10.21228/M8M888 This work is supported by NIH grant, U2C- DK119886.


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Study IDST000222
Study TitleBile acid targeted metabolomics of the small intestine in malnourished and control mice
Study TypeTargeted metabolomics
Study SummaryA total of 8 samples from 6 week old, female C57BL/6 mice, treated for 3 weeks with a malnourished diet or a control-fed isocaloric diet. Samples were taken from the small intestinal fecal content at the terminus of the ileum for targeted bile acid analysis.
University of Victoria
DepartmentThe Uvic Proteomics and Metabolomics Innovation Centre
Last NameBorchers
First NameChristoph
Address#3101-4464 Markham St Victoria, BC Canada, V8Z 7X8
Submit Date2015-06-08
Num Groups2
Total Subjects8*
Study Comments*One sample failed quality control in the malnourished group, thus was not included in the study
Raw Data AvailableYes
Raw Data File Type(s)wiff
Uploaded File Size4.0 M
Analysis Type DetailLC-MS
Release Date2015-06-08
Release Version1
Christoph Borchers Christoph Borchers application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR000182
Project DOI:doi: 10.21228/M8M888
Project Title:Metabolomic analysis of the small intestinal content of malnourished mice
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
Funding Source:Canadian Institutes for Health Research


Subject ID:SU000241
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6
Age Or Age Range:6 weeks at collection
Animal Animal Supplier:Jackson Labs
Animal Housing:Conventional
Animal Feed:Low Protein, Low Fat Malnourished Diet/Isocaloric Control Diet
Cell Primary Immortalized:Malnourished/Control
Species Group:Mammal


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

mb_sample_id local_sample_id Diet
Showing results 1 to 8 of 8


Collection ID:CO000229
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 ID:TR000249
Treatment Summary:4 mice were given a malnourished diet and 4 mice were untreated, fed a control diet

Sample Preparation:

Sampleprep ID:SP000243
Sampleprep Summary:Bile-acid targeted metabolomics. Each sample was homogenized in LC-MS grade water at a ratio of 150 ?L per 10 mg raw material and with the aid of 5-mm stainless steel metal balls. Bile acids were extracted by addition of acetonitrile at a ratio of 350 ?L per 10 mg raw material followed by vortexing and sonication (1 min) in an ice-water ultrasonic bath. The samples were centrifuged. 20 ?L of the supernatants were precisely taken out and mixed with a predefined mix of 14 deuterium-labeled bile acids as the internal standards. The mixtures were subjected to phospholipid-depletion solid-phase extraction according to a validated protocol for sample cleanup and bile acid enrichment62. The flow-through fractions were collected and then dried under a gentle nitrogen flow. The dried residues were dissolved in 200 ?L of 50% methonal. 10 ?L were injected for quantitation by UPLC-MRM/MS. A Dionex UPLC system was connected to an AB Sciex 4000 QTRAP mass spectrometer which was operated in the negative ion multiple-reaction monitoring (MRM) mode and with electrospray ionization. UPLC separation was carried out on a 15 cm long C-18 UPLC column with water-acetonitrile-formic acid as the mobile phase for binary gradient elution using a developed and validated protocol for comprehensive analysis of bile acids in biological samples (Han, etc. manuscript submitted to Analytical Chemistry). The column temperature was 45 oC and the flow rate was 0.35 mL/min. 45 bile acids (including the 19 targeted bile acids) were involved in the quantitation by UPLC/scheduled MRM/MS. Concentrations of the detected bile acids were calculated with internal standard calibration from the linearly regressed standard calibration curves of individual bile acids. The lower limits of quantitation were 0.08 nmoles/mg for all the bile acids.

Combined analysis:

Analysis ID AN000331
Analysis type MS
Chromatography type
Chromatography system
MS instrument type Triple quadrupole
MS instrument name ABI Sciex API 4000 QTrap
Units nM/mg


Chromatography ID:CH000248


MS ID:MS000280
Analysis ID:AN000331
Instrument Name:ABI Sciex API 4000 QTrap
Instrument Type:Triple quadrupole