Summary of Study ST003253

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 PR002019. The data can be accessed directly via it's Project DOI: 10.21228/M8N23M 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 IDST003253
Study TitleMetabolomics studies on mouse liver samples on a Western diet
Study SummaryTargeted metabolomics was performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS).to measure polar metabolites in both positive and negative ionization mode on cardiac mice tissue acquired after a 30 week dietary intervention.
Institute
University of Sydney
DepartmentSchool of Medical Sciences
LaboratoryCardiometabolic Disease
Last NameLiu
First NameRenping
AddressCharles Perkins Centre
Emailrenping.liu@sydney.edu.au
Phone+61432953638
Submit Date2024-05-03
Num Groups4
Total Subjects35
Num Males35
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailAPI
Release Date2024-08-26
Release Version1
Renping Liu Renping Liu
https://dx.doi.org/10.21228/M8N23M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002019
Project DOI:doi: 10.21228/M8N23M
Project Title:4-diet multi-organ and multi-omic crosstalk
Project Type:Targeted MS quantitative analysis
Project Summary:Presently, dietary patterns have undergone significant shifts, and understanding the intricate interplay between diet, particularly high fat and high sucrose diets, the gut microbiome, and cardiometabolic health has become paramount. These dietary patterns have been consistently associated with heightened cardiometabolic risk factors including obesity, insulin resistance, dyslipidemia, and hypertension. High-fat diets, in particular, contribute to increased adiposity and ectopic fat deposition, exacerbating systemic inflammation and oxidative stress, thereby promoting the development of metabolic dysfunction. Similarly, high sucrose diets have been implicated in the dysregulation of glucose homeostasis, leading to insulin resistance and hyperglycemia, key hallmarks of cardiometabolic diseases such as type 2 diabetes mellitus. Amidst this, the exploration of multi-omic profiles alongside the gut microbial landscape has emerged as a pivotal avenue for unraveling the complexities of cardiometabolic health dynamics affected by the effects of high-fat and high-sucrose diets. The approach of using a multi-omic comparison between organs offers a comprehensive lens through which the intricate molecular signatures underlying the impact of dietary compositions, particularly high fat and high sucrose, on metabolic health, can be examined.
Institute:University of Sydney
Department:School of Medical Sciences
Laboratory:Cardiometabolic Disease
Last Name:Liu
First Name:Renping
Address:The Hub, Charles Perkins Centre, D17, The University of Sydney, NSW, 2006
Email:renping.liu@sydney.edu.au
Phone:+61432953638

Subject:

Subject ID:SU003372
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6J
Age Or Age Range:6 weeks old
Gender:Male
Animal Animal Supplier:Australian Resource Centre
Animal Housing:3 per cage
Animal Light Cycle:12-hour light-dark cycle

Factors:

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

mb_sample_id local_sample_id Sample source Diet
SA353582C62.2liver tissue chow
SA353583C59.2liver tissue chow
SA353584C62.3liver tissue chow
SA353585C59.1liver tissue chow
SA353586C62.1liver tissue chow
SA353587C61.2liver tissue chow
SA353588C61.1liver tissue chow
SA353589C61.3liver tissue chow
SA353590HF58.1liver tissue hfd
SA353591HF58.2liver tissue hfd
SA353592HF65.1liver tissue hfd
SA353593HF65.2liver tissue hfd
SA353594HF65.3liver tissue hfd
SA353595HF67.1liver tissue hfd
SA353596HF67.2liver tissue hfd
SA353597HF67.3liver tissue hfd
SA353598HFHS66.2liver tissue hfhsd
SA353599HFHS66.3liver tissue hfhsd
SA353600HFHS57.1liver tissue hfhsd
SA353601HFHS66.1liver tissue hfhsd
SA353602HFHS57.3liver tissue hfhsd
SA353603HFHS56.2liver tissue hfhsd
SA353604HFHS56.1liver tissue hfhsd
SA353605HS60.1liver tissue hsd
SA353606HS60.2liver tissue hsd
SA353607HS63.1liver tissue hsd
SA353608HS63.2liver tissue hsd
SA353609HS63.3liver tissue hsd
SA353610HS64.1liver tissue hsd
SA353611HS64.2liver tissue hsd
SA353612HS64.3liver tissue hsd
Showing results 1 to 31 of 31

Collection:

Collection ID:CO003365
Collection Summary:Mouse liver samples were collected at the end of the experimental design (after 30-weeks on the diet) during the cull. These samples were immediately clamped with metal clamps and snap-frozen in liquid nitrogen and stored in -80 degrees Celsius until further analysis. This process was approved by the University of Sydney’s Ethics Committee (USYD # 2017/1294).
Sample Type:Liver
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003381
Treatment Summary:36 male C57BL/6J mice were allocated to four different diets (n = 7-8) consisting of a control diet (Chow), a high-sucrose diet (HSD), a high-fat diet (HFD), and a high-fat high-sucrose (western) diet (HFHSD) at 8 weeks of age. Mice had ad libitum access to their food and autoclaved water. One mouse was euthanised prior to the expected experimental endpoint due to the loss of body condition and was excluded from this study. 4 samples were not collected after euthanisation making the groups (n = 7-8)
Treatment:Chow, HFD, HSD, HFHSD

Sample Preparation:

Sampleprep ID:SP003379
Sampleprep Summary:Approximately 50 mg of ground liver tissue was weighed into 2 mL Eppendorf tube and subjected to a two-phase extraction protocol involving tissue, ice-cold extraction medium (methanol:water, and chloroform). Samples were then centrifuged at 14 000 x g at 4 °C for 25 min. The aqueous layer was transferred into a new microfuge tube and reconstituted in the acetonitrile/methanol/formic acid (75:25:0.2; v/v/v, HPLC grade; Thermo Fisher Scientific) for the HILIC analysis, and acetonitrile/methanol (25:25; v/v/v, HPLC grade) for the AMIDE and NAD analysis.

Combined analysis:

Analysis ID AN005330 AN005331 AN005332
Analysis type MS MS MS
Chromatography type Reversed phase HILIC HILIC
Chromatography system Agilent 1260 Agilent 1260 Agilent 1260
Column Waters Atlantis T3 (150 x 4.6mm,5um) Waters XBridge BEH Amide (100 x 2.1mm,2.5um) Waters XBridge BEH Amide (100 x 2.1mm,2.5um)
MS Type API API API
MS instrument type Triple quadrupole Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex 6500 QTrap ABI Sciex 6500 QTrap ABI Sciex 6500 QTrap
Ion Mode POSITIVE NEGATIVE NEGATIVE
Units abundance abundance abundance

Chromatography:

Chromatography ID:CH004032
Chromatography Summary:Chromatographic method to detect analytes such as amino acids, endocannabinoids, fatty acid β-oxidation intermediates, gut-derived metabolites, nucleotides, neurotransmitters, cofactors and vitamins.
Instrument Name:Agilent 1260
Column Name:Waters Atlantis T3 (150 x 4.6mm,5um)
Column Temperature:40
Flow Gradient:The LC gradient program begins with an initial condition of 5% solvent A and 95% solvent B, with a flow rate of 0.25 mL/min, which is held for 0.5 minutes to establish system equilibration. The gradient then proceeds as follows: at 6 minutes, the mobile phase composition shifts to 60% solvent A and 40% solvent B for 3minutes; at 10 minutes, it changes back to 5% solvent A and 95% solvent B; at 11 minutes, the flow rate increases to 0.4 mL/min while maintaining a composition of 5% solvent A and 95% solvent B for a duration of 12.5 minutes; and at 24.5 minutes, the flow rate decreases back to 0.25 mL/min. The final condition is maintained for 1 minutes to ensure stability before subsequent analyses.
Flow Rate:0.250 – 0.400 mL/min
Solvent A:100% water; 0.1% formic acid; 10 mM ammonium formate (pH ~2.5)
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH004033
Chromatography Summary:Chromatographic method to detect analytes such as amino acids, endocannabinoids, fatty acid β-oxidation intermediates, gut-derived metabolites, nucleotides, neurotransmitters, cofactors and vitamins.
Instrument Name:Agilent 1260
Column Name:Waters XBridge BEH Amide (100 x 2.1mm,2.5um)
Column Temperature:40
Flow Gradient:The LC gradient program is initialized with an initial mobile phase composition of 15% solvent A and 85% solvent B at a flow rate of 0.25 mL/min. Over the course of 8 minutes, the mobile phase composition undergoes a transition to 65% solvent A and 35% solvent B. Subsequently, at 8 minutes, the composition shifts to 98% solvent A and 2% solvent B, maintained for 1 minute. The mobile phase reverts back to the initial composition of 15% solvent A and 85% solvent B at 10 minutes. At 12.5 minutes, the flow rate is increased to 0.4 mL/min, while maintaining a constant mobile phase composition of 15% solvent A and 85% solvent B for a period of 2.5 minutes. Finally, at 15 minutes, the flow rate is reduced back to 0.25 mL/min. To ensure system stability, the final condition is maintained for 1 minute prior to subsequent analyses.
Flow Rate:0.250 – 0.400 mL/min
Solvent A:95% acetonitrile/5% water; 20mM ammonium acetate; 20mM ammonium hydroxide (pH 9.0)
Solvent B:100% acetonitrile
Chromatography Type:HILIC
  
Chromatography ID:CH004034
Chromatography Summary:Chromatographic method to detect analytes of NAD products
Instrument Name:Agilent 1260
Column Name:Waters XBridge BEH Amide (100 x 2.1mm,2.5um)
Column Temperature:40
Flow Gradient:The LC gradient program is initialized with an initial mobile phase composition of 15% solvent A and 85% solvent B at a flow rate of 0.25 mL/min. Over the course of 8 minutes, the mobile phase composition undergoes a transition to 65% solvent A and 35% solvent B. Subsequently, at 8 minutes, the composition shifts to 98% solvent A and 2% solvent B, maintained for 1 minute. The mobile phase reverts back to the initial composition of 15% solvent A and 85% solvent B at 10 minutes. At 12.5 minutes, the flow rate is increased to 0.4 mL/min, while maintaining a constant mobile phase composition of 15% solvent A and 85% solvent B for a period of 2.5 minutes. Finally, at 15 minutes, the flow rate is reduced back to 0.25 mL/min. To ensure system stability, the final condition is maintained for 1 minute prior to subsequent analyses.
Flow Rate:0.250 – 0.400 mL/min
Solvent A:95% acetonitrile/5% water; 20mM ammonium acetate; 20mM ammonium hydroxide (pH 9.0)
Solvent B:100% acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS005060
Analysis ID:AN005330
Instrument Name:ABI Sciex 6500 QTrap
Instrument Type:Triple quadrupole
MS Type:API
MS Comments:Targeted metabolite profiling was performed using MS multiple reaction-monitoring transitions. Multiple Reaction Monitoring (MRM) Q1/Q3 peak integration of the raw data files (Analyst software, v.1.6.2; ABSciex) was performed using software MultiQuant 3.0 (ABSciex).
Ion Mode:POSITIVE
  
MS ID:MS005061
Analysis ID:AN005331
Instrument Name:ABI Sciex 6500 QTrap
Instrument Type:Triple quadrupole
MS Type:API
MS Comments:Targeted metabolite profiling was performed using MS multiple reaction-monitoring transitions. Multiple Reaction Monitoring (MRM) Q1/Q3 peak integration of the raw data files (Analyst software, v.1.6.2; ABSciex) was performed using software MultiQuant 3.0 (ABSciex).
Ion Mode:NEGATIVE
  
MS ID:MS005062
Analysis ID:AN005332
Instrument Name:ABI Sciex 6500 QTrap
Instrument Type:Triple quadrupole
MS Type:API
MS Comments:Targeted metabolite profiling was performed using MS multiple reaction-monitoring transitions. Multiple Reaction Monitoring (MRM) Q1/Q3 peak integration of the raw data files (Analyst software, v.1.6.2; ABSciex) was performed using software MultiQuant 3.0 (ABSciex).
Ion Mode:NEGATIVE
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