Summary of Study ST001848

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 PR001165. The data can be accessed directly via it's Project DOI: 10.21228/M8411V This work is supported by NIH grant, U2C- DK119886.

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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 IDST001848
Study TitleUntargeted mass spectrometry reveals impact of high fat diet on peripheral amino acid regulation in a mouse model of Alzheimer’s Disease
Study Typeuntargeted metabolomics analysis
Study SummaryAPPSwe/PS1ΔE9 (APP/PSEN1) transgenic mice (to represent familial or early-onset AD) and wild-type litter mater controls were fed either a high-fat diet (HFD, 60% kcal from lard), low-fat diet (LFD, 10% kcal from lard) from 2 months of age, or reversal diet (REV, high-fat followed by low-fat from 9.5 months).
Institute
Vanderbilt University
DepartmentChemistry
LaboratoryCenter for Innovative Technology
Last NameCodreanu
First NameSimona
Address3009, Liberty Hills Drive
EmailSIMONA.CODREANU@VANDERBILT.EDU
Phone6153477458
Submit Date2021-06-03
Num Groups6
Total Subjects36
Num Males18
Num Females18
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-08-31
Release Version1
Simona Codreanu Simona Codreanu
https://dx.doi.org/10.21228/M8411V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001165
Project DOI:doi: 10.21228/M8411V
Project Title:Untargeted mass spectrometry reveals impact of high fat diet on peripheral amino acid regulation in a mouse model of Alzheimer’s Disease
Project Type:Untargeted Metabolomics analysis
Project Summary:Recent research regarding amino acid metabolism has shown that there may be a link between obesity and Alzheimer’s Disease (AD). This work reports a metabolomics study using untargeted mass spectrometry-based metabolomic strategies to investigate the metabolic changes that occur in AD and obesity. APPSwe/PS1ΔE9 (APP/PSEN1) transgenic mice (to represent familial or early-onset AD) and wild-type litter mater controls were fed either a high-fat diet (HFD, 60% kcal from lard), low-fat diet (LFD, 10% kcal from lard) from 2 months of age, or reversal diet (REV, high-fat followed by low-fat from 9.5 months).
Institute:Vanderbilt University
Department:Chemistry
Laboratory:Center for Innovative Technology
Last Name:Codreanu
First Name:Simona
Address:3009, Liberty Hills Drive
Email:SIMONA.CODREANU@VANDERBILT.EDU
Phone:6153477458

Subject:

Subject ID:SU001925
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:APPSwe/PS1ΔE9 (APP/PSEN1)
Age Or Age Range:12 month
Gender:Male and female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id gender genotype treatment
SA171968S29F APP HFD
SA171969S30F APP HFD
SA171970S28F APP HFD
SA171971S24F APP LFD
SA171972S23F APP LFD
SA171973S22F APP LFD
SA171974S34F APP REV
SA171975S36F APP REV
SA171976S35F APP REV
SA171977S26F WT HFD
SA171978S25F WT HFD
SA171979S27F WT HFD
SA171980S21F WT LFD
SA171981S20F WT LFD
SA171982S19F WT LFD
SA171983S31F WT REV
SA171984S32F WT REV
SA171985S33F WT REV
SA171986S10M APP HFD
SA171987S11M APP HFD
SA171988S12M APP HFD
SA171989S05M APP LFD
SA171990S04M APP LFD
SA171991S06M APP LFD
SA171992S18M APP REV
SA171993S17M APP REV
SA171994S16M APP REV
SA171995S09M WT HFD
SA171996S07M WT HFD
SA171997S08M WT HFD
SA171998S03M WT LFD
SA171999S02M WT LFD
SA172000S01M WT LFD
SA172001S14M WT REV
SA172002S13M WT REV
SA172003S15M WT REV
Showing results 1 to 36 of 36

Collection:

Collection ID:CO001918
Collection Summary:Liver samples from male and female APPSwe/PS1ΔE9 (APP/PSEN1) transgenic mice and wild-type (WT) littermates were collected after sacrifice at 12 months. These mice are a subset of mice for which behavioral and biochemical data have already been published, including weight change and diabetic state as assessed by glucose tolerance tests.After sacrifice, liver tissue samples were taken and put immediately on dry ice and stored at −80°C until used in the analytical workflow described herein.
Sample Type:Liver
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001937
Treatment Summary:Briefly, at 2-months of age, standard lab chow (Purina 5001, 4% kcal/fat) was replaced with either HFD in which 60% kcal are derived from lard, 20% from carbohydrate and 20% from protein, or low-fat diet (LFD) control in which 10% kcal are derived from lard and additional calories are derived from corn starch, with 70% from carbohydrates and 20% from protein.33 For the reversal group (REV), a subset of mice on the HFD was provided with a LFD, at 9.5 months of age, for the study duration.33 All other mice were maintained on their original experimental diets until the end of the study, which was an additional 10 weeks.

Sample Preparation:

Sampleprep ID:SP001931
Sampleprep Summary:For liver samples, frozen tissues were first individually pulverized using a mortar and pestle followed by lysing in 1 mL ice-cold lysis buffer ((1:1:2, ACN:MeOH:ammonium bicarbonate (0.1 M, pH 8.0) (LC-MS grade)). Individual samples were sonicated using a probe tip sonicator, 10 pulses, at 30% power, and cooled on ice between samples. A bicinchoninic acid (BCA) protein assay was used to determine the protein concentration for each individual sample and adjusted to a total amount of protein of 200 µg. For untargeted MS studies, SIL-ISs biotin-D2 and phenylalanine-D8 were added to each sample to assess sample processing steps (metabolite extraction and reconstitution). Following lysis and addition of SIL-ISs, protein precipitation was performed by adding 800 µL of ice-cold methanol (4x by volume). Samples were incubated at -80°C overnight. Following incubation, samples were centrifuged at 10,000 rpm for 10 min. The supernatant containing metabolites were dried in vacuo and metabolite extracts were stored frozen at -80 °C until ready to use.
Processing Storage Conditions:-80℃
Extraction Method:Following lysis and standard addition, protein precipitation was performed by adding 800µL of ice-cold methanol (4x by volume). Samples were incubated at -80°C overnight. Following incubation, samples were centrifuged at 10,000 rpm for 10 min to eliminate proteins. The supernatants containing metabolites were dried via speed-vacuum.
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002992
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Thermo Hypersil Gold (100 x 2. mm,1.9um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode POSITIVE
Units time_m/z

Chromatography:

Chromatography ID:CH002219
Instrument Name:Thermo Vanquish
Column Name:Thermo Hypersil Gold (100 x 2. mm,1.9um)
Column Temperature:40
Flow Gradient:0.250
Flow Rate:0.25 mL/min
Injection Temperature:8
Sample Injection:5
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile, 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS002781
Analysis ID:AN002992
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:XCalibur software for data acquisition Progenesis QI 2.0 for data processing
Ion Mode:POSITIVE
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