Summary of Study ST002152

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 PR001365. The data can be accessed directly via it's Project DOI: 10.21228/M88Q5H 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 IDST002152
Study TitleMetabolomics analysis of mouse liver with or without SIRT5 deficiency
Study Summary8 Wild-type (WT) and 8 Sirt5-/- (SIRT5 KO) mice on 129 background were maintained on a standard chow diet (Teklad Global 18% Protein Rodent Diet, ENVIGO, Cat.#2018) until they were put on euthanized. Liver metabolites were extracted (5-10 mg) were extracted using 80% methanol/water as the extraction solvent. Metabolite extract was split into two tubes (one for polar metabolite analysis and the other one for acyl-CoA analysis), and then extraction solvent was evaporated using a speed vacuum concentrator. Dry pellets were stored in −80 °C freezer until ready for LC-MS analysis. For acyl-CoA analysis, dry pellets were reconstituted into 30 μL of sample solvent (water containing 50 mM ammonium acetate) per 6 mg tissue, and 8 μL was injected into the LC-MS. For non-acyl-CoA polar metabolite analysis, pellets were reconstituted into 30 μL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v/v) per 3 mg tissue, and 3 μL was injected into the LC-MS.
Institute
North Carolina State University
Last NameLiu
First NameXiaojing
AddressPolk Hall, RM 128
Emailxliu68@ncsu.edu
Phone9195154387
Submit Date2022-04-14
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-05-09
Release Version1
Xiaojing Liu Xiaojing Liu
https://dx.doi.org/10.21228/M88Q5H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001365
Project DOI:doi: 10.21228/M88Q5H
Project Title:Metabolomics analysis of mouse liver with or without SIRT5 deficiency
Project Summary:Lysine succinylation is a post-translational modification that has been implicated in the regulation of various metabolic pathways. However, the biological relevance of lysine succinylation remains largely uncertain due to methodological difficulties in determining high-impact succinylation sites. In the present study, multiple high stoichiometry lysine sites were identified in argininosuccinate synthase (ASS1), a key enzyme in urea cycle, are regulated by SIRT5. Metabolomics profiling confirms that SIRT5 deficiency decreases urea cycle activity in liver. Importantly, SIRT5 deficiency compromises ammonia tolerance, and reduces locomotor and exploratory activity in male mice upon high-ammonium diet (HAD) feeding. Therefore, lysine succinylation plays a functionally important role in ammonia metabolism.
Institute:North Carolina State University
Last Name:Liu
First Name:Xiaojing
Address:Polk Hall, RM 128
Email:xliu68@ncsu.edu
Phone:9195154387

Subject:

Subject ID:SU002238
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 Sample Source
SA206325KO_6.rawSIRT5 knockout
SA206326KO_5.rawSIRT5 knockout
SA206327KO_4.rawSIRT5 knockout
SA206328KO_7.rawSIRT5 knockout
SA206329KO_8.rawSIRT5 knockout
SA206330KO_1_luna.rawSIRT5 knockout
SA206331KO_2_luna.rawSIRT5 knockout
SA206332KO_3.rawSIRT5 knockout
SA206333KO_2.rawSIRT5 knockout
SA206334KO_7_luna.rawSIRT5 knockout
SA206335KO_8_luna.rawSIRT5 knockout
SA206336KO_6_luna.rawSIRT5 knockout
SA206337KO_5_luna.rawSIRT5 knockout
SA206338KO_1.rawSIRT5 knockout
SA206339KO_3_luna.rawSIRT5 knockout
SA206340KO_4_luna.rawSIRT5 knockout
SA206341WT_7_luna.rawWild type
SA206342WT_8_luna.rawWild type
SA206343WT_6_luna.rawWild type
SA206344WT_1_luna.rawWild type
SA206345WT_5.rawWild type
SA206346WT_6.rawWild type
SA206347WT_4.rawWild type
SA206348WT_3.rawWild type
SA206349WT_2.rawWild type
SA206350WT_7.rawWild type
SA206351WT_8.rawWild type
SA206352WT_4_luna.rawWild type
SA206353WT_3_luna.rawWild type
SA206354WT_2_luna.rawWild type
SA206355WT_1.rawWild type
SA206356WT_5_luna.rawWild type
Showing results 1 to 32 of 32

Collection:

Collection ID:CO002231
Collection Summary:Wild-type (WT) and Sirt5-/- (SIRT5 KO) mice on 129 background were maintained on a standard chow diet (Teklad Global 18% Protein Rodent Diet, ENVIGO, Cat.#2018) until they were euthanized. Metabolites extracted from eight WT and eight Sirt5-/- mouse livers were analyzed by LC/MS. Intracellular metabolites and acyl-CoA from cells were harvested as described previously using 80% methanol/water as solvent (PMID: 24410464, PMID: 24894601, PMID: 25795660) and dry pellets were stored in -80 °C freezer until ready for LC-MS analysis. For acyl-CoA and 5-methyltetrahydrofolate analysis, dry pellets were reconstituted into 30 μL of sample solvent (water containing 50 mM ammonium acetate), and 8 μL was injected into the LC-MS. For non-acyl-CoA polar metabolite analysis, pellets were reconstituted into 30 μL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v), and 3 μL was injected into the LC-MS.
Sample Type:Liver

Treatment:

Treatment ID:TR002250
Treatment Summary:Eight Wild-type (WT) and eight Sirt5-/- (SIRT5 KO) mice on 129 background were maintained on a standard chow diet (Teklad Global 18% Protein Rodent Diet, ENVIGO, Cat.#2018) until they were euthanized. Mice had free access to food and water. Mouse body weight and food intake were monitored weekly.

Sample Preparation:

Sampleprep ID:SP002244
Sampleprep Summary:Intracellular metabolites and acyl-CoA from mouse liver tissues were harvested as described previously using 80% methanol/water as solvent (PMID: 24410464, PMID: 24894601, PMID: 25795660) and dry pellets were stored in -80 °C freezer until ready for LC-MS analysis. For acyl-CoA and 5-methyltetrahydrofolate analysis, dry pellets were reconstituted into 30 μL of sample solvent (water containing 50 mM ammonium acetate), and 8 μL was injected into the LC-MS. For non-acyl-CoA polar metabolite analysis, pellets were reconstituted into 30 μL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v), and 3 μL was injected into the LC-MS.

Combined analysis:

Analysis ID AN003523 AN003524 AN003525
Analysis type MS MS MS
Chromatography type HILIC HILIC Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters Xbridge amide (100 × 2.1 mm i.d., 3.5 μm) Waters Xbridge amide (100 × 2.1 mm i.d., 3.5 μm) Phenomenex Luna C18 (100 × 2.0 mm i.d., 3 μm)
MS Type ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE
Units ion counts ion counts ion counts

Chromatography:

Chromatography ID:CH002602
Chromatography Summary:HILIC method is for general metabolomics analysis.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters Xbridge amide (100 × 2.1 mm i.d., 3.5 μm)
Chromatography Type:HILIC
  
Chromatography ID:CH002603
Chromatography Summary:RPLC is for acyl-CoA and folate analysis.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Luna C18 (100 × 2.0 mm i.d., 3 μm)
Chromatography Type:Reversed phase

MS:

MS ID:MS003281
Analysis ID:AN003523
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:It was operated in the full-scan mode with a scan range of 60-900 and the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch.
Ion Mode:POSITIVE
  
MS ID:MS003282
Analysis ID:AN003524
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:It was operated in the full-scan mode with a scan range of 60-900 and the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch.
Ion Mode:NEGATIVE
  
MS ID:MS003283
Analysis ID:AN003525
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:It was operated in the full-scan mode with a scan range of 150-1000 and the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch.
Ion Mode:POSITIVE
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