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.

Study ID	ST002152
Study Title	Metabolomics analysis of mouse liver with or without SIRT5 deficiency
Study Summary	8 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 Name	Liu
First Name	Xiaojing
Address	Polk Hall, RM 128
Email	xliu68@ncsu.edu
Phone	9195154387
Submit Date	2022-04-14
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2022-05-09
Release Version	1

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
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Sample Source
SA206325	KO_6.raw	SIRT5 knockout
SA206326	KO_5.raw	SIRT5 knockout
SA206327	KO_4.raw	SIRT5 knockout
SA206328	KO_7.raw	SIRT5 knockout
SA206329	KO_8.raw	SIRT5 knockout
SA206330	KO_1_luna.raw	SIRT5 knockout
SA206331	KO_2_luna.raw	SIRT5 knockout
SA206332	KO_3.raw	SIRT5 knockout
SA206333	KO_2.raw	SIRT5 knockout
SA206334	KO_7_luna.raw	SIRT5 knockout
SA206335	KO_8_luna.raw	SIRT5 knockout
SA206336	KO_6_luna.raw	SIRT5 knockout
SA206337	KO_5_luna.raw	SIRT5 knockout
SA206338	KO_1.raw	SIRT5 knockout
SA206339	KO_3_luna.raw	SIRT5 knockout
SA206340	KO_4_luna.raw	SIRT5 knockout
SA206341	WT_7_luna.raw	Wild type
SA206342	WT_8_luna.raw	Wild type
SA206343	WT_6_luna.raw	Wild type
SA206344	WT_1_luna.raw	Wild type
SA206345	WT_5.raw	Wild type
SA206346	WT_6.raw	Wild type
SA206347	WT_4.raw	Wild type
SA206348	WT_3.raw	Wild type
SA206349	WT_2.raw	Wild type
SA206350	WT_7.raw	Wild type
SA206351	WT_8.raw	Wild type
SA206352	WT_4_luna.raw	Wild type
SA206353	WT_3_luna.raw	Wild type
SA206354	WT_2_luna.raw	Wild type
SA206355	WT_1.raw	Wild type
SA206356	WT_5_luna.raw	Wild type

Showing results 1 to 32 of 32

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.

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 x 2.1mm,3.5um)	Waters Xbridge amide (100 x 2.1mm,3.5um)	Phenomenex Luna C18 (100 x 2.0mm,3um)
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 x 2.1mm,3.5um)
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 x 2.0mm,3um)
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