Summary of Study ST003188

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 PR001984. The data can be accessed directly via it's Project DOI: 10.21228/M88J0W 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	ST003188
Study Title	A metabolic atlas of mouse aging
Study Summary	Humans are living longer, but this is accompanied by an increased incidence of age-related chronic diseases. Many of these diseases are influenced by age-associated metabolic dysregulation, but how metabolism changes in multiple organs during aging in males and females is not known. Answering this could reveal new mechanisms of aging and age-targeted therapeutics. In this study, we describe how metabolism changes in 12 organs in male and female mice at 5 different ages. Organs show distinct patterns of metabolic aging that are affected by sex differently. Hydroxyproline shows the most consistent change across the dataset, decreasing with age in 11 out of 12 organs investigated. We also developed a metabolic aging clock that predicts biological age and identified alpha-ketoglutarate, previously shown to extend lifespan in mice, as a key predictor of age. Our results reveal fundamental insights into the aging process and identify new therapeutic targets to maintain organ health.
Institute	University of Southern California
Department	Keck School of Medicine
Laboratory	Mullen Lab
Last Name	Pilley
First Name	Steven
Address	1501 San Pablo St., Los Angeles, CA, 90033, USA
Email	pilley@usc.edu
Phone	+13234427555
Submit Date	2024-05-02
Num Groups	10
Total Subjects	70
Num Males	35
Num Females	35
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-11-18
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001984
Project DOI:	doi: 10.21228/M88J0W
Project Title:	A metabolic atlas of mouse aging
Project Summary:	Humans are living longer, but this is accompanied by an increased incidence of age-related chronic diseases. Many of these diseases are influenced by age-associated metabolic dysregulation, but how metabolism changes in multiple organs during aging in males and females is not known. Answering this could reveal new mechanisms of aging and age-targeted therapeutics. In this study, we describe how metabolism changes in 12 organs in male and female mice at 5 different ages. Organs show distinct patterns of metabolic aging that are affected by sex differently. Hydroxyproline shows the most consistent change across the dataset, decreasing with age in 11 out of 12 organs investigated. We also developed a metabolic aging clock that predicts biological age and identified alpha-ketoglutarate, previously shown to extend lifespan in mice, as a key predictor of age. Our results reveal fundamental insights into the aging process and identify new therapeutic targets to maintain organ health.
Institute:	University of Southern California
Department:	Keck School of Medicine
Laboratory:	Mullen Lab
Last Name:	Pilley
First Name:	Steven
Address:	1501 San Pablo St., Los Angeles, CA, 90033, USA
Email:	pilley@usc.edu
Phone:	+13234427555
Funding Source:	Impetus Grants 014746-00001

Subject:

Subject ID:	SU003307
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	C57BL/6NCrl
Age Or Age Range:	1-24 months
Gender:	Male and female
Animal Animal Supplier:	Charles River
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Sample source	Age (months)	Sex	Organ
SA346837	L55	Bladder	18	Female	Bladder
SA346838	L56	Bladder	18	Female	Bladder
SA346839	L54	Bladder	18	Female	Bladder
SA346840	L53	Bladder	18	Female	Bladder
SA346841	L50	Bladder	18	Female	Bladder
SA346842	L51	Bladder	18	Female	Bladder
SA346843	L52	Bladder	18	Female	Bladder
SA346844	L19	Bladder	18	Male	Bladder
SA346845	L21	Bladder	18	Male	Bladder
SA346846	L18	Bladder	18	Male	Bladder
SA346847	L20	Bladder	18	Male	Bladder
SA346848	L17	Bladder	18	Male	Bladder
SA346849	L15	Bladder	18	Male	Bladder
SA346850	L16	Bladder	18	Male	Bladder
SA346851	L39	Bladder	1	Female	Bladder
SA346852	L41	Bladder	1	Female	Bladder
SA346853	L40	Bladder	1	Female	Bladder
SA346854	L38	Bladder	1	Female	Bladder
SA346855	L42	Bladder	1	Female	Bladder
SA346856	L36	Bladder	1	Female	Bladder
SA346857	L37	Bladder	1	Female	Bladder
SA346858	L1	Bladder	1	Male	Bladder
SA346859	L7	Bladder	1	Male	Bladder
SA346860	L6	Bladder	1	Male	Bladder
SA346861	L5	Bladder	1	Male	Bladder
SA346862	L4	Bladder	1	Male	Bladder
SA346863	L2	Bladder	1	Male	Bladder
SA346864	L3	Bladder	1	Male	Bladder
SA346865	L59	Bladder	21	Female	Bladder
SA346866	L58	Bladder	21	Female	Bladder
SA346867	L60	Bladder	21	Female	Bladder
SA346868	L61	Bladder	21	Female	Bladder
SA346869	L63	Bladder	21	Female	Bladder
SA346870	L57	Bladder	21	Female	Bladder
SA346871	L62	Bladder	21	Female	Bladder
SA346872	L23	Bladder	21	Male	Bladder
SA346873	L25	Bladder	21	Male	Bladder
SA346874	L24	Bladder	21	Male	Bladder
SA346875	L28	Bladder	21	Male	Bladder
SA346876	L26	Bladder	21	Male	Bladder
SA346877	L27	Bladder	21	Male	Bladder
SA346878	L22	Bladder	21	Male	Bladder
SA346879	L64	Bladder	24	Female	Bladder
SA346880	L70	Bladder	24	Female	Bladder
SA346881	L69	Bladder	24	Female	Bladder
SA346882	L68	Bladder	24	Female	Bladder
SA346883	L67	Bladder	24	Female	Bladder
SA346884	L65	Bladder	24	Female	Bladder
SA346885	L66	Bladder	24	Female	Bladder
SA346886	L35	Bladder	24	Male	Bladder
SA346887	L34	Bladder	24	Male	Bladder
SA346888	L29	Bladder	24	Male	Bladder
SA346889	L33	Bladder	24	Male	Bladder
SA346890	L32	Bladder	24	Male	Bladder
SA346891	L30	Bladder	24	Male	Bladder
SA346892	L31	Bladder	24	Male	Bladder
SA346893	L47	Bladder	3	Female	Bladder
SA346894	L46	Bladder	3	Female	Bladder
SA346895	L48	Bladder	3	Female	Bladder
SA346896	L49	Bladder	3	Female	Bladder
SA346897	L44	Bladder	3	Female	Bladder
SA346898	L43	Bladder	3	Female	Bladder
SA346899	L45	Bladder	3	Female	Bladder
SA346900	L9	Bladder	3	Male	Bladder
SA346901	L8	Bladder	3	Male	Bladder
SA346902	L14	Bladder	3	Male	Bladder
SA346903	L10	Bladder	3	Male	Bladder
SA346904	L13	Bladder	3	Male	Bladder
SA346905	L12	Bladder	3	Male	Bladder
SA346906	L11	Bladder	3	Male	Bladder
SA346907	G solvent-2	Blank	NA	NA	NA
SA346908	G solvent-1	Blank	NA	NA	NA
SA346909	I solvent-1	Blank	NA	NA	NA
SA346910	F solvent-2	Blank	NA	NA	NA
SA346911	H solvent-2	Blank	NA	NA	NA
SA346912	I solvent-2	Blank	NA	NA	NA
SA346913	E solvent-1	Blank	NA	NA	NA
SA346914	C solvent-2	Blank	NA	NA	NA
SA346915	D solvent -1	Blank	NA	NA	NA
SA346916	D solvent-2	Blank	NA	NA	NA
SA346917	E solvent-2	Blank	NA	NA	NA
SA346918	F solvent -1	Blank	NA	NA	NA
SA346919	H solvent -1	Blank	NA	NA	NA
SA346920	L solvent-2	Blank	NA	NA	NA
SA346921	A solvent.d-1	Blank	NA	NA	NA
SA346922	L solvent-1	Blank	NA	NA	NA
SA346923	B solvent -1	Blank	NA	NA	NA
SA346924	J solvent -1	Blank	NA	NA	NA
SA346925	A solvent-2	Blank	NA	NA	NA
SA346926	L solvent -1	Blank	NA	NA	NA
SA346927	K solvent-1	Blank	NA	NA	NA
SA346928	C solvent-1	Blank	NA	NA	NA
SA346929	B solvent-2	Blank	NA	NA	NA
SA346930	J solvent-2	Blank	NA	NA	NA
SA346931	K solvent-2	Blank	NA	NA	NA
SA346932	F53	Brain	18	Female	Brain
SA346933	F56	Brain	18	Female	Brain
SA346934	F52	Brain	18	Female	Brain
SA346935	F55	Brain	18	Female	Brain
SA346936	F51	Brain	18	Female	Brain

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Collection:

Collection ID:	CO003300
Collection Summary:	We purchased male and virgin female C57BL/6NCrl mice from Charles River (RRID:IMSR_CRL:027) and housed them at USC. Mice were housed under identical conditions at both Charles River and USC (12 hr/12 hr light dark cycle) and fed the same diet ad libitum (NIH-31 diet). The 1-month-old, 3-month-old, and 18-month-old mice were kept at USC for one week before harvesting. The 21-month-old and 24-month-old mice arrived aged 18 months and were aged at USC for the remaining 3 months and 6 months respectively. All tissues were collected beginning at 3 pm on each day of harvest. We used 4% isoflurane to anaesthetize the mice. We then weighed the mice and collected blood via cardiac puncture into EDTA collection tubes and placed them on ice. We then collected organs in the following order: heart, thymus, lungs, liver, pancreas, spleen, kidney, bladder, quadriceps muscle, tongue, and brain. The organs were immediately snap frozen in liquid nitrogen and stored at -80C until metabolite extraction. Organ collection finished by 5 pm. All animal care and procedures were approved by the USC Department of Animal Research.
Sample Type:	Blood (plasma), heart, pancreas, liver, kidney, brain, spleen, quadriceps muscle, lung, thymus, tongue, bladder

Treatment:

Treatment ID:	TR003316
Treatment Summary:	We purchased male and virgin female C57BL/6NCrl mice from Charles River (RRID:IMSR_CRL:027) and housed them at USC. Mice were housed under identical conditions at both Charles River and USC (12 hr/12 hr light dark cycle) and fed the same diet ad libitum (NIH-31 diet). The 1-month-old, 3-month-old, and 18-month-old mice were kept at USC for one week before harvesting. The 21-month-old and 24-month-old mice arrived aged 18 months and were aged at USC for the remaining 3 months and 6 months respectively.

Treatment ID:

TR003316

Treatment Summary:

We purchased male and virgin female C57BL/6NCrl mice from Charles River (RRID:IMSR_CRL:027) and housed them at USC. Mice were housed under identical conditions at both Charles River and USC (12 hr/12 hr light dark cycle) and fed the same diet ad libitum (NIH-31 diet). The 1-month-old, 3-month-old, and 18-month-old mice were kept at USC for one week before harvesting. The 21-month-old and 24-month-old mice arrived aged 18 months and were aged at USC for the remaining 3 months and 6 months respectively.

Sample Preparation:

Sampleprep ID:	SP003314
Sampleprep Summary:	To obtain plasma, we centrifuged EDTA-tubes containing blood at 4°C at 2,000 g for 15 minutes. We collected supernatants and added 20 μL to 80 μL 100% LC-grade methanol. For tissue homogenization, we put tissue samples in 10 μL ice-cold 4:1 LC-grade Methanol:Ultrapure-water per mg tissue and homogenized them using a bead homogenizer (Bead Mill 4, Fisherbrand). We centrifuged plasma supernatants and tissue homogenates at 4°C at 21,300 g for 10 minutes and collected the metabolite-containing supernatants. We dried down 100 μL of supernatant from each sample (equivalent to 10 mg of tissue) using a vacuum centrifuge and stored them at -80°C until further processing. Dried supernatants reconstituted in 50ul of LC-grade Methanol: Ultrapure-water mix (1:1) and then analyzed using the Agilent 1290 Infinity II LC –6470 Triple Quadrupole (QqQ) tandem mass spectrometer (MS/MS).

Sampleprep ID:

SP003314

Sampleprep Summary:

To obtain plasma, we centrifuged EDTA-tubes containing blood at 4°C at 2,000 g for 15 minutes. We collected supernatants and added 20 μL to 80 μL 100% LC-grade methanol. For tissue homogenization, we put tissue samples in 10 μL ice-cold 4:1 LC-grade Methanol:Ultrapure-water per mg tissue and homogenized them using a bead homogenizer (Bead Mill 4, Fisherbrand). We centrifuged plasma supernatants and tissue homogenates at 4°C at 21,300 g for 10 minutes and collected the metabolite-containing supernatants. We dried down 100 μL of supernatant from each sample (equivalent to 10 mg of tissue) using a vacuum centrifuge and stored them at -80°C until further processing. Dried supernatants reconstituted in 50ul of LC-grade Methanol: Ultrapure-water mix (1:1) and then analyzed using the Agilent 1290 Infinity II LC –6470 Triple Quadrupole (QqQ) tandem mass spectrometer (MS/MS).

Chromatography:

Chromatography ID:	CH003963
Instrument Name:	Agilent 1290 Infinity II
Column Name:	Agilent ZORBAX RRHD SB-C18 (150 x 2.1mm,1.8um)
Column Temperature:	35
Flow Gradient:	0.25 mL/min, 0–2.5 min, 100% A; 7.5 min, 80% A and 20% B; 13 min 55% A and 45% B; 20 min, 1% A and 99% B; 24 min, 1% A and 99% B; 24.05 min, 1% A and 99% C; 27 min, 1% A and 99% C; at 0.8 mL/min, 27.5–31.35 min, 1% A and 99% C; at 0.6 mL/min, 31.50 min, 1% A and 99% C; at 0.4 mL/min, 32.25–39.9 min, 100% A; and at 0.25 mL/min, 40 min, 100% A.
Flow Rate:	0.25-0.8 mL/min
Solvent A:	97% water/3% methanol;15 mM acetic acid; 10 mM tributylamine at pH 5
Solvent B:	100% methanol; 15 mM acetic acid; 10 mM tributylamine
Chromatography Type:	Reversed phase
Solvent C:	100% acetonitrile, wash solvent.

Analysis:

Analysis ID:	AN005236
Laboratory Name:	Lyssiotis Lab
Analysis Type:	MS
Operator Name:	Li Zhang
Chromatography ID:	CH003963
Num Factors:	133
Num Metabolites:	190
Units:	AU