Summary of Study ST001353

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 PR000923. The data can be accessed directly via it's Project DOI: 10.21228/M8CT2B 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 ID	ST001353
Study Title	Untargeted metabolomics in skeletal muscle of mice with chronic kidney disease
Study Type	MS quantitative analysis
Study Summary	This study performed untargeted metabolomics analysis of skeletal muscle obtained form mice with and without chronic kidney disease.
Institute	University of Florida
Last Name	Ryan
First Name	Terence
Address	1864 Stadium Rd, FLG 114, Gainesville, FL, 32611, USA
Email	ryant@ufl.edu
Phone	352-294-1700
Submit Date	2020-04-02
Num Groups	4
Total Subjects	18
Num Males	8
Num Females	10
Study Comments	two control male samples processed mistakenly were from soles muscles, while all other samples were gastrocnemius muscles. Due to differences in fiber type proportions, soleus muscles were not used in final analysis
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2020-12-31
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000923
Project DOI:	doi: 10.21228/M8CT2B
Project Title:	Untargeted metabolomics in skeletal muscle of mice with chronic kidney disease
Project Type:	MS Quantitative analysis
Project Summary:	This project performed untargeted metabolomics analysis in skeletal muscle (gastrocnemius) in mice with and without chronic kidney disease.
Institute:	University of Florida
Department:	Applied Physiology and Kinesiology
Last Name:	Ryan
First Name:	Terence
Address:	1864 Stadium Rd, FLG 114, Gainesville, FL, 32611, USA
Email:	ryant@ufl.edu
Phone:	352-294-1700
Funding Source:	NIH/NHLBI R01-HL149704 and R01-HL148597

Subject:

Subject ID:	SU001427
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	C57BL6J
Age Or Age Range:	18-20 weeks
Weight Or Weight Range:	20-30g
Gender:	Male and female
Animal Animal Supplier:	Jackson Laboratories
Animal Housing:	5/cage
Animal Light Cycle:	12h
Animal Feed:	Ad libitum. Control mice received custom casein-diet. Chronic kidney disease was induced by supplementing casein-based diet with 0.15% adenine
Animal Water:	Ad libitum

Factors:

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

mb_sample_id	local_sample_id	Group
SA098167	CKD015	CKD
SA098168	CKD014	CKD
SA098169	CKD012	CKD
SA098170	CKD016	CKD
SA098171	CKD013	CKD
SA098172	CKD017	CKD
SA098173	Pooled_CKD_Female	CKD
SA098174	Pooled_CKD_Male	CKD
SA098175	CKD018	CKD
SA098176	CKD010	CKD
SA098177	CKD011	CKD
SA098178	CKD009	CKD
SA098179	Pooled_Control_Female	Control
SA098180	Pooled_Control_Male	Control
SA098181	Con012	Control
SA098182	Con011	Control
SA098183	Con010	Control
SA098184	Con013	Control
SA098185	Con014	Control
SA098186	Con018	Control
SA098187	Con017	Control
SA098188	Con016	Control
SA098189	Con015	Control
SA098190	Con009	Control

Showing results 1 to 24 of 24

Showing results 1 to 24 of 24

Collection:

Collection ID:	CO001422
Collection Summary:	Skeletal muscle was quickly dissected, trimmed of fat and connective tissues and rinsed in PBS to remove and blood. Dissection occurred under ketamine/xylazine anesthesia and snap frozen in liquid nitrogen. Frozen muscles were stored at -80C until processing.
Sample Type:	Muscle
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR001442
Treatment Summary:	We utilized an established adenine-diet model to induce CKD in mice. Mice were assigned to a casein-based chow diet for 7 days, followed by induction of renal tubular injury by supplementing the diet with 0.2% adenine for 7 days, and were subsequently maintained on a 0.15% adenine diet for 7 more weeks. CKD mice were then placed back on control casein diet for 2 weeks to prior to euthanasia and terminal experiments. Control mice received casein diet for the duration of the study.
Animal Anesthesia:	Ketamine/Xylazine
Animal Endp Euthanasia:	Ketamine/Xylazine

Sample Preparation:

Sampleprep ID:	SP001435
Sampleprep Summary:	Muscles were thawed on ice, weighed, and homogenized with a Teflon-tipped conical pestle with a metal rod (Micro-Tube Sample Pestle with Conical Teflon Tip, fits 1.5ml Tubes, autoclavable at 121°F; Research Products International Corp; 199221; Fisher Scientific). The pestle was rinsed with 2-Propanol, water, and methanol and patted dry with a KimWipe in between samples. The samples were centrifuged to pellet the tissue debris and protein concentrations were quantified on the QuBit. The samples were normalized to 500µg/mL of protein with 5mM Ammonium Acetate in water prior to extraction for a total volume of 100µL. 25µL of sample was aliquoted into a clean tube and extracted with 5µL of Global Metabolomics IS and 200µL of 8:1:1 Acetonitrile:Methanol:Acetone to precipitate proteins. The samples were incubated at 4°C for 30 min and centrifuged at 20,000xg at 4°C for 10min. 200µL of supernatant was transferred to a clean Eppendorf tube and dried under nitrogen gas at 30°C and then reconstituted at 25µL in Global Metabolomics Inj. Std. Mix.

Sampleprep ID:

SP001435

Sampleprep Summary:

Muscles were thawed on ice, weighed, and homogenized with a Teflon-tipped conical pestle with a metal rod (Micro-Tube Sample Pestle with Conical Teflon Tip, fits 1.5ml Tubes, autoclavable at 121°F; Research Products International Corp; 199221; Fisher Scientific). The pestle was rinsed with 2-Propanol, water, and methanol and patted dry with a KimWipe in between samples. The samples were centrifuged to pellet the tissue debris and protein concentrations were quantified on the QuBit. The samples were normalized to 500µg/mL of protein with 5mM Ammonium Acetate in water prior to extraction for a total volume of 100µL. 25µL of sample was aliquoted into a clean tube and extracted with 5µL of Global Metabolomics IS and 200µL of 8:1:1 Acetonitrile:Methanol:Acetone to precipitate proteins. The samples were incubated at 4°C for 30 min and centrifuged at 20,000xg at 4°C for 10min. 200µL of supernatant was transferred to a clean Eppendorf tube and dried under nitrogen gas at 30°C and then reconstituted at 25µL in Global Metabolomics Inj. Std. Mix.

Combined analysis:

Analysis ID	AN002251	AN002252
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Dionex	Thermo Dionex
Column	ACE 5 C18-300 (100 x 2.1mm)	ACE 5 C18-300 (100 x 2.1mm)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Exactive Plus Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	peak height	peak height

Chromatography:

Chromatography ID:	CH001655
Chromatography Summary:	samples were processed on a Thermo Q-Exactive Oribtrap mass spectrometer with Dionex UHPLC and autosampler. All samples were analyzed in positive and negative heated electrospray ionization with a mass resolution of 35,000 at m/z 200 as separate injections. Separation was achieved on an ACE 18-pfp 100 x 2.1 mm, 2 µm column with mobile phase A as 0.1% formic acid in water and mobile phase B as acetonitrile. This is a polar embedded stationary phase that provides comprehensive coverage, but does have some limitation is the coverage of very polar species. The flow rate was 350 µL/min with a column temperature of 25°C. 4 µL was injected for negative ions and 2 µL for positive ions.
Instrument Name:	Thermo Dionex
Column Name:	ACE 5 C18-300 (100 x 2.1mm)
Column Temperature:	25C
Flow Rate:	350ul/min
Sample Injection:	4ul for negative ion, 2ul for positive ion
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002096
Analysis ID:	AN002251
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	samples were processed on a Thermo Q-Exactive Oribtrap mass spectrometer with Dionex UHPLC and autosampler. All samples were analyzed in positive and negative heated electrospray ionization with a mass resolution of 35,000 at m/z 200 as separate injections. Separation was achieved on an ACE 18-pfp 100 x 2.1 mm, 2 µm column with mobile phase A as 0.1% formic acid in water and mobile phase B as acetonitrile. This is a polar embedded stationary phase that provides comprehensive coverage, but does have some limitation is the coverage of very polar species. The flow rate was 350 µL/min with a column temperature of 25°C. 4 µL was injected for negative ions and 2 µL for positive ions. Data from positive and negative ion modes were separately subjected to statistical analyses. MZmine (freeware) was used to identify features, deisotope, align features and perform gap filling to fill in any features that may have been missed in the first alignment algorithm. All adducts and complexes were identified and removed from the data set. The primary source of feature identification was performed by mapping against an internal retention time metabolite library established by the SECIM. Additional metabolite searches were performed using HMDB (http://www.hmdb.ca) and the Metabolomics Workbench (https://www.metabolomicsworkbench.org) through a search of the m/z ratio with a [M+H] adduct and a tolerance of 0.002 m/z.
Ion Mode:	POSITIVE

MS ID:	MS002097
Analysis ID:	AN002252
Instrument Name:	Thermo Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	samples were processed on a Thermo Q-Exactive Oribtrap mass spectrometer with Dionex UHPLC and autosampler. All samples were analyzed in positive and negative heated electrospray ionization with a mass resolution of 35,000 at m/z 200 as separate injections. Separation was achieved on an ACE 18-pfp 100 x 2.1 mm, 2 µm column with mobile phase A as 0.1% formic acid in water and mobile phase B as acetonitrile. This is a polar embedded stationary phase that provides comprehensive coverage, but does have some limitation is the coverage of very polar species. The flow rate was 350 µL/min with a column temperature of 25°C. 4 µL was injected for negative ions and 2 µL for positive ions. Data from positive and negative ion modes were separately subjected to statistical analyses. MZmine (freeware) was used to identify features, deisotope, align features and perform gap filling to fill in any features that may have been missed in the first alignment algorithm. All adducts and complexes were identified and removed from the data set. The primary source of feature identification was performed by mapping against an internal retention time metabolite library established by the SECIM. Additional metabolite searches were performed using HMDB (http://www.hmdb.ca) and the Metabolomics Workbench (https://www.metabolomicsworkbench.org) through a search of the m/z ratio with a [M+H] adduct and a tolerance of 0.002 m/z.
Ion Mode:	NEGATIVE