Summary of Study ST001367

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 PR000935. The data can be accessed directly via it's Project DOI: 10.21228/M8TT3R 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	ST001367
Study Title	Malnutrition and Liver Metabolomics Pre-Intervention (part-I)
Study Summary	RP-UPLC-FTMS (+/- ion detection) and HILIC-FTMS (+/- ion detection) were conducted on murine livers from healthy (CON) and malnourished (MAL) mice. To examine the impact of gut microbes and malnutrition, data was also collected from a third group (MBG).
Institute	University of British Columbia
Department	Microbiology and Immunology
Laboratory	B. Brett Finlay
Last Name	Bauer
First Name	Kylynda
Address	Michael Smith Laboratories, #301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4
Email	kcbauer@msl.ubc.ca
Phone	(604) 822-2210
Submit Date	2020-04-20
Num Groups	3
Total Subjects	12
Num Females	12
Analysis Type Detail	LC-MS
Release Date	2020-08-03
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000935
Project DOI:	doi: 10.21228/M8TT3R
Project Title:	Malnutrition Gut microbes and Liver Metabolomics
Project Summary:	Examining the role of malnutrition and gut microbes on fatty liver using the MAL-BG murine model. RP-UPLC-FTMS and HILIC-FTMS were conducted on murine livers prior and following dietary intervention. This submission contains prior intervention raw data.
Institute:	University of British Columbia
Department:	Microbiology and Immunology
Laboratory:	Finlay
Last Name:	Bauer
First Name:	Kylynda
Address:	#301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4
Email:	kcbauer@msl.ubc.ca
Phone:	(604) 822-2210
Project Comments:	Pre-Intervention
Contributors:	B. Brett Finlay

Subject:

Subject ID:	SU001441
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	C57BL/6J
Age Or Age Range:	~7 weeks (Pre-intervention)
Gender:	Female
Animal Animal Supplier:	Jackson Laboratories

Factors:

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

mb_sample_id	local_sample_id	Treatment	Start Diet	Final Diet
SA099377	CONA_4	CON	Healthy	Healthy
SA099378	CONA_3	CON	Healthy	Healthy
SA099379	CONA_1	CON	Healthy	Healthy
SA099380	CONA_2	CON	Healthy	Healthy
SA099381	MALA_4	MAL	Malnourished	Malnourished
SA099382	MALA_3	MAL	Malnourished	Malnourished
SA099383	MALA_2	MAL	Malnourished	Malnourished
SA099384	MALA_1	MAL	Malnourished	Malnourished
SA099385	MBGA_4	MBG	Malnourished	Malnourished
SA099386	MBGA_2	MBG	Malnourished	Malnourished
SA099387	MBGA_1	MBG	Malnourished	Malnourished
SA099388	MBGA_3	MBG	Malnourished	Malnourished

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO001436
Collection Summary:	Following sacrifice, murine liver lobes were isolated and stored at -70/80 C prior to untargeted metabolomics.
Sample Type:	Liver

Treatment:

Treatment ID:	TR001456
Treatment Summary:	CON = control mice placed on a healthy (standard mouse chow), MAL = mice placed on an isocaloric malnourished diet (protein/fat deficient), MBG = MAL mice with repeated exposure to fecal microbes, mice were placed on the respective treatments for one month following weaning.

Sample Preparation:

Sampleprep ID:	SP001449
Sampleprep Summary:	RP-UPLC-FTMS: Individual mouse liver samples were mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added to an Eppendorf tube. The tissue was homogenized on a MM 400 mill mixer at a vibrating frequency of 30 Hz for 1 min twice. After 5-s spin-down, a mixture of methanol-chloroform (4:1) was added, at 25 μL per mg tissue, to each tube. The sample was homogenized again for metabolite extraction using the same setup for 1 min twice, followed by sonication in an ice-water bath for 5 min. The tube was centrifuged at 15,000 rpm and at 10 0C for 20 min. The clear supernatant was transferred to a 1.5-mL Eppendorf tube. A 60-μL aliquot from each sample was dried down inside the same nitrogen evaporator and the residue was reconstituted in 40 μL of 80% methanol. 10 μL was injected for reversed-phase RP-UPLC-FTMS. HILIC-FTMS: Individual sample supernatants were mixed with 120 μL of water, 180 μL of methanol and 195 μL of chloroform. The mixture was vortex mixed at 3000 rpm for 30 s before centrifugal clarification. 300 μL of the upper, aqueous phase was precisely taken out and transferred to a “V”-shape LC injection microvial and was dried down under a gentle nitrogen gas flow in the nitrogen evaporator. The residue was reconstituted in 50 μL of 80% acetonitrile. 10 μL was injected for HILIC-FTMS. *See Methods

Sampleprep ID:

SP001449

Sampleprep Summary:

RP-UPLC-FTMS: Individual mouse liver samples were mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added to an Eppendorf tube. The tissue was homogenized on a MM 400 mill mixer at a vibrating frequency of 30 Hz for 1 min twice. After 5-s spin-down, a mixture of methanol-chloroform (4:1) was added, at 25 μL per mg tissue, to each tube. The sample was homogenized again for metabolite extraction using the same setup for 1 min twice, followed by sonication in an ice-water bath for 5 min. The tube was centrifuged at 15,000 rpm and at 10 0C for 20 min. The clear supernatant was transferred to a 1.5-mL Eppendorf tube. A 60-μL aliquot from each sample was dried down inside the same nitrogen evaporator and the residue was reconstituted in 40 μL of 80% methanol. 10 μL was injected for reversed-phase RP-UPLC-FTMS. HILIC-FTMS: Individual sample supernatants were mixed with 120 μL of water, 180 μL of methanol and 195 μL of chloroform. The mixture was vortex mixed at 3000 rpm for 30 s before centrifugal clarification. 300 μL of the upper, aqueous phase was precisely taken out and transferred to a “V”-shape LC injection microvial and was dried down under a gentle nitrogen gas flow in the nitrogen evaporator. The residue was reconstituted in 50 μL of 80% acetonitrile. 10 μL was injected for HILIC-FTMS. *See Methods

Combined analysis:

Analysis ID	AN002275	AN002276	AN002277	AN002278
Analysis type	MS	MS	MS	MS
Chromatography type	Reversed phase	Reversed phase	HILIC	HILIC
Chromatography system	Thermo Dionex Ultimate 3000	Thermo Dionex Ultimate 3000	Thermo Dionex Ultimate 3000	Thermo Dionex Ultimate 3000
Column	Waters BEH C8 (50 x 2.1mm,1.7um)	Waters BEH C8 (50 x 2.1mm,1.7um)	Waters HILIC (100 x 2.1mm,1.8um)	Waters HILIC (100 x 2.1mm,1.8um)
MS Type	ESI	ESI	ESI	ESI
MS instrument type	Orbitrap	Orbitrap	Orbitrap	Orbitrap
MS instrument name	Thermo LTQ-Orbitrap Velos Pro	Thermo LTQ-Orbitrap Velos Pro	Thermo LTQ-Orbitrap Velos Pro	Thermo LTQ-Orbitrap Velos Pro
Ion Mode	POSITIVE	NEGATIVE	POSITIVE	NEGATIVE
Units	Abundance	abundance	Abundance	abundance

Chromatography:

Chromatography ID:	CH001673
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Waters BEH C8 (50 x 2.1mm,1.7um)
Chromatography Type:	Reversed phase

Chromatography ID:	CH001674
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Waters HILIC (100 x 2.1mm,1.8um)
Chromatography Type:	HILIC

MS:

MS ID:	MS002119
Analysis ID:	AN002275
Instrument Name:	Thermo LTQ-Orbitrap Velos Pro
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	For relative quantitation, the MS instrument was run in the survey scan mode with FTMS detection at a mass resolution of 60,000 FWHM at m/z 400. The mass scan range was m/z 80 to 1800, with a reference lock-mass for real-time calibration. Two UPLC-FTMS datasets were acquired for each sample, one with positive-ion detection and the other with negative-ion detection. LC-MS/MS data was also acquired from each sample set with collision induced dissociation (CID) at different levels of normalized collision energy (from publication methods).
Ion Mode:	POSITIVE

MS ID:	MS002120
Analysis ID:	AN002276
Instrument Name:	Thermo LTQ-Orbitrap Velos Pro
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	For relative quantitation, the MS instrument was run in the survey scan mode with FTMS detection at a mass resolution of 60,000 FWHM at m/z 400. The mass scan range was m/z 80 to 1800, with a reference lock-mass for real-time calibration. Two UPLC-FTMS datasets were acquired for each sample, one with positive-ion detection and the other with negative-ion detection. LC-MS/MS data was also acquired from each sample set with collision induced dissociation (CID) at different levels of normalized collision energy (from publication methods).
Ion Mode:	NEGATIVE

MS ID:	MS002121
Analysis ID:	AN002277
Instrument Name:	Thermo LTQ-Orbitrap Velos Pro
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The MS instrument was run in the survey scan mode with FTMS detection at a mass resolution of 60,000 FWHM at m/z 400. Two HILIC-FTMS datasets were acquired for each sample, one with positive-ion detection and the other with negative-ion detection. The mass scan range was m/z 80 to 800 (from publication methods).
Ion Mode:	POSITIVE

MS ID:	MS002122
Analysis ID:	AN002278
Instrument Name:	Thermo LTQ-Orbitrap Velos Pro
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The MS instrument was run in the survey scan mode with FTMS detection at a mass resolution of 60,000 FWHM at m/z 400. Two HILIC-FTMS datasets were acquired for each sample, one with positive-ion detection and the other with negative-ion detection. The mass scan range was m/z 80 to 800 (from publication methods).
Ion Mode:	NEGATIVE