Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA099387

Local Sample ID:	MBGA_1
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

Select appropriate tab below to view additional metadata details:

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:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
MBGA_1	SA099387	FL014062	MBG	Treatment
MBGA_1	SA099387	FL014062	Malnourished	Start Diet
MBGA_1	SA099387	FL014062	Malnourished	Final Diet

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