Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA099375

Local Sample ID:	MAL_4
Subject ID:	SU001440
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	C57BL/6J
Age Or Age Range:	7 weeks
Gender:	Female
Animal Animal Supplier:	Jackson Laboratories

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Subject:

Subject ID:	SU001440
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	C57BL/6J
Age Or Age Range:	7 weeks
Gender:	Female
Animal Animal Supplier:	Jackson Laboratories

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
MAL_4	SA099375	FL014059	MAL	Treatment
MAL_4	SA099375	FL014059	Malnourished	Diet
MAL_4	SA099375	FL014059	No	Bacterial Exposure

Collection:

Collection ID:	CO001435
Collection Summary:	Following sacrifice, murine liver lobes were isolated and stored at -70/80 C prior to untargeted metabolomics.
Sample Type:	Hippocampus

Treatment:

Treatment ID:	TR001455
Treatment Summary:	CON = control mice on healthy diet, MAL = mice placed on a protein/fat deficient diet (malnourished), MAL-BG = MAL mice plus iterative E.coli/Bacteroidales exposure

Sample Preparation:

Sampleprep ID:	SP001448
Sampleprep Summary:	Methods reported in methodology .zip folder / Metabolomics were completed by TMIC (The Metabolomics Innovation Centre). Each mouse hippocampal sample in an Eppendorf tube was mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added. 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. Two rounds of sample injections were made, with positive- and negative-ion detection, respectively.

Sampleprep ID:

SP001448

Sampleprep Summary:

Methods reported in methodology .zip folder / Metabolomics were completed by TMIC (The Metabolomics Innovation Centre). Each mouse hippocampal sample in an Eppendorf tube was mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added. 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. Two rounds of sample injections were made, with positive- and negative-ion detection, respectively.

Combined analysis:

Analysis ID	AN002273	AN002274
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	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)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo LTQ-Orbitrap Velos Pro	Thermo LTQ-Orbitrap Velos Pro
Ion Mode	POSITIVE	NEGATIVE
Units	abundance	abundance

Chromatography:

Chromatography ID:	CH001672
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Waters BEH C8 (50 x 2.1mm,1.7um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002117
Analysis ID:	AN002273
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:	MS002118
Analysis ID:	AN002274
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