Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA047146

Local Sample ID:	ms6021-6
Subject ID:	SU000881
Subject Type:	Mouse
Subject Species:	Mus musculus
Taxonomy ID:	10090
Species Group:	Mammal

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Subject:

Subject ID:	SU000881
Subject Type:	Mouse
Subject Species:	Mus musculus
Taxonomy ID:	10090
Species Group:	Mammal

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
ms6021-6	SA047146	FL009342	K6+/+	group
ms6021-6	SA047146	FL009342	P90	time

Collection:

Collection ID:	CO000875
Collection Summary:	Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are two different genotypes (K6+/+ and K6-/-) and 20 samples total, n=5 for each group that includes P21(K6+/+); P90 (K6+/+); P21 (K6-/-); and P90 (K6-/-). We would like to make comparisons across the 4 groups.
Sample Type:	Spinal cord

Treatment:

Treatment ID:	TR000895
Treatment Summary:	A 3g Clip produces moderate SCI including demyelination and clinical impairment and we recently published a detailed methodology. At 1 week after injury, the 3g injured mice are expected to have an average Basso Mouse Scale score (BMS)=5 on a 9 point scale such that they have frequent plantar stepping with no or some coordination. This level of impairment was chosen to provide a sufficient window to observe recovery.

Treatment ID:

TR000895

Treatment Summary:

A 3g Clip produces moderate SCI including demyelination and clinical impairment and we recently published a detailed methodology. At 1 week after injury, the 3g injured mice are expected to have an average Basso Mouse Scale score (BMS)=5 on a 9 point scale such that they have frequent plantar stepping with no or some coordination. This level of impairment was chosen to provide a sufficient window to observe recovery.

Sample Preparation:

Sampleprep ID:	SP000888
Sampleprep Summary:	FFA composition of mouse spinal cord Lipids will be quantified in myelin isolated in high yield and purity by subcellular fractionation from the lumbosacral spinal cord. While there are no absolutely ‘myelin-specific’ lipids, galactocerebroside is the most typical of myelin in the adult nervous system being directly proportional to the amount of myelin. Sulfatide is another galactolipid enriched in myelin. Together with cholesterol, these form 78% of the total amount of lipid in the myelin membrane and each will be quantified using LC/MS/MS. A highly sensitive assay for galactocerebroside was recently established by the Mayo Metabolomics Core and can be implemented immediately. The LC/MS/MS panel for free fatty acids, including the very long chain fatty acids found in myelin is also routinely performed by the Core. Cholesterol will be quantified using an NMR-based approach by the Mayo Dept. of Laboratory Medicine Clinical Core. Additionally, we have a plan in place with the Metabolomics Core to develop LC/MS/MS assays for sulfatide and sphingomyelin during the Pilot proposal. Having quantitative assays for each of these key myelin lipids will facilitate our goal to comprehensively profile myelin lipid metabolism and will form foundational assays for a future NIH grant focused on myelin metabolism.

Sampleprep ID:

SP000888

Sampleprep Summary:

FFA composition of mouse spinal cord Lipids will be quantified in myelin isolated in high yield and purity by subcellular fractionation from the lumbosacral spinal cord. While there are no absolutely ‘myelin-specific’ lipids, galactocerebroside is the most typical of myelin in the adult nervous system being directly proportional to the amount of myelin. Sulfatide is another galactolipid enriched in myelin. Together with cholesterol, these form 78% of the total amount of lipid in the myelin membrane and each will be quantified using LC/MS/MS. A highly sensitive assay for galactocerebroside was recently established by the Mayo Metabolomics Core and can be implemented immediately. The LC/MS/MS panel for free fatty acids, including the very long chain fatty acids found in myelin is also routinely performed by the Core. Cholesterol will be quantified using an NMR-based approach by the Mayo Dept. of Laboratory Medicine Clinical Core. Additionally, we have a plan in place with the Metabolomics Core to develop LC/MS/MS assays for sulfatide and sphingomyelin during the Pilot proposal. Having quantitative assays for each of these key myelin lipids will facilitate our goal to comprehensively profile myelin lipid metabolism and will form foundational assays for a future NIH grant focused on myelin metabolism.

Combined analysis:

Analysis ID	AN001378
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Cohesive TX2
Column	Altma HP HILIC (150 x 2.1mm,5um)
MS Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	ABI Sciex 6500 QTrap
Ion Mode	NEGATIVE
Units	% total

Chromatography:

Chromatography ID:	CH000963
Instrument Name:	Cohesive TX2
Column Name:	Altma HP HILIC (150 x 2.1mm,5um)
Chromatography Type:	HILIC

MS:

MS ID:	MS001270
Analysis ID:	AN001378
Instrument Name:	ABI Sciex 6500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
Ion Mode:	NEGATIVE