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MB Sample ID: SA099381
Local Sample ID: | MALA_4 |
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 |
---|---|---|---|---|
MALA_4 | SA099381 | FL014061 | MAL | Treatment |
MALA_4 | SA099381 | FL014061 | Malnourished | Start Diet |
MALA_4 | SA099381 | FL014061 | 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 |
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 |