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MB Sample ID: SA338999
| Local Sample ID: | SP_HetHFD_3 |
| Subject ID: | SU003245 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003245 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| SP_HetHFD_3 | SA338999 | FL040142 | Serum | Sample source |
| SP_HetHFD_3 | SA338999 | FL040142 | CHCHD10 S55L Het | Genotype |
| SP_HetHFD_3 | SA338999 | FL040142 | High Fat Diet | Treatment |
| SP_HetHFD_3 | SA338999 | FL040142 | 250 | Age (d) |
| SP_HetHFD_3 | SA338999 | FL040142 | F | Sex |
Collection:
| Collection ID: | CO003238 |
| Collection Summary: | Blood was collected by cheek bleeds into serum separator tubes. Serum was separated after 30 minutes of clotting at room temperature and centrifugation at 2000xg for 15 min. |
| Sample Type: | Blood (serum) |
Treatment:
| Treatment ID: | TR003254 |
| Treatment Summary: | CHCHD10 WT and CHCHD10 S55L heterozygous mice were treated with either a control diet (70% Carbohydrate, 20% Protein, 10% Fat) or High Fat Diet (60% Fat, 20% Protein, 20% Carbohydrate). |
Sample Preparation:
| Sampleprep ID: | SP003252 |
| Sampleprep Summary: | Untargeted and targeted metabolomics: Serum metabolites were extracted with 80% methanol. The extracts were clarified by centrifugation at 15,000 g for 10 min. The supernatant was collected and dried down using a SpeedVac. For lipidomics analyses: 180 µl of 90% isopropanol was added to 20 µl serum. Samples were vortexed for 2 min, sonicated for 1 min using a probe sonicator and centrifuged at 15,000 g for 10 min. The supernatant was collected and dried down using a SpeedVac. The dried samples were reconstituted using acetonitrile/isopropanol/water 65:30:5 containing stable isotope labeled internal lipid standards (Splash Lipidomix, Avanti Polar Lipids) prior to LC-MS analysis. Free Fatty Acids: Free fatty acids were extracted from serum using 90% methanol (LC/MS grade, Thermo Scientific). The extracts were clarified by centrifugation at 15,000 g for 10 min. The supernatant was collected and dried down using a SpeedVac. The dried sample was reconstituted using 50% methanol prior to LC-MS analysis. |
Combined analysis:
| Analysis ID | AN005128 | AN005129 | AN005130 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | HILIC | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish |
| Column | SeQuant ZIC-pHILIC (150 x 2.1mm, 5um) | Imtakt Cadenza CD-C18 (150 x 2.1 mm, 3um) | Imtakt Cadenza CD-C18 (150 x 2.1 mm, 3um) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED | NEGATIVE | POSITIVE |
| Units | Peak Intensity | Peak Intensity | Peak Intensity |
Chromatography:
| Chromatography ID: | CH003880 |
| Chromatography Summary: | Serum targeted and untargeted metabolomics |
| Methods Filename: | Serum_MS_and_Data_Analysis.pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | SeQuant ZIC-pHILIC (150 x 2.1mm, 5um) |
| Column Temperature: | 35 |
| Flow Gradient: | 85% to 30% A in 20 min followed by a wash with 30% A and re-equilibration at 85% A |
| Flow Rate: | 150 µl/min |
| Solvent A: | 100% acetonitrile |
| Solvent B: | 100% water; 0.1% ammonium hydroxide; 20 mM ammonium acetate |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003881 |
| Chromatography Summary: | Serum free fatty acids |
| Methods Filename: | Serum_MS_and_Data_Analysis.pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Imtakt Cadenza CD-C18 (150 x 2.1 mm, 3um) |
| Column Temperature: | 35 |
| Flow Gradient: | 0–1.5 min, 50% B; 1.5-3 min, 50-90% B; 3-5.5 min, 90-95% B; 5.5-10 min, 95% B, followed by 5 min of re-equilibration |
| Flow Rate: | 150 µl/min |
| Solvent A: | 100% water; 5 mM ammonium acetate |
| Solvent B: | 85% isopropanol/10% acetonitrile/5% water; 5 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003882 |
| Chromatography Summary: | Serum lipidomics |
| Methods Filename: | Serum_MS_and_Data_Analysis.pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Imtakt Cadenza CD-C18 (150 x 2.1 mm, 3um) |
| Column Temperature: | 35 |
| Flow Gradient: | 0–1.5 min, 32% B; 1.5-4 min, 32-45% B; 4-5 min, 45-52% B; 5-8 min, 52-58% B; 8-11 min, 58-66% B; 11-14 min, 66-70% B; 14-18 min, 70-75% B; 21-25 min, isocratic 97% B, 25-25.1 min 97-32% B |
| Flow Rate: | 200 µl/min |
| Solvent A: | 60% acetonitrile/40% water; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004864 |
| Analysis ID: | AN005128 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The MS data was processed using XCalibur 4.1 (Thermo Scientific) to obtain the metabolite signal intensity for relative quantitation. Targeted identification was available for 205 metabolites based on an in-house library established using known chemical standards. Identification required exact mass (within 5ppm) and standard retention times. For untargeted metabolomics, metabolites were identified by mass matching of the MS signal to metabolites in the HMDB database. If multiple metabolites in the database were matched to a certain MS signal, all matched metabolites were grouped into a single identification, and ordered based on the number of references included in the HMDB database (high to low). |
| Ion Mode: | UNSPECIFIED |
| Analysis Protocol File: | Serum_MS_and_Data_Analysis.pdf |
| MS ID: | MS004865 |
| Analysis ID: | AN005129 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Identification of free fatty acids was based on accurate masses within 5 ppm and standard retention times from compound standards. Relative quantitation was performed based on MS signal intensities. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | Serum_MS_and_Data_Analysis.pdf |
| MS ID: | MS004866 |
| Analysis ID: | AN005130 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | A data-dependent mass spectrometric acquisition method was used for lipid identification. In this method, each MS survey scan was followed by up to 10 MS/MS scans performed on the most abundant ions. The LC-MS results were processed using MS-DIAL software (version 4.9) for lipid identification and relative quantitation. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | Serum_MS_and_Data_Analysis.pdf |
