Return to study ST001323 main page
MB Sample ID: SA095968
| Local Sample ID: | S5D |
| Subject ID: | SU001397 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001397 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| S5D | SA095968 | FL013568 | HighFat | Diet |
| S5D | SA095968 | FL013568 | DCA | BileAcid |
Collection:
| Collection ID: | CO001392 |
| Collection Summary: | Mouse serum lipids were extracted using the lipid extraction method by Matyash et al(J Lipid Res 2008, 49, (5), 1137-46). Mouse serum (30 µL) was added to 215 µL of ice-cold methanol containing 50 µg/mL butylated hydroxytoluene (BHT). Samples were homogenized by three rounds of vortex mixing for 30 seconds, freezing in liquid nitrogen for one minute, thawing for two minutes and sonicating for 10 minutes at 15°C, power 100% in a Grant XUB18 bath sonicator. |
| Sample Type: | Blood (serum) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001412 |
| Treatment Summary: | C57BL/6 mice (n=44) were divided into 4 groups (n=11 per group) and fed High-fat diet (HFD), 1% deoxycholic acid (DCA) in drinking water, both, or left as control for 9 months. Serum samples were collected and analyzed by targeted lipidomics as described in Supplemental Information. The two treatments were selected to demonstrate the ability of lipidomics to detect gross changes induced by HFD in the serum lipidome, as well as specific/minor changes induced by the secondary bile acid (DCA) through regulation of liver lipid metabolism. |
Sample Preparation:
| Sampleprep ID: | SP001405 |
| Sampleprep Summary: | Mouse serum lipids were extracted using the lipid extraction method by Matyash et al. Mouse serum (30 µL) was added to 215 µL of ice-cold methanol containing 50 µg/mL butylated hydroxytoluene (BHT). Samples were homogenized by three rounds of vortex mixing for 30 seconds, freezing in liquid nitrogen for one minute, thawing for two minutes and sonicating for 10 minutes at 15°C, power 100% in a Grant XUB18 bath sonicator. SPLASH LipidoMix Mass Spec Standard (10 µL, undiluted) and Cer/Sph mixture II (10 µL, undiluted) internal standards mixes from Avanti Polar Lipids were then added to each sample. After overnight incubation at -30°C, 750 µL MTBE was added and each tube was vortex mixed for 10 seconds and shaken for 10 minutes on a tube rotator (4°C). MilliQ water (188 µL) was then added, and the tube was vortex mixed for 30 seconds to form a biphasic separation. After centrifuging for 15 minutes at 15,000 ×g, the clear upper phase containing lipids in MTBE was transferred to another tube and dried down using a gentle stream of nitrogen. Prior to LC-MS/MS analysis, the samples were resuspended in a mixture of 50 µL methanol (containing 50 µg/mL BHT)/toluene (90/10%, v/v) and 4µL was used as the injection volume. |
| Processing Storage Conditions: | On ice |
Combined analysis:
| Analysis ID | AN002199 | AN002200 | AN002201 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | HILIC | HILIC | HILIC |
| Chromatography system | Agilent 1290 Infinity | Agilent 1290 Infinity | Agilent 1290 Infinity |
| Column | Agilent HILIC Plus RRHD (100 x 2.1mm, 1.8um) | Agilent HILIC Plus RRHD (100 x 2.1mm, 1.8um) | Agilent HILIC Plus RRHD (100 x 2.1mm, 1.8um) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole |
| MS instrument name | Agilent 6490 QQQ | Agilent 6490 QQQ | Agilent 6490 QQQ |
| Ion Mode | UNSPECIFIED | POSITIVE | UNSPECIFIED |
| Units | intensity | intensity | intensity |
Chromatography:
| Chromatography ID: | CH001613 |
| Chromatography Summary: | buffer A contained 50% acetonitrile and buffer B contained 95% acetonitrile in water. Buffers were supplemented with 25 mM ammonium formate (pH 4.6) and 0.1% formic acid. |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Agilent HILIC Plus RRHD (100 x 2.1mm, 1.8um) |
| Solvent A: | 50% acetonitrile/50% water; 10 mM ammonium acetate, pH 7.6 |
| Solvent B: | 95% acetonitrile/5% water; 10 mM ammonium acetate, pH 7.6 |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001614 |
| Chromatography Summary: | buffer A contained 50% acetonitrile and buffer B contained 95% acetonitrile in water. Buffers were supplemented with 25 mM ammonium formate (pH 4.6) and 0.1% formic acid. |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Agilent HILIC Plus RRHD (100 x 2.1mm, 1.8um) |
| Solvent A: | 50% acetonitrile/50% water; 10 mM ammonium acetate, pH 7.6 |
| Solvent B: | 95% acetonitrile/5% water; 10 mM ammonium acetate, pH 7.6 |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001615 |
| Chromatography Summary: | buffer A contained 50% acetonitrile and buffer B contained 95% acetonitrile in water. Buffers were supplemented with 10 mM ammonium acetate (pH 7.6). |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Agilent HILIC Plus RRHD (100 x 2.1mm, 1.8um) |
| Solvent A: | 50% acetonitrile/50% water; 10 mM ammonium acetate, pH 7.6 |
| Solvent B: | 95% acetonitrile/5% water; 10 mM ammonium acetate, pH 7.6 |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002045 |
| Analysis ID: | AN002199 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Targeted lipidomics were performed on an Agilent Technologies 1290 Infinity UHPLC system with an Agilent HILIC Plus RRHD 2.1×100 mm 1.8-micron column, coupled online to an Agilent 6490A Triple Quadrupole mass spectrometer with iFunnel and Agilent Jet Stream (AJS) electrospray ionization (ESI) source, operated in dynamic MRM mode. The source nitrogen gas temperature was set to 250°C at a flow of 15 L/min and a sheath gas temperature of 400°C at a flow of 12 L/min. The capillary voltage was set to 4000 V for positive mode and 5000 V for negative mode and the nebulizer operated at 30 psi. Ion funnel high and low pressure in positive and negative mode were 150 and 120. Check tunes were performed in wide, unit and enhanced modes prior to each experiment to confirm the performance of the mass spectrometer. The quadrupole was tuned to reference masses 118.09, 322.05, 622.03, 922.01 and 1221.99 in positive ionization mode; 112.99, 302.00, 601.98, 1033.99 and 1333.97 in negative ionization mode. |
| Ion Mode: | UNSPECIFIED |
| MS ID: | MS002046 |
| Analysis ID: | AN002200 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Targeted lipidomics were performed on an Agilent Technologies 1290 Infinity UHPLC system with an Agilent HILIC Plus RRHD 2.1×100 mm 1.8-micron column, coupled online to an Agilent 6490A Triple Quadrupole mass spectrometer with iFunnel and Agilent Jet Stream (AJS) electrospray ionization (ESI) source, operated in dynamic MRM mode. The source nitrogen gas temperature was set to 250°C at a flow of 15 L/min and a sheath gas temperature of 400°C at a flow of 12 L/min. The capillary voltage was set to 4000 V for positive mode and 5000 V for negative mode and the nebulizer operated at 30 psi. Ion funnel high and low pressure in positive and negative mode were 150 and 120. Check tunes were performed in wide, unit and enhanced modes prior to each experiment to confirm the performance of the mass spectrometer. The quadrupole was tuned to reference masses 118.09, 322.05, 622.03, 922.01 and 1221.99 in positive ionization mode; 112.99, 302.00, 601.98, 1033.99 and 1333.97 in negative ionization mode. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002047 |
| Analysis ID: | AN002201 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Targeted lipidomics were performed on an Agilent Technologies 1290 Infinity UHPLC system with an Agilent HILIC Plus RRHD 2.1×100 mm 1.8-micron column, coupled online to an Agilent 6490A Triple Quadrupole mass spectrometer with iFunnel and Agilent Jet Stream (AJS) electrospray ionization (ESI) source, operated in dynamic MRM mode. The source nitrogen gas temperature was set to 250°C at a flow of 15 L/min and a sheath gas temperature of 400°C at a flow of 12 L/min. The capillary voltage was set to 4000 V for positive mode and 5000 V for negative mode and the nebulizer operated at 30 psi. Ion funnel high and low pressure in positive and negative mode were 150 and 120. Check tunes were performed in wide, unit and enhanced modes prior to each experiment to confirm the performance of the mass spectrometer. The quadrupole was tuned to reference masses 118.09, 322.05, 622.03, 922.01 and 1221.99 in positive ionization mode; 112.99, 302.00, 601.98, 1033.99 and 1333.97 in negative ionization mode. |
| Ion Mode: | UNSPECIFIED |
