Summary of study ST001323

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000900. The data can be accessed directly via it's Project DOI: 10.21228/M8BX09 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001323
Study TitleEffect of high-fat diet on serum lipidome in mice
Study SummaryWe analyzed mouse serum samples from a mouse dietary intervention experiment. Briefly, 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. For quality control, 12 TQC samples and 2 blanks were also included in the analysis (total 58 samples and 6 groups). 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.
Institute
QIMR Berghofer Medical Research Institute
Last NameMohamed
First NameAhmed
Address300 Herston Road
Emailahmed.mohamed@qimrberghofer.edu.au
Phone+61738453992
Submit Date2020-03-02
Raw Data AvailableYes
Raw Data File Type(s).d
Analysis Type DetailLC-MS
Release Date2020-03-20
Release Version1
Ahmed Mohamed Ahmed Mohamed
https://dx.doi.org/10.21228/M8BX09
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000900
Project DOI:doi: 10.21228/M8BX09
Project Title:Effect of high-fat diet on serum lipidome in mice
Project Summary:We analyzed mouse serum samples from a mouse dietary intervention experiment. Briefly, 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. For quality control, 12 TQC samples and 2 blanks were also included in the analysis (total 58 samples and 6 groups). 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.
Institute:QIMR Berghofer Medical Research Institute
Department:Precision & Systems Biomedicine
Last Name:Mohamed
First Name:Ahmed
Address:300 Herston Road, Herston, QLD, 4006, Australia
Email:ahmed.mohamed@qimrberghofer.edu.au
Phone:+61738453992

Subject:

Subject ID:SU001397
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Diet BileAcid
SA096024Blank_1blank blank
SA096025Blank_2blank blank
SA095968S5DHighFat DCA
SA095969S4DHighFat DCA
SA095970S1DHighFat DCA
SA095971S6DHighFat DCA
SA095972S2DHighFat DCA
SA095973S3DHighFat DCA
SA095974S7DHighFat DCA
SA095975S11DHighFat DCA
SA095976S10DHighFat DCA
SA095977S9DHighFat DCA
SA095978S8DHighFat DCA
SA095979S4CHighFat water
SA095980S5CHighFat water
SA095981S3CHighFat water
SA095982S6CHighFat water
SA095983S2CHighFat water
SA095984S10CHighFat water
SA095985S1CHighFat water
SA095986S11CHighFat water
SA095987S9CHighFat water
SA095988S7CHighFat water
SA095989S8CHighFat water
SA095990S3BNormal DCA
SA095991S2BNormal DCA
SA095992S1BNormal DCA
SA095993S11BNormal DCA
SA095994S4BNormal DCA
SA095995S5BNormal DCA
SA095996S9BNormal DCA
SA095997S10BNormal DCA
SA095998S7BNormal DCA
SA095999S8BNormal DCA
SA096000S6BNormal DCA
SA096001S7ANormal water
SA096002S5ANormal water
SA096003S3ANormal water
SA096004S2ANormal water
SA096005S4ANormal water
SA096006S6ANormal water
SA096007S8ANormal water
SA096008S1ANormal water
SA096009S11ANormal water
SA096010S9ANormal water
SA096011S10ANormal water
SA096012TQC_9QC QC
SA096013TQC_8QC QC
SA096014TQC_12QC QC
SA096015TQC_7QC QC
SA096016TQC_11QC QC
SA096017TQC_10QC QC
SA096018TQC_4QC QC
SA096019TQC_1QC QC
SA096020TQC_6QC QC
SA096021TQC_2QC QC
SA096022TQC_3QC QC
SA096023TQC_5QC QC
Showing results 1 to 58 of 58

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)
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)
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)
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
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