Summary of Study ST003220

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 PR002008. The data can be accessed directly via it's Project DOI: 10.21228/M8281N This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST003220
Study Title	Obesity, sex, and depot drive distinct lipid profiles in murine white adipose tissue
Study Summary	To investigate how the lipid composition of the adipose tissue changes with obesity, sex, and depot, we performed comprehensive untargeted lipidomics on the whole adipose tissue of the inguinal and perigonadal adipose depot from lean and obese, male and female mice. The screen allowed us to identify lipid signatures sufficient to differentiate different adipose tissue samples. Such that, increased levels of OxTG and CL, increase in DG and Cer, and increase in HexCer were all able to differentiate adipose tissue based on obesity, sex, or depot, respectively.
Institute	University of Utah
Last Name	Hilgendorf
First Name	Keren
Address	EEJMRB 5520
Email	keren.hilgendorf@biochem.utah.edu
Phone	(801) 587-1071
Submit Date	2023-10-25
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2024-06-12
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002008
Project DOI:	doi: 10.21228/M8281N
Project Title:	Obesity, sex, and depot drive distinct lipid profiles in murine white adipose tissue
Project Summary:	To investigate how the lipid composition of the adipose tissue changes with obesity, sex, and depot, we performed comprehensive untargeted lipidomics on the whole adipose tissue of the inguinal and perigonadal adipose depot from lean and obese, male and female mice.
Institute:	University of Utah
Department:	Biochemistry
Laboratory:	Keren Hilgendorf
Last Name:	Hilgendorf
First Name:	Keren
Address:	EEJMRB 5520
Email:	keren.hilgendorf@biochem.utah.edu
Phone:	(801) 587-1071

Subject:

Subject ID:	SU003339
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

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

mb_sample_id	local_sample_id	Sample source	Tissue type	Sex
SA352012	IPA02	-	-	-
SA352013	IPA01	-	-	-
SA352014	IPA03	-	-	-
SA352015	IPA04	-	-	-
SA352016	QC 00	-	-	-
SA352017	IPA05	-	-	-
SA352018	double blank 02	-	-	-
SA352019	double blank 01	-	-	-
SA352020	blank 01	-	-	-
SA352021	blank 00	-	-	-
SA352022	blank 02	-	-	-
SA352023	blank 03	-	-	-
SA352024	double blank 00	-	-	-
SA352025	QC 01	-	-	-
SA352026	QC 02	-	-	-
SA352027	QC 06	-	-	-
SA352028	QC 07	-	-	-
SA352029	QC 04	-	-	-
SA352030	QC 05	-	-	-
SA352031	QC 03	-	-	-
SA352032	4-FLI	whole adipose tissue	Inguinal	Female
SA352033	3-FLI	whole adipose tissue	Inguinal	Female
SA352034	1-FLI	whole adipose tissue	Inguinal	Female
SA352035	2-FLI	whole adipose tissue	Inguinal	Female
SA352036	5-FLI	whole adipose tissue	Inguinal	Female
SA352037	13-FOI	whole adipose tissue	Inguinal	Female
SA352038	11-FOI	whole adipose tissue	Inguinal	Female
SA352039	14-FO1	whole adipose tissue	Inguinal	Female
SA352040	12-FOI	whole adipose tissue	Inguinal	Female
SA352041	15-FOI	whole adipose tissue	Inguinal	Female
SA352042	35-MOI	whole adipose tissue	Inguinal	Male
SA352043	34-MOI	whole adipose tissue	Inguinal	Male
SA352044	31-MOI	whole adipose tissue	Inguinal	Male
SA352045	33-MOI	whole adipose tissue	Inguinal	Male
SA352046	25-MLI	whole adipose tissue	Inguinal	Male
SA352047	23-MLI	whole adipose tissue	Inguinal	Male
SA352048	22-MLI	whole adipose tissue	Inguinal	Male
SA352049	21-MLI	whole adipose tissue	Inguinal	Male
SA352050	32-MOI	whole adipose tissue	Inguinal	Male
SA352051	24-MLI	whole adipose tissue	Inguinal	Male
SA352052	16-FOPG	whole adipose tissue	Perigonadal	Female
SA352053	17-FOPG	whole adipose tissue	Perigonadal	Female
SA352054	18-FOPG	whole adipose tissue	Perigonadal	Female
SA352055	19-FOPG	whole adipose tissue	Perigonadal	Female
SA352056	10-FLPG	whole adipose tissue	Perigonadal	Female
SA352057	9-FLPG	whole adipose tissue	Perigonadal	Female
SA352058	6-FLPG	whole adipose tissue	Perigonadal	Female
SA352059	7-FLPG	whole adipose tissue	Perigonadal	Female
SA352060	8-FLPG	whole adipose tissue	Perigonadal	Female
SA352061	20-FOPG	whole adipose tissue	Perigonadal	Female
SA352062	36-MOPG	whole adipose tissue	Perigonadal	Male
SA352063	27-MLPG	whole adipose tissue	Perigonadal	Male
SA352064	28-MLPG	whole adipose tissue	Perigonadal	Male
SA352065	29-MLPG	whole adipose tissue	Perigonadal	Male
SA352066	26-MLPG	whole adipose tissue	Perigonadal	Male
SA352067	40-MOPG	whole adipose tissue	Perigonadal	Male
SA352068	37-MOPG	whole adipose tissue	Perigonadal	Male
SA352069	38-MOPG	whole adipose tissue	Perigonadal	Male
SA352070	39-MOPG	whole adipose tissue	Perigonadal	Male
SA352071	30-MLPG	whole adipose tissue	Perigonadal	Male

Showing results 1 to 60 of 60

Showing results 1 to 60 of 60

Collection:

Collection ID:	CO003332
Collection Summary:	Adipose tissue from inguinal or perigonadal depot was isolated, weighted, placed into bead mill tubes and flash-frozen for downstream analysis.
Sample Type:	Adipose tissue

Treatment:

Treatment ID:	TR003348
Treatment Summary:	Lean mice were fed rodent chow diet (LabDiet 5053), ad libitum. For high-fat feeding studies, animals were fed 60% fat diet (Research Diets, D12492), ad libitum starting at 6 weeks of age for 15 weeks prior to adipose tissue isolation.

Sample Preparation:

Sampleprep ID:	SP003346
Sampleprep Summary:	Extraction of lipids was carried out using a biphasic solvent system of cold methanol (MeOH), methyl tert-butyl ether (MTBE), and water as described by Matyash et al. (J Lipid Res 49(5) (2008) 1137-1146) with some modifications. To begin, tissues were homogenized in PBS so that each samples final concentration was equal to 159.6 mg/mL. From each sample, 188 µL was aliquoted into a separate, labelled microcentrifuge tube (polypropylene 1.7 mL, VWR, USA), equal to 30 mg of sample. Tissue lipids were extracted in a solution of 750 µL MTBE and 225 µL MeOH with internal standards. Samples were sonicated for 2 minutes then rested on ice for 1 hr with occasional vortexing. Samples were then centrifuged at 15,000 x g for 10 minutes at 4 °C, and the upper phases were collected. Another aliquot of 1 mL MTBE/MeOH/water (10/3/2.5, v/v/v) was added to the bottom aqueous layer followed by a brief vortex. Samples were then centrifuged at 15,000 x g for 10 minutes at 4 °C, the upper phases were combined and evaporated to dryness under speedvac. After dry down, there was approximately 200 µL of undried material left over. This prompted re-extraction. To each sample was added 1 mL of MTBE/MeOH (7.5/1, v/v), followed by a brief vortex, centrifugation at 15,000 x g for 10 minutes at 4 °C, and collection of upper phases. Another addition of 1 mL MTBE/MeOH (7.5/1, v/v) was added to the bottom aqueous layer followed by a brief vortex, centrifugation at 15,000 x g for 10 minutes at 4 °C, and the combination of upper phases which were evaporated to dryness under speedvac. Lipid extracts were reconstituted in IPA/ACN/water (4:1:1, v/v/v). Concurrently, a process blank sample and pooled quality control (QC) samples were prepared.

Sampleprep ID:

SP003346

Sampleprep Summary:

Extraction of lipids was carried out using a biphasic solvent system of cold methanol (MeOH), methyl tert-butyl ether (MTBE), and water as described by Matyash et al. (J Lipid Res 49(5) (2008) 1137-1146) with some modifications. To begin, tissues were homogenized in PBS so that each samples final concentration was equal to 159.6 mg/mL. From each sample, 188 µL was aliquoted into a separate, labelled microcentrifuge tube (polypropylene 1.7 mL, VWR, USA), equal to 30 mg of sample. Tissue lipids were extracted in a solution of 750 µL MTBE and 225 µL MeOH with internal standards. Samples were sonicated for 2 minutes then rested on ice for 1 hr with occasional vortexing. Samples were then centrifuged at 15,000 x g for 10 minutes at 4 °C, and the upper phases were collected. Another aliquot of 1 mL MTBE/MeOH/water (10/3/2.5, v/v/v) was added to the bottom aqueous layer followed by a brief vortex. Samples were then centrifuged at 15,000 x g for 10 minutes at 4 °C, the upper phases were combined and evaporated to dryness under speedvac. After dry down, there was approximately 200 µL of undried material left over. This prompted re-extraction. To each sample was added 1 mL of MTBE/MeOH (7.5/1, v/v), followed by a brief vortex, centrifugation at 15,000 x g for 10 minutes at 4 °C, and collection of upper phases. Another addition of 1 mL MTBE/MeOH (7.5/1, v/v) was added to the bottom aqueous layer followed by a brief vortex, centrifugation at 15,000 x g for 10 minutes at 4 °C, and the combination of upper phases which were evaporated to dryness under speedvac. Lipid extracts were reconstituted in IPA/ACN/water (4:1:1, v/v/v). Concurrently, a process blank sample and pooled quality control (QC) samples were prepared.

Combined analysis:

Analysis ID	AN005280	AN005281
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Agilent 1290 Infinity	Agilent 1290 Infinity
Column	Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)	Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	Agilent 6545 QTOF	Agilent 6545 QTOF
Ion Mode	POSITIVE	NEGATIVE
Units	pmol/mg tissue	pmol/mg tissue

Chromatography:

Chromatography ID:	CH003994
Chromatography Summary:	Pos mode, RP setup where mobile phase A consisted of ACN:H2O (60:40, v/v) in 10 mM ammonium formate and 0.1% formic acid, and mobile phase B consisted of IPA:ACN:H2O (90:9:1, v/v/v) in 10 mM ammonium formate and 0.1% formic acid.
Instrument Name:	Agilent 1290 Infinity
Column Name:	Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:	65
Flow Gradient:	The chromatography gradient for both positive and negative modes started at 15% mobile phase B then increased to 30% B over 2.4 min, it then increased to 48% B from 2.4 – 3.0 min, then increased to 82% B from 3 – 13.2 min, then increased to 99% B from 13.2 – 13.8 min where it’s held until 16.7 min and then returned to the initial conditions and equilibriated for 5 min
Flow Rate:	0.4 mL/min
Solvent A:	acetonitrile:water (60:40, v/v); 10 mM ammonium formate; 0.1% formic acid
Solvent B:	isopropyl alcohol:acetonitrile:water (90:9:1, v/v/v); 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:	Reversed phase

Chromatography ID:	CH003995
Chromatography Summary:	Neg mode, RP set up where Mobile phase A consisted of ACN:H2O (60:40, v/v) in 10 mM ammonium acetate, and mobile phase B consisted of IPA:ACN:H2O (90:9:1, v/v/v) in 10 mM ammonium acetate.
Instrument Name:	Agilent 1290 Infinity
Column Name:	Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:	65
Flow Gradient:	The chromatography gradient for both positive and negative modes started at 15% mobile phase B then increased to 30% B over 2.4 min, it then increased to 48% B from 2.4 – 3.0 min, then increased to 82% B from 3 – 13.2 min, then increased to 99% B from 13.2 – 13.8 min where it’s held until 16.7 min and then returned to the initial conditions and equilibriated for 5 min
Flow Rate:	0.4 mL/min
Solvent A:	acetonitrile:water (60:40, v/v); 10 mM ammonium acetate
Solvent B:	isopropyl alcohol:acetonitrile:water (90:9:1, v/v/v); 10 mM ammonium acetate
Chromatography Type:	Reversed phase

MS:

MS ID:	MS005011
Analysis ID:	AN005280
Instrument Name:	Agilent 6545 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	For positive mode, the source gas temperature was set to 225 °C, with a drying gas flow of 11 L/min, nebulizer pressure of 40 psig, sheath gas temp of 350 °C and sheath gas flow of 11 L/min. VCap voltage is set at 3500 V, nozzle voltage 500V, fragmentor at 110 V, skimmer at 85 V and octopole RF peak at 750 V. For negative mode, the source gas temperature was set to 300 °C, with a drying gas flow of 11 L/min, a nebulizer pressure of 30 psig, sheath gas temp of 350 °C and sheath gas flow 11 L/min. VCap voltage was set at 3500 V, nozzle voltage 75 V, fragmentor at 175 V, skimmer at 75 V and octopole RF peak at 750 V. Data processing was performed using Agilent MassHunter (MH) Workstation and software packages MH Qualitiative and MH Quantitative. The pooled QC (n=8) and process blank (n=4) were injected throughout the sample queue to ensure the reliability of acquired lipidomics data. For lipid annotation, accurate mass and MS/MS spectral matching was used with LipidMatch library (Koelmel et al., BMC bioinformatics 18.1 (2017): 1-11.). Results from the positive and negative ionization modes from Lipid Annotator were merged based on the class of lipid identified. Data exported from MH Quantitative was evaluated using Excel where initial lipid targets are parsed based on the following criteria. Only lipids with relative standard deviations (RSD) less than 30% in QC samples are used for data analysis. Additionally, only lipids with background AUC counts in process blanks that are less than 30% of QC are used for data analysis. The parsed excel data tables are normalized based on the ratio to class-specific internal standards prior to statistical analysis.
Ion Mode:	POSITIVE

MS ID:	MS005012
Analysis ID:	AN005281
Instrument Name:	Agilent 6545 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The source gas temperature was set to 225 °C, with a drying gas flow of 11 L/min, nebulizer pressure of 40 psig, sheath gas temp of 350 °C and sheath gas flow of 11 L/min. VCap voltage is set at 3500 V, nozzle voltage 500V, fragmentor at 110 V, skimmer at 85 V and octopole RF peak at 750 V. For negative mode, the source gas temperature was set to 300 °C, with a drying gas flow of 11 L/min, a nebulizer pressure of 30 psig, sheath gas temp of 350 °C and sheath gas flow 11 L/min. VCap voltage was set at 3500 V, nozzle voltage 75 V, fragmentor at 175 V, skimmer at 75 V and octopole RF peak at 750 V. Data processing was performed using Agilent MassHunter (MH) Workstation and software packages MH Qualitiative and MH Quantitative. The pooled QC (n=8) and process blank (n=4) were injected throughout the sample queue to ensure the reliability of acquired lipidomics data. For lipid annotation, accurate mass and MS/MS spectral matching was used with LipidMatch library (Koelmel et al., BMC bioinformatics 18.1 (2017): 1-11.). Results from the positive and negative ionization modes from Lipid Annotator were merged based on the class of lipid identified. Data exported from MH Quantitative was evaluated using Excel where initial lipid targets are parsed based on the following criteria. Only lipids with relative standard deviations (RSD) less than 30% in QC samples are used for data analysis. Additionally, only lipids with background AUC counts in process blanks that are less than 30% of QC are used for data analysis. The parsed excel data tables are normalized based on the ratio to class-specific internal standards prior to statistical analysis.
Ion Mode:	NEGATIVE