Summary of Study ST003077

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 PR001916. The data can be accessed directly via it's Project DOI: 10.21228/M82B0Z 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	ST003077
Study Title	Data-dependent and -independent acquisition lipidomics analysis reveals the tissue-dependent effect of metformin on lipid metabolism (Adipose tissue measurements)
Study Summary	Lipidomics analysis of 6 mouse tissues and plasma using MS/MS combining BRI-DIA and DDA allowed a systemic evaluation of lipidomic changes induced by metformin in different tissues. We observed that 1) the degrees of lipidomic changes induced by metformin treatment overly correlated with tissue concentrations of metformin; 2) the impact on lysophosphorylcholine and cardiolipins was positively correlated with tissue concentrations of metformin, while neutral lipids such as triglycerides did not correlate with the corresponding tissue metformin concentrations.
Institute	North Carolina State University
Last Name	Liu
First Name	Xiaojing
Address	128 Polk Hall, 120 W Broughton Dr.
Email	xliu68@ncsu.edu
Phone	919.515.4387
Submit Date	2024-02-06
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2024-03-01
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001916
Project DOI:	doi: 10.21228/M82B0Z
Project Title:	Data-dependent and -independent acquisition lipidomics analysis reveals the tissue-dependent effect of metformin on lipid metabolism
Project Summary:	Free fatty acids and polar metabolite analysis were conducted on six mouse tissues and plasma using HILIC chromatography coupled to a Q Exactive Plus mass spectrometer. This enabled a comprehensive assessment of fatty acid and metabolic changes induced by metformin across various tissues.
Institute:	North Carolina State University
Last Name:	Liu
First Name:	Xiaojing
Address:	128 Polk Hall, 120 W Broughton Dr.
Email:	xliu68@ncsu.edu
Phone:	919.515.4387

Subject:

Subject ID:	SU003192
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	Treatment
SA332539	Heart504	metformin
SA332540	Intestine502	metformin
SA332541	Adipose503	metformin
SA332542	Heart505	metformin
SA332543	Adipose505	metformin
SA332544	Intestine501	metformin
SA332545	Intestine505	metformin
SA332546	Kidney502	metformin
SA332547	Kidney503	metformin
SA332548	Kidney504	metformin
SA332549	Kidney505	metformin
SA332550	Kidney501	metformin
SA332551	Adipose501	metformin
SA332552	Intestine504	metformin
SA332553	Heart503	metformin
SA332554	Adipose502	metformin
SA332555	Intestine503	metformin
SA332556	Liver504	metformin
SA332557	P14	metformin
SA332558	Muscle501	metformin
SA332559	Muscle502	metformin
SA332560	P13	metformin
SA332561	P12	metformin
SA332562	P10	metformin
SA332563	P11	metformin
SA332564	Heart502	metformin
SA332565	Muscle503	metformin
SA332566	Liver502	metformin
SA332567	Liver503	metformin
SA332568	Muscle504	metformin
SA332569	Heart501	metformin
SA332570	Muscle505	metformin
SA332571	Liver501	metformin
SA332572	Liver505	metformin
SA332525	Pooled_muscle_neg	Mix
SA332526	Pooled_liver_neg	Mix
SA332527	Pooled_intestine_pos	Mix
SA332528	Pooled_plasma_pos	Mix
SA332529	Pooled_plasma_neg	Mix
SA332530	Pooled_kidney_pos	Mix
SA332531	Pooled_adipose_pos	Mix
SA332532	Pooled_intestine_neg	Mix
SA332533	Pooled_heart_neg	Mix
SA332534	Pooled_heart_pos	Mix
SA332535	Pooled_kidney_neg	Mix
SA332536	Pooled_adipose_neg	Mix
SA332537	Pooled_liver_pos	Mix
SA332538	Pooled_muscle_pos	Mix
SA332573	Adipose493	water
SA332574	Adipose494	water
SA332575	Adipose492	water
SA332576	Intestine494	water
SA332577	Muscle494	water
SA332578	Liver491	water
SA332579	Liver492	water
SA332580	Liver493	water
SA332581	Muscle493	water
SA332582	Muscle492	water
SA332583	P2	water
SA332584	P3	water
SA332585	P4	water
SA332586	Muscle491	water
SA332587	Liver494	water
SA332588	Heart491	water
SA332589	Kidney491	water
SA332590	Kidney492	water
SA332591	Kidney493	water
SA332592	Kidney494	water
SA332593	P1	water
SA332594	Intestine493	water
SA332595	Heart492	water
SA332596	Heart494	water
SA332597	Intestine491	water
SA332598	Adipose491	water

Showing results 1 to 74 of 74

Showing results 1 to 74 of 74

Collection:

Collection ID:	CO003185
Collection Summary:	Blood was collected into tubes containing EDTA anticoagulant via cardiac puncture. Plasma was obtained by centrifugation of whole blood at 1,500 g for 10 min at 4 °C and stored at -80 °C freezer.
Sample Type:	plasma, adipose, liver, muscle, heart, kidney, intestine, adipose

Treatment:

Treatment ID:	TR003201
Treatment Summary:	C57BL/6 mice were housed North Carolina State University Biological Resources Facility with ad libitum access to food (Laboratory Rodent Diet 5001) and water on a 12-hour light/dark cycle. At the age of 8 weeks, mice were administrated metformin in their drinking water (1mg/ml) for 12 days. Before tissue and blood collection, mice were fasted for 5 hours (6am-11am). Mice were then anesthetized with isoflurane and sacrificed via cervical dislocation.

Treatment ID:

TR003201

Treatment Summary:

C57BL/6 mice were housed North Carolina State University Biological Resources Facility with ad libitum access to food (Laboratory Rodent Diet 5001) and water on a 12-hour light/dark cycle. At the age of 8 weeks, mice were administrated metformin in their drinking water (1mg/ml) for 12 days. Before tissue and blood collection, mice were fasted for 5 hours (6am-11am). Mice were then anesthetized with isoflurane and sacrificed via cervical dislocation.

Sample Preparation:

Sampleprep ID:	SP003198
Sampleprep Summary:	All tissue sample was first homogenized in liquid nitrogen and then 10-20 mg tissues were weighed into a new 1.7 ml Eppendorf tube. Ice cold extraction solvent (400 ul 80% methanol/water) and 10 ul metformin-d6 (50 ng/ul in water) was added to each sample. Geno/Grinder homogenizer was used (1500 rpm, 1 to 2 min) to further break down the tissue chunk and form an even suspension. 200 ul supernatant containing polar metabolites was removed after centrifugation at 20,000 g at 4 °C for 10 min and transferred to LC vial for polar metabolite analysis using LC-HRMS. The rest samples (200 ul solvent and insoluble pellet) were briefly homogenized using Geno/Grinder again (1500 rpm, 30 sec) to loosen the bottom pellet and better mix with extraction solvent. 480 ul MTBE and 10 ul internal standard solution were added. After rigorous vortexing, 120 ul water was added to initiate phase separation. All samples were centrifuged at 20,000 g at 4 °C for 10 min. The supernatant containing lipids was transferred to a new Eppendorf tube and dried using speed vacuum. Dry pellets were stored in -80 °C freezer until ready for LC-HRMS analysis. To extract metabolites and lipids from mouse plasma, 10 ul plasma was mixed with 10 l water containing internal standards (50 ng/ul metformin-d6, 5 mM [U-13C]-glucose and [U-13C]-lactate, and 80 ul ice cold methanol was added. After vortex for 1 min, the mixture was centrifuged with a speed of 20,000 g at 4 °C for 10 min, and 20 ul was transferred directly to LC vial without solvent evaporation, followed by LC-HRMS analysis (injection volume, 3 ul) of polar metabolites such as glucose and metformin. To the rest samples (80 l solvent and pellet), 192 ul MTBE and 10 ul lipid internal standard solution were added. After rigorous vortexing, 48 ul water was added to initiate phase separation. All samples were centrifuged at 20,000 g at 4 °C for 10 min. The supernatant containing lipids was transferred to a new Eppendorf tube and dried using speed vacuum. The dry pellets of lipids from mouse tissues or plasma were reconstituted into (300 ul for tissue and 50 ul for plasma) sample solvent (isopropanol: ethyl acetate, 1:1, v/v), and 3 ul was injected to LC-HRMS for lipidomics analysis.

Sampleprep ID:

SP003198

Sampleprep Summary:

All tissue sample was first homogenized in liquid nitrogen and then 10-20 mg tissues were weighed into a new 1.7 ml Eppendorf tube. Ice cold extraction solvent (400 ul 80% methanol/water) and 10 ul metformin-d6 (50 ng/ul in water) was added to each sample. Geno/Grinder homogenizer was used (1500 rpm, 1 to 2 min) to further break down the tissue chunk and form an even suspension. 200 ul supernatant containing polar metabolites was removed after centrifugation at 20,000 g at 4 °C for 10 min and transferred to LC vial for polar metabolite analysis using LC-HRMS. The rest samples (200 ul solvent and insoluble pellet) were briefly homogenized using Geno/Grinder again (1500 rpm, 30 sec) to loosen the bottom pellet and better mix with extraction solvent. 480 ul MTBE and 10 ul internal standard solution were added. After rigorous vortexing, 120 ul water was added to initiate phase separation. All samples were centrifuged at 20,000 g at 4 °C for 10 min. The supernatant containing lipids was transferred to a new Eppendorf tube and dried using speed vacuum. Dry pellets were stored in -80 °C freezer until ready for LC-HRMS analysis. To extract metabolites and lipids from mouse plasma, 10 ul plasma was mixed with 10 l water containing internal standards (50 ng/ul metformin-d6, 5 mM [U-13C]-glucose and [U-13C]-lactate, and 80 ul ice cold methanol was added. After vortex for 1 min, the mixture was centrifuged with a speed of 20,000 g at 4 °C for 10 min, and 20 ul was transferred directly to LC vial without solvent evaporation, followed by LC-HRMS analysis (injection volume, 3 ul) of polar metabolites such as glucose and metformin. To the rest samples (80 l solvent and pellet), 192 ul MTBE and 10 ul lipid internal standard solution were added. After rigorous vortexing, 48 ul water was added to initiate phase separation. All samples were centrifuged at 20,000 g at 4 °C for 10 min. The supernatant containing lipids was transferred to a new Eppendorf tube and dried using speed vacuum. The dry pellets of lipids from mouse tissues or plasma were reconstituted into (300 ul for tissue and 50 ul for plasma) sample solvent (isopropanol: ethyl acetate, 1:1, v/v), and 3 ul was injected to LC-HRMS for lipidomics analysis.

Combined analysis:

Analysis ID	AN005035
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Thermo Vanquish
Column	Xbridge BEH C18 column (100 × 2.1 mm, 2.5 um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Orbitrap Exploris 480
Ion Mode	UNSPECIFIED
Units	arbitrary unit

Chromatography:

Chromatography ID:	CH003806
Instrument Name:	Thermo Vanquish
Column Name:	Xbridge BEH C18 column (100 × 2.1 mm, 2.5 um)
Column Temperature:	40 °C
Flow Gradient:	Linear gradient was: 0 min, 40% B; 1.5 min, 40% B; 5.0 min, 85% B; 12.0 min, 97% B; 16.0 min, 97% B; 16.5 min, 40% B; 21.0 min, 40% B.
Flow Rate:	The flow rate was: 0.15 ml/min.
Solvent A:	80% water/20% acetonitrile; 0.1% formic acid; mM ammonium formate,
Solvent B:	90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004774
Analysis ID:	AN005035
Instrument Name:	Thermo Orbitrap Exploris 480
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The relevant parameters of Orbitrap Exploris 480 were as listed: vaporizer temperature, 350 °C; ion transfer tube temperature, 300 °C; sheath gas, 35; auxiliary gas, 7; sweep gas, 1; spray voltage, 3.5 kV for positive mode and 2.5 kV for negative mode; RF-lens (%), 45. The resolution was set at 120,000 (at m/z 200). The scan range was 200 to 1600 (m/z). Automatic maximum injection time (max IT) and automatic gain control (AGC) were used. MS/MS scan was acquired using Hybrid mode (BRI-DIA followed by DDA) with the inclusion list containing precursor ions in positive and negative ion mode (described in the Supplementary table 1 of our prior publication PMID: 35842862). The MS/MS condition for positive or negative ion mode was set as follows: precursor isolation window was set at 1 (m/z) for all three methods, HCD collision energy was set at 25%, orbitrap resolution of full scan and MS/MS scan was set at 60,000 and 15,000, respectively. Intensity threshold for DDA and DIA MS/MS scan was set at 10,000. LC-MS peak extraction and integration were performed using MS-DIAL with default settings.
Ion Mode:	UNSPECIFIED