Summary of Study ST003316

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 PR002063. The data can be accessed directly via it's Project DOI: 10.21228/M8Z823 This work is supported by NIH grant, U2C- DK119886.

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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.

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Study IDST003316
Study TitleEffects of LDAH overexpression on the lipidome of oxLDL-treated mouse peritoneal macrophages
Study SummaryMouse peritoneal macrophages from LDAH-transgenic mice and wild-type littermate controls were harvested 5 days after aged 3% thioglycolate injection. 4–5 × 106 cells were plated in 60mm culture dishes, and cultured overnight in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS). The media was replaced by DMEM-1% FBS supplemented with Hi-TBAR oxLDL (50 μg/ml, Alfa Aesar J65261) for 48h.
Institute
Albany Medical College
DepartmentMCP
LaboratoryPaul
Last NamePaul
First NameAntoni
Address47 New Scotland Avenue, MC-8, Albany, NY-12208
Emailpaula@amc.edu
Phone518-262-1158
Submit Date2024-07-05
Num Groups2
Total Subjects12
Analysis Type DetailLC-MS
Release Date2024-07-18
Release Version1
Antoni Paul Antoni Paul
https://dx.doi.org/10.21228/M8Z823
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002063
Project DOI:doi: 10.21228/M8Z823
Project Title:Effects of LDAH on the lipidome of oxLDL-treated mouse peritoneal macrophages
Project Summary:Lipid droplet-associated hydrolase (LDAH) has a lipase structure and high affinity for lipid droplets of macrophages/foam cells. However, LDAH's functions and lipid substrates remain poorly understood. In this project we treated mouse peritoneal macrophages isolated from LDAH-transgenic mice and wild-type littermate controls with oxidized low-density lipoprotein (oxLDL) and analyzed the effects of LDAH overexpression on their lipidome.
Institute:Albany Medical College
Department:MCP
Laboratory:Paul
Last Name:Paul
First Name:Antoni
Address:47 New Scotland Avenue, MC-8, albany, NY-12208
Email:paula@amc.edu
Phone:518-262-1158

Subject:

Subject ID:SU003437
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:LDAH wild-type and LDAH-transgenic mice in C57BL/6 background

Factors:

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

mb_sample_id local_sample_id Sample source Genotype Treatment
SA359529T1Peritoneal Macrophages LDAH-Transgenic oxLDL
SA359530T2Peritoneal Macrophages LDAH-Transgenic oxLDL
SA359531T3Peritoneal Macrophages LDAH-Transgenic oxLDL
SA359532T4Peritoneal Macrophages LDAH-Transgenic oxLDL
SA359533T5Peritoneal Macrophages LDAH-Transgenic oxLDL
SA359534T6Peritoneal Macrophages LDAH-Transgenic oxLDL
SA359535W1Peritoneal Macrophages Wild-type oxLDL
SA359536W2Peritoneal Macrophages Wild-type oxLDL
SA359537W3Peritoneal Macrophages Wild-type oxLDL
SA359538W4Peritoneal Macrophages Wild-type oxLDL
SA359539W5Peritoneal Macrophages Wild-type oxLDL
SA359540W6Peritoneal Macrophages Wild-type oxLDL
Showing results 1 to 12 of 12

Collection:

Collection ID:CO003430
Collection Summary:Cells were collected, centrifuged, and washed 3x in cold PBS. Cells were immediately frozen and stored at -80C.
Sample Type:Peritoneal macrophages

Treatment:

Treatment ID:TR003446
Treatment Summary:Cells were treated with Hi-TBAR oxLDL (50 μg/ml, Alfa Aesar J65261) for 48h in DMEM-1% FBS.

Sample Preparation:

Sampleprep ID:SP003444
Sampleprep Summary:Monophasic lipid extracts were diluted into isopropanol: methanol (2:1,v:v) containing 20 mM ammonium formate and analyzed by flow injection high resolution/accurate MS and tandem MS.

Combined analysis:

Analysis ID AN005430
Analysis type MS
Chromatography type None (Direct infusion)
Chromatography system none
Column none
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Velos LTQ Orbitrap
Ion Mode POSITIVE
Units Normalized intensity

Chromatography:

Chromatography ID:CH004119
Chromatography Summary:Lipids were analyzed by flow injection high resolution/accurate MS and tandem MS. Lipid species were identified using the Lipid Mass Spectrum Analysis (LIMSA) v.1.0 software linear fit algorithm, in conjunction with a user-defined database of hypothetical lipid compounds for automated peak finding and correction of 13C isotope effects. Relative quantification of lipid abundance between samples was performed by normalization of target lipid ion peak areas to the di-myristoyl phosphatidylcholine internal standard.
Instrument Name:none
Column Name:none
Column Temperature:none
Flow Gradient:none
Flow Rate:none
Solvent A:none
Solvent B:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS005156
Analysis ID:AN005430
Instrument Name:Thermo Velos LTQ Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Lipid sample was introduced via nanoESI to a high resolution / accurate mass Thermo Scientific model LTQ Orbitrap Velos mass spectrometer (San Jose, CA) using an Advion Triversa Nanomate nESI source (Advion, Ithaca, NY) operating with a spray voltage of 1.4 kV and a gas pressure of 0.3 psi. The ion source interface settings (inlet temperature of 100°C and S-Lens value of 50%) were optimized to maximize the sensitivity of the precursor ions while minimizing ‘in-source’ fragmentation.
Ion Mode:POSITIVE
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