Summary of Study ST003058
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 PR001905. The data can be accessed directly via it's Project DOI: 10.21228/M8GH8F 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.
Download mwTab file (text) | Download mwTab file(JSON) | Download data files (Contains raw data)
| Study ID | ST003058 |
| Study Title | Spatiotemporal mapping of lipid disturbance in heart injury - Part 2 |
| Study Summary | The project consists of 3 studies in total, this is the second part, in this study, mouse plasma were collected for LC-MS/MS based lipidomics. The plasma sample from mouse underwent I/R injury at different time points (0h, 3h, 24h, 3d, 7d) were collected for investigation. |
| Institute | National University of Singapore |
| Last Name | Chenyuan |
| First Name | Huang |
| Address | 14 Medical Drive, MD6, #08-01, Singapore |
| huangchenyuan@u.nus.edu | |
| Phone | 80384853 |
| Submit Date | 2024-01-25 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-01-30 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001905 |
| Project DOI: | doi: 10.21228/M8GH8F |
| Project Title: | Spatiotemporal mapping of lipid disturbance in heart injury |
| Project Summary: | Disturbance of myocardial lipid metabolism occurring in response to cardiac injury has been closely associated with heart failure. However, the spatial and temporal myocardial lipid profiles in heart injury remain unexplored. Here, we employ the matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and liquid chromatography tandem mass spectrometry (LC-MS/MS) to analyze myocardial lipid profiles in heart injury induced by myocardial ischemia/reperfusion (I/R) in both mice and pigs. |
| Institute: | National University of Singapore |
| Last Name: | chenyuan |
| First Name: | huang |
| Address: | 14 Medical Drive, MD6, Singapore |
| Email: | huangchenyuan@u.nus.edu |
| Phone: | 80384853 |
Subject:
| Subject ID: | SU003173 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Time |
|---|---|---|
| SA331786 | 101922 | 24h |
| SA331787 | 101913 | 24h |
| SA331788 | 101925 | 24h |
| SA331789 | 101912 | 24h |
| SA331790 | 101923 | 24h |
| SA331791 | 101924 | 24h |
| SA331792 | 101915 | 3d |
| SA331793 | 101916 | 3d |
| SA331794 | 101927 | 3d |
| SA331795 | 101917 | 3d |
| SA331796 | 101914 | 3d |
| SA331797 | 101926 | 3d |
| SA331798 | 101909 | 3h |
| SA331799 | 101921 | 3h |
| SA331800 | 101920 | 3h |
| SA331801 | 101911 | 3h |
| SA331802 | 101908 | 3h |
| SA331803 | 101910 | 3h |
| SA331804 | 101930 | 7d |
| SA331805 | 101929 | 7d |
| SA331806 | 101928 | 7d |
| SA331807 | 101919 | 7d |
| SA331808 | 101918 | 7d |
| SA331809 | 101931 | 7d |
| SA331810 | 101936 | baseline |
| SA331811 | 101935 | baseline |
| SA331812 | 101937 | baseline |
| SA331813 | 101933 | sham |
| SA331814 | 101934 | sham |
| Showing results 1 to 29 of 29 |
Collection:
| Collection ID: | CO003166 |
| Collection Summary: | Mice were sacrificed at different time points after I/R injury, blood was collected in EDTA-coated tubes (Greiner Bio-One, Kremsmünster, Austria) via submandibular vein by cheek puncture and was subsequently centrifuged at 4 °C, 2000 g for 10 min, to obtain plasma. The hearts were perfused with saline, and the atria and right ventricles were removed. Left ventricles were divided transversally, the bottom parts were dissected for LC-MS/MS and upper part was later used for MALDI-MSI. Sham surgery was performed (referred to as control) where all procedures were the same as the experimental group except for the LAD ligation. Tissue and blood from sham group were collected 24 hours after surgery to serve as baseline lipid levels (control). |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR003182 |
| Treatment Summary: | There is no treatment, but the factor contains different time and collection region of the tissue |
Sample Preparation:
| Sampleprep ID: | SP003179 |
| Sampleprep Summary: | 10 µL plasma was mixed with 100 µL butanol/methanol (1:1, v:v; Merck Millipore, Massachusetts, USA) spiked with the following internal standards: 400 nM phosphatidylethanolamine (PE) 17:0/17:0, 2.4 nM ceramide (Cer) d18:1/8:0, 200 nM phosphatidylcholine (PC) 13:0/13:0, 1.7 nM hexosylceramide (HexCer) d18:1/8:0, 400 nM lysophosphatidylcholine (LPC) 13:0, 400 nM lysophosphatidylethanolamine (LPE) 14:0, 400 nM phosphatidylserine (PS) 17:0/17:0, 3.6 nM sphingomyelin (SM) d18:1/6:0, 0.8 nM sphingosine d18:1 d7 and 0.8 nM sphingosine d18:0 d7 from Avanti Polar Lipids; 400 nM triacylglycerides (TAG) 12:0/12:0/12:0 from Sigma Aldrich. The samples were sonicated for 30 min followed by centrifugation at 14,000 g for 10 min at 22°C. The supernatant was analysed by LC-MS |
| Extraction Method: | one phase extraction with 1:1 butanol/methanol |
| Extract Cleanup: | by taking the supernatant |
| Extract Storage: | On ice |
Combined analysis:
| Analysis ID | AN005013 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 |
| Column | Agilent ZORBAX Eclipse Plus C18 (50 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6495 QQQ |
| Ion Mode | POSITIVE |
| Units | umol |
Chromatography:
| Chromatography ID: | CH003786 |
| Chromatography Summary: | The supernatant was analysed using an Agilent 1290 series UHPLC system connected to an Agilent 6495 QQQ mass spectrometer after separation on a ZORBAX Eclipse plus C18 column (2.1 x 50 mm, 1.8 µm, 95 Å, Agilent) at 40 °C. The injection volume was 2 µL. Solvent A consisted of 60% water/40% acetonitrile (v/v) with 10 mM ammonium formate; solvent B consisted of 90% isopropanol/10% acetonitrile (v/v) with 10 mM ammonium formate. The gradient started with a flow rate of 0.4 mL/min at 20% B and increased to 60% B at 2 min, 100% B at 7 min, held at 100% B until 9 min, followed by equilibration with 20% B from 9.01 min until 10.8 min. |
| Instrument Name: | Agilent 1290 |
| Column Name: | Agilent ZORBAX Eclipse Plus C18 (50 x 2.1mm,1.8um) |
| Column Temperature: | 40 |
| Flow Gradient: | 20% B and increased to 60% B at 2 min, 100% B at 7 min, held at 100% B until 9 min, followed by equilibration with 20% B from 9.01 min until 10.8 min |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 60% water/40% acetonitrile (v/v) with 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile (v/v) with 10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004752 |
| Analysis ID: | AN005013 |
| Instrument Name: | Agilent 6495 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Column effluent was introduced to the mass spectrometer via AJS-ESI ion source operating under the following conditions: gas temperature, 200 °C; gas flow, 14 L/min; nebulizer, 20 psi; sheath gas temperature, 250 °C; sheath gas flow, 11 L/min; capillary, 3500 V. Mass spectrometry analysis was performed in positive ion mode with dynamic multiple reaction monitoring (dMRM). Mass spectrometry settings, LC-MS gradient and MRM transitions for each lipid class were adapted from a published method 65. Relative quantification of lipids was based on one-point calibration with class specific internal standards and was further normalized to the total protein content within each sample. The data were then analyzed by MassHunter |
| Ion Mode: | POSITIVE |
