Summary of Study ST002422
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 PR001559. The data can be accessed directly via it's Project DOI: 10.21228/M85X3W 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 | ST002422 |
| Study Title | UBXD8 lipidomics from whole cells (Part 2) |
| Study Summary | The intimate association between the endoplasmic reticulum (ER) and mitochondrial membranes at ER-mitochondria contact sites (ERMCS) serves as a platform for several critical cellular processes, in particular lipid synthesis. Enzymes involved in lipid biosynthesis are enriched at contacts and membrane lipid composition at contacts is distinct relative to surrounding membranes. How contacts are remodeled and the subsequent biological consequences of altered contacts such as perturbed lipid metabolism remains poorly understood. Here we investigate if the ER-tethered ubiquitin-X domain adaptor 8 (UBXD8) regulates the lipids found in mitochondria-associated membranes (MAM). LC-MS/MS lipidomics found significant changes in distinct lipid species in the MAM fraction of UBXD8 knockout cells. Our results suggest that lipids in MAM are regulated by UBXD8. |
| Institute | University of Arizona |
| Department | Immunobiology |
| Laboratory | Purdy Lab |
| Last Name | Purdy |
| First Name | John |
| Address | PO Box 245221, Tucson, Arizona, 85724, USA |
| purdylab@gmail.com | |
| Phone | 520-626-4371 |
| Submit Date | 2023-01-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-01-16 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003944 | AN003945 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters ACQUITY UPLC CSH C18 (150 x 2.1mm,1.7um) | Waters ACQUITY UPLC CSH C18 (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH002920 |
| Chromatography Summary: | Lipids were identified and quantitatively measured using ultra high-performance liquid-chromatography high-resolution tandem MS/MS (UHPLC-MS/MS) as recently described89,90. Separation of lipids was done by reverse-phase chromatography using a Waters ACQUITY CSH C18 column (150x2.1mm; 1.7um) at 60°C using a Vanquish UHPLC system (Thermo Scientific) and two solvents: solvent A (40:60 water-methanol plus 10mM ammonium formate and 0.1% formic acid) and solvent B (10:90 methanol-isopropanol plus 10mM ammonium formate and 0.1% formic acid). UHPLC was performed at a 0.25 ml per min flow rate for 30 min per sample, starting at 25% solvent B and ending at 100% solvent B as described. The column was washed and equilibrated between samples. Samples were run in a semi-random order where WT or UBXD8 KO samples were interspersed with blank samples. Each sample was repeatedly analyzed using various injection volumes (4, 8, 16ul for positive mode and 5, 10, and 15ul for negative mode). |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC CSH C18 (150 x 2.1mm,1.7um) |
| Column Temperature: | 60 |
| Flow Gradient: | 25% to 100% |
| Flow Rate: | 0.25mL per min |
| Solvent A: | 40% water; 60% methanol 10mM ammonium formate and 0.1% formic acid |
| Solvent B: | 10% methanol; 90% isopropanol 10mM ammonium formate and 0.1% formic acid |
| Chromatography Type: | Reversed phase |
