Summary of Study ST003114
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 PR001935. The data can be accessed directly via it's Project DOI: 10.21228/M8M430 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 | ST003114 |
| Study Title | Lipidomics analyses in model membranes, isolated mitochondria and cellular systems to study how the local lipid environment affects BAX and BAK function during apoptosis. |
| Study Summary | To investigate how the local lipid environment affects BAX and BAK function during apoptosis, we performed quantitative analyses of different lipid classes (glycerophospholipids, fatty acids, ceramides and sphingomyelins) in cultured cells, isolated mitochondria and lipid nanodics formed by Styrene-Malic Acid (SMA) co-polymers. Ceramides, sphingomyelins, fatty acids and cardiolipins were analyzed by Liquid Chromatography coupled to Tandem Mass Spectrometry (LC-MS/MS). For glycerophospholipids (PC, PE, PI, PS, PG, PA) we applied direct infusion MS approaches (Shotgun Lipidomics). |
| Institute | University of Cologne |
| Department | Faculty of Medicine and University Hospital of Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD) |
| Laboratory | CECAD Lipidomics/Metabolomics Facility |
| Last Name | Brodesser |
| First Name | Susanne |
| Address | Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany |
| susanne.brodesser@uk-koeln.de | |
| Phone | +49 221 478 84015 |
| Submit Date | 2023-08-16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-03-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005102 | AN005103 | AN005104 | AN005105 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | None (Direct infusion) | Normal phase | Reversed phase | Reversed phase |
| Chromatography system | Advion TriVersa NanoMate | Agilent 1260 | Shimadzu Nexera X2 | Shimadzu Nexera X2 |
| Column | None | Macherey-Nagel Nucleosil NH2 (50×2 mm, 3 um, 120 Å) | Waters Acquity BEH Shield RP18 (100×2.1 mm, 1.7 um) | Phenomenex Core-Shell Kinetex Biphenyl (100×3.0 mm, 2.6 um, 100 Å) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | QTRAP | QTRAP | QTRAP | QTRAP |
| MS instrument name | SCIEX QTRAP 6500 | SCIEX QTRAP 6500 | SCIEX QTRAP 6500 | SCIEX QTRAP 6500 |
| Ion Mode | POSITIVE | POSITIVE | POSITIVE | NEGATIVE |
| Units | counts per second (cps) | counts per second (cps) | counts per second (cps) | counts per second (cps) |
MS:
| MS ID: | MS004839 |
| Analysis ID: | AN005102 |
| Instrument Name: | SCIEX QTRAP 6500 |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | PC, PE, PI, PS, PG, and PA species were analyzed by Nano-Electrospray Ionization Tandem Spectrometry (Nano-ESI-MS/MS) with direct infusion of the lipid extract (Shotgun Lipidomics) as previously described (Kumar et al., J Cell Biol 2015, 211, 1057). |
| Ion Mode: | POSITIVE |
| MS ID: | MS004840 |
| Analysis ID: | AN005103 |
| Instrument Name: | SCIEX QTRAP 6500 |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | LC-ESI-MS/MS analysis of ceramides and sphingomyelins was conducted as previously published (Oteng et al., J Lipid Res 2017, 58, 1100; Schwamb et al., Blood 2012, 120, 3978). |
| Ion Mode: | POSITIVE |
| MS ID: | MS004841 |
| Analysis ID: | AN005104 |
| Instrument Name: | SCIEX QTRAP 6500 |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | Cardiolipin (CL) species were analyzed by Liquid Chromatography coupled to Electrospray Ionization Tandem Mass Spectrometry (LC-ESI-MS/MS). CL species were monitored in the positive ion mode using the following Multiple Reaction Monitoring (MRM) transitions: CL 68:4, m/z 1418.9 to 575.4; CL 70:4, m/z 1446.9 to 575.4; CL 72:4 m/z 1475.0 to 603.4; CL 61:1 (internal standard), m/z 1326.9 to 535.4. For all MRM transitions the values for declustering potential, entrance potential, collision energy, and cell exit potential were 140 V, 10 V, 45 V, and 7 V, respectively (Tatsuta, Methods Mol Biol 2017, 1567, 79). The instrument settings for nebulizer gas (Gas 1), turbo gas (Gas 2), curtain gas, and collision gas were 50 psi, 50 psi, 40 psi, and medium, respectively. The Turbo V ESI source temperature was 500 °C, and the ionspray voltage was 4.5 kV. The LC chromatogram peaks of the endogenous CL species and the internal standard CL 61:1 were integrated using the MultiQuant 3.0.2 software (SCIEX). |
| Ion Mode: | POSITIVE |
| MS ID: | MS004842 |
| Analysis ID: | AN005105 |
| Instrument Name: | SCIEX QTRAP 6500 |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | Fatty acid levels were determined by LC-ESI-MS/MS: Fatty acids were monitored in the negative ion mode using “pseudo” Multiple Reaction Monitoring (MRM) transitions (Hellmuth et al., Anal Chem 2012, 84, 1483). The instrument settings for nebulizer gas (Gas 1), turbo gas (Gas 2), curtain gas, and collision gas were 60 psi, 90 psi, 40 psi, and medium, respectively. The Turbo V ESI source temperature was 650 °C, and the ionspray voltage was -4 kV. The LC chromatogram peaks of the endogenous fatty acids and the internal standard palmitic-d31 acid were integrated using the MultiQuant 3.0.2 software (SCIEX). |
| Ion Mode: | NEGATIVE |
