Summary of Study ST002358
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 PR001514. The data can be accessed directly via it's Project DOI: 10.21228/M80H6B 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 | ST002358 |
| Study Title | Effect of hypoxia and reoxygenation on the juvenile hooded seal brain lipidome |
| Study Summary | Brain samples from juvenile hooded seals (Cystophora cristata) were subjected to hypoxia and reoxygenation in vitro and lipid composition was compared. |
| Institute | University of Hamburg |
| Last Name | Martens |
| First Name | Gerrit Alexander |
| Address | Martin-Luther-King-Platz 3, 20146 Hamburg, Germany |
| gerrit.alexander.martens@uni-hamburg.de | |
| Phone | +49 40 42838-3934 |
| Submit Date | 2022-11-23 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-04-12 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003850 | AN003851 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Dionex Ultimate 3000 UPLC system (Dionex, Idstein, Germany) | Dionex Ultimate 3000 UPLC system (Dionex, Idstein, Germany) |
| Column | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Bruker Daltonics maXis 3G | Bruker Daltonics maXis 3G |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak Area | Peak Area |
MS:
| MS ID: | MS003591 |
| Analysis ID: | AN003850 |
| Instrument Name: | Bruker Daltonics maXis 3G |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The data were recorded at 1 Hz over a mass range of m/z 80-1100. Further parameters were: end plate offset -500 V, capillary -4500 V, nebulizer pressure 4.0 bar, dry gas 9.0 L/min at 200 °C dry temperature. At the beginning of the measurements, the mass spectrometer was calibrated using sodium formate clusters. At the end of each sample run, a further calibration was carried out using the cluster solutions. Acquired experimental mass spectra were recalibrated with Bruker Data Analysis Software 4.2 (Bruker Daltonics, Bremen, Germany) using the mentioned sodium formate clusters. Afterwards, data were exported to netCDF file format. Data preprocessing was performed with R package xcms 3.6.2 (Smith et al. 2006) in R version 3.6.3 (R Core Team 2021). Parameters for processing were optimized based on existing tools and scripts (Libiseller et al. 2015; Manier et al. 2019). After reading in recalibrated netCDF files, features were detected with findChromPeaks function and CentWaveParam (peakwidth = c(10, 40), ppm = 20, snthresh = 10, mzdiff = 0.015, prefilter = c(0, 0), noise = 0)). Retention time was corrected with adjustRtime function and ObiwarpParam (binSize = 1.0). Feature correspondence was achieved with groupChromPeaks function and PeakDensityParam (sampleGroups = xdata$sample_group, bw = 1) as well as missing value imputation with fillChromPeaks function with FillChromPeaksParam (fixedRt = ChromPeakwidth/2)). ChromPeakwidth was calculated as average peak width of detected chromatographic peaks. Adducts and isotopes of features were annotated using R package CAMERA 1.40.0 (Kuhl et al. 2012). Features in the QC samples with a relative standard deviation over 30%, blank intensity contribution over 10% and QC sample count below 60% were removed before further statistical analysis. |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | -4500 V |
| Dry Gas Flow: | 9.0 L/min |
| Dry Gas Temp: | 200 °C |
| Nebulizer: | 4.0 bar |
| MS ID: | MS003592 |
| Analysis ID: | AN003851 |
| Instrument Name: | Bruker Daltonics maXis 3G |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The data were recorded at 1 Hz over a mass range of m/z 80-1100. Further parameters were: end plate offset -500 V, capillary +4500 V, nebulizer pressure 4.0 bar, dry gas 9.0 L/min at 200 °C dry temperature. At the beginning of the measurements, the mass spectrometer was calibrated using sodium acetate clusters. At the end of each sample run, a further calibration was carried out using the cluster solutions. Acquired experimental mass spectra were recalibrated with Bruker Data Analysis Software 4.2 (Bruker Daltonics, Bremen, Germany) using the mentioned sodium acetate clusters. Afterwards, data were exported to netCDF file format. Data preprocessing was performed with R package xcms 3.6.2 (Smith et al. 2006) in R version 3.6.3 (R Core Team 2021). Parameters for processing were optimized based on existing tools and scripts (Libiseller et al. 2015; Manier et al. 2019). After reading in recalibrated netCDF files, features were detected with findChromPeaks function and CentWaveParam (peakwidth = c(10, 40), ppm = 20, snthresh = 10, mzdiff = 0.015, prefilter = c(0, 0), noise = 0)). Retention time was corrected with adjustRtime function and ObiwarpParam (binSize = 1.0). Feature correspondence was achieved with groupChromPeaks function and PeakDensityParam (sampleGroups = xdata$sample_group, bw = 1) as well as missing value imputation with fillChromPeaks function with FillChromPeaksParam (fixedRt = ChromPeakwidth/2)). ChromPeakwidth was calculated as average peak width of detected chromatographic peaks. Adducts and isotopes of features were annotated using R package CAMERA 1.40.0 (Kuhl et al. 2012). Features in the QC samples with a relative standard deviation over 30%, blank intensity contribution over 10% and QC sample count below 60% were removed before further statistical analysis. |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | +4500 V |
| Dry Gas Flow: | 9.0 L/min |
| Dry Gas Temp: | 200 °C |
| Nebulizer: | 4.0 bar |
