Summary of Study ST002880
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 PR001801. The data can be accessed directly via it's Project DOI: 10.21228/M8X43S 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 | ST002880 |
| Study Title | Hypoxia-driven dynamics of tomato root lipidome |
| Study Summary | A distinct, hypoxia-related lipid composition of Solanum lycopersicum root tissue was observed. Out of 965 lipid species, 33 were exclusively detected in this condition. Among the lipid classes observed, glycerolipids and glycerophospholipids dominated by far (77%). Significantly, the abundance of triacylglycerols increased with hypoxic stress, while sitosterol esters, digalactosyldiacylglycerols, and phosphatidylcholine decreased. Alongside, an increased level of polyunsaturation was observed in the fatty acid chains, with 18:2, 18:3 residues showing a significant increase. Of note, hexadecatetraenoic acid (16:4) was identified in hypoxia condition samples. |
| Institute | Leibniz Institute for Plasma Science and Technology |
| Last Name | Wende |
| First Name | Kristian |
| Address | F.-Hausdorff-Str. 2, D-17489 Greifswald |
| kristian.wende@inp-greifswald.de | |
| Phone | +49 3834 554 3923 |
| Submit Date | 2023-09-15 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-10-16 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN004719 | AN004720 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore C30 (150 x 2.1mm,2.6um) | Thermo Accucore C30 (150 x 2.1mm,2.6um) |
| 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 | normalized relative abundance | normalized relative abundance (a.u.) |
MS:
| MS ID: | MS004465 |
| Analysis ID: | AN004719 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS raw files were analysed with the software LipidSearch (version 4.2.27, Thermo Fisher) using the following parameters: retention time interval 0.01 min, m-score threshold 5, precursor tolerance 5 ppm, product tolerance 8 ppm, ID quality filter A (fatty acid chain and class identified completely) and B (class and some fatty acid chains identified). The resulting text files were processed with an in-house KNIME workflow and filtered for ppm error, peak quality and area score. The area of identical lipids with different ion adducts was summed up. The resulting excel file was processed in R (v 4.0.2) with manual inspection of raw areas (Figure S1). Lipids in the blanks or blank extracts were excluded from the data, if not at least 5-fold lower in intensity in blank controls. Lipid areas were normalized to the respective lipids in the EquiSplash standard, and median normalization was applied (Figure S2). Lipids present in less than 20% of samples were excluded from subsequent analysis of lipid species. For principal component analyses (PCA), lipid species identified in at least 50% of samples were considered, and the three independent replicates were batch-adjusted using the ComBat algorithm. Lipids were annotated on the molecular species level in accordance with the proposed nomenclature by the LIPID MAPS consortium since no information on the sn-position of acyl/alkyl constituents was available |
| Ion Mode: | POSITIVE |
| MS ID: | MS004466 |
| Analysis ID: | AN004720 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS raw files were analysed with the software LipidSearch (version 4.2.27, Thermo Fisher) using the following parameters: retention time interval 0.01 min, m-score threshold 5, precursor tolerance 5 ppm, product tolerance 8 ppm, ID quality filter A (fatty acid chain and class identified completely) and B (class and some fatty acid chains identified). The resulting text files were processed with an in-house KNIME workflow and filtered for ppm error, peak quality and area score. The area of identical lipids with different ion adducts was summed up. The resulting excel file was processed in R (v 4.0.2) with manual inspection of raw areas (Figure S1). Lipids in the blanks or blank extracts were excluded from the data, if not at least 5-fold lower in intensity in blank controls. Lipid areas were normalized to the respective lipids in the EquiSplash standard, and median normalization was applied (Figure S2). Lipids present in less than 20% of samples were excluded from subsequent analysis of lipid species. For principal component analyses (PCA), lipid species identified in at least 50% of samples were considered, and the three independent replicates were batch-adjusted using the ComBat algorithm. Lipids were annotated on the molecular species level in accordance with the proposed nomenclature by the LIPID MAPS consortium since no information on the sn-position of acyl/alkyl constituents was available |
| Ion Mode: | NEGATIVE |
