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.

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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.

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Study IDST002880
Study TitleHypoxia-driven dynamics of tomato root lipidome
Study SummaryA 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 NameWende
First NameKristian
AddressF.-Hausdorff-Str. 2, D-17489 Greifswald
Emailkristian.wende@inp-greifswald.de
Phone+49 3834 554 3923
Submit Date2023-09-15
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-10-16
Release Version1
Kristian Wende Kristian Wende
https://dx.doi.org/10.21228/M8X43S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001801
Project DOI:doi: 10.21228/M8X43S
Project Title:Biomolecule oxidation by cold plasma generated ROS/RNS
Project Summary:In an extensive study, the oxidation pattern of lipids and proteins by plasma-generated species was mapped. The dominant reaction partners and reaction locations were identified. Conclusions on plasma source design and medical implications were drawn.
Institute:Leibniz Institute for Plasma Science and Technology
Department:PFE
Last Name:Wende
First Name:Kristian
Address:F.-Hausdorff-Str. 4, D-17489 Greifswald
Email:kristian.wende@inp-greifswald.de
Phone:+49 3834 554 3923
Funding Source:BMBF 03Z22DN12

Subject:

Subject ID:SU002993
Subject Type:Plant
Subject Species:Lycopersicon esculentum

Factors:

Subject type: Plant; Subject species: Lycopersicon esculentum (Factor headings shown in green)

mb_sample_id local_sample_id condition
SA314678Control_2_4_negcontrol
SA314679Control_2_4_poscontrol
SA314680Control_2_5_poscontrol
SA314681Control_2_3_poscontrol
SA314682Control_2_3_negcontrol
SA314683Control_2_2_negcontrol
SA314684Control_2_2_poscontrol
SA314685Control_2_6_negcontrol
SA314686Control_2_7_negcontrol
SA314687Control_2_9_negcontrol
SA314688Control_2_9_poscontrol
SA314689Control_1_1_negcontrol
SA314690Control_2_8_poscontrol
SA314691Control_2_8_negcontrol
SA314692Control_2_1_poscontrol
SA314693Control_2_7_poscontrol
SA314694Control_2_6_poscontrol
SA314695Control_2_5_negcontrol
SA314696Control_1_4_negcontrol
SA314697Control_1_4_poscontrol
SA314698Control_1_5_negcontrol
SA314699Control_1_3_poscontrol
SA314700Control_1_3_negcontrol
SA314701Control_1_1_poscontrol
SA314702Control_2_1_negcontrol
SA314703Control_1_2_poscontrol
SA314704Control_1_5_poscontrol
SA314705Control_1_2_negcontrol
SA314706Control_1_8_poscontrol
SA314707Control_1_9_poscontrol
SA314708Control_1_6_negcontrol
SA314709Control_1_8_negcontrol
SA314710Control_1_9_negcontrol
SA314711Control_1_7_poscontrol
SA314712Control_1_6_poscontrol
SA314713Control_1_7_negcontrol
SA314714Hypoxia_2_4_neghypoxia
SA314715Hypoxia_2_5_neghypoxia
SA314716Hypoxia_2_4_poshypoxia
SA314717Hypoxia_2_3_neghypoxia
SA314718Hypoxia_2_5_poshypoxia
SA314719Hypoxia_2_2_neghypoxia
SA314720Hypoxia_2_2_poshypoxia
SA314721Hypoxia_2_3_poshypoxia
SA314722Hypoxia_2_8_neghypoxia
SA314723Hypoxia_2_9_neghypoxia
SA314724Hypoxia_2_9_poshypoxia
SA314725Hypoxia_2_1_poshypoxia
SA314726Hypoxia_2_8_poshypoxia
SA314727Hypoxia_2_7_poshypoxia
SA314728Hypoxia_2_6_poshypoxia
SA314729Hypoxia_2_7_neghypoxia
SA314730Hypoxia_2_6_neghypoxia
SA314731Hypoxia_1_1_neghypoxia
SA314732Hypoxia_1_4_neghypoxia
SA314733Hypoxia_1_4_poshypoxia
SA314734Hypoxia_1_5_neghypoxia
SA314735Hypoxia_1_3_poshypoxia
SA314736Hypoxia_1_3_neghypoxia
SA314737Hypoxia_1_1_poshypoxia
SA314738Hypoxia_1_2_neghypoxia
SA314739Hypoxia_1_2_poshypoxia
SA314740Hypoxia_1_5_poshypoxia
SA314741Hypoxia_1_6_neghypoxia
SA314742Hypoxia_1_8_poshypoxia
SA314743Hypoxia_1_9_neghypoxia
SA314744Hypoxia_1_9_poshypoxia
SA314745Hypoxia_1_8_neghypoxia
SA314746Hypoxia_1_7_poshypoxia
SA314747Hypoxia_1_6_poshypoxia
SA314748Hypoxia_1_7_neghypoxia
SA314749Hypoxia_2_1_neghypoxia
Showing results 1 to 72 of 72

Collection:

Collection ID:CO002986
Collection Summary:Control or hypoxia-exposed tomato roots were collected, minced, and extracted. Subsequently, lipidome profile was determined by LC-HRMS/MS
Collection Protocol Filename:experimental procedure.pdf
Sample Type:Plant roots
Collection Frequency:48h after hypoxia applied
Storage Conditions:-20℃

Treatment:

Treatment ID:TR003002
Treatment Summary:Solanum lycopersicum (L.) cv. Moneymaker was cultivated under greenhouse conditions (14 h light 18 °C / 10 h dark 22 °C). Tomato plants grew on quartz sand culture for four weeks with a nutrient solution containing 5 mM NO3- [18,19]. Tomato roots were waterlogged for 48 h to apply hypoxic conditions.
Treatment:watterlogging
Treatment Doseduration:48h
Plant Light Period:14h
Plant Temp:18°C

Sample Preparation:

Sampleprep ID:SP002999
Sampleprep Summary:Lipids from tomato roots were extracted with a modified procedure adapted from Shiva and colleagues [20]. In brief, 0.1 g of grinded roots (cooled on liquid nitrogen) were added to a glass reaction tube filled with isopropanol supplemented with 0.01 % BHT. The mixture was incubated for 15 min at 75 °C and cooled on ice afterward. To the cooled-down mixture, 0.5 volume of chloroform, 0.2 volume of water and 3 µL of EquiSPLASH Lipidomix were added. Lipids were extracted for 1 h on ice with occasional vortexing in between. Reaction tubes were centrifuged at 5000 x g to induce phase separation, and the organic phase was transferred to another glass reaction tube. To the remaining water phase, 1.33 volumes of a chloroform:methanol mixture (2:1, v/v) supplemented with 0.1 % BHT was added and incubated for 30 min on ice with occasional vortexing. Reaction tubes were again centrifuged at 5000 rpm, and the chloroform phase was transferred to the second glass vial. The chloroform:methanol extraction step was repeated with the remaining water phase 3 times. Afterward, 0.33 volumes of KCl (1 M) were added to the combined lipid extracts and vortexed. The upper water phase was removed, and 0.66 volumes of water were added and vortexed. The upper phase was again removed, and sodium sulfate was added to remove the remaining water. Finally, the lipid extract was dried under constant N2-flow with a TurboVap sample evaporator (Biotage, Sweden) and frozen at -80°C until MS analysis.
Processing Storage Conditions:On ice
Extract Storage:-80℃
Sample Resuspension:chloroform:methanol:isopropanol (1:2:4 v/v/v, supplemented with 5 mM ammonium formate)
Sample Derivatization:none
Sample Spiking:EquiSPLASH

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.)

Chromatography:

Chromatography ID:CH003553
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore C30 (150 x 2.1mm,2.6um)
Column Temperature:50°C
Flow Gradient:30% - 99% B 30min
Flow Rate:350µl/min
Solvent A:60% acetonitrile/40% water;10 mM ammonium formate; 0.1 % formic acid
Solvent B:90% isopropanol/10% acetonitrile; 10 mM ammonium formate; 0.1 % formic acid
Chromatography Type:Reversed phase

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
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