Summary of Study ST002148

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 PR001361. The data can be accessed directly via it's Project DOI: 10.21228/M8SQ6J 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 IDST002148
Study TitleUntargeted MS-based metabolomics analysis of the responses to drought stress in Quercus ilex leaf seedlings, and identification of putative compounds related to tolerance
Study TypeUntargeted MS-based metabolomics
Study SummaryThe effect and responses to drought stress have been analyzed in Quercus ilex seedlings by using a non-targeted metabolomic approach, implementing previous studies pub-lished in which other -omics platforms, transcriptomics, and proteomics, have been em-ployed. This work is aimed at characterizing the Q. ilex leaf metabolome, determining possible mechanisms and molecular markers of drought tolerance, and identifying puta-tive bioactive compounds. Six-month-old seedling leaves, subjected to drought stress im-posed by water withholding under high temperature and irradiance conditions, were col-lected when leaf fluorescence decreased by 20 % (day 17) and 45 % (day 24) relative to ir-rigated seedlings. A total of 3934 compounds were resolved, with 616 being variable, and 342 identified, belonging to five chemical families. Out of the identified compounds 33 were variable, mostly corresponding to amino acids, carboxylic acids, benzenoids, flavo-noids and isoprenoids. Epigallocatechin, ellagic acid, pulegone, indole-3-acrylic acid and dihydrozeatin-O-glucoside were up-accumulated under drought conditions at both sam-pling times. An integrated multi-omics analysis of phenolic compounds and related en-zymes was performed, revealing that some enzymes involved in the flavonoid pathways (chalcone synthase, anthocyanidin synthase and anthocyanidin reductase) were up-accumulated at day 24 in non-irrigated seedlings. Some putative markers of drought tol-erance to drought in Q. ilex are proposed for assisting breeding programs based on the se-lection of elite genotypes.
Institute
Universidad de Córdoba
DepartmentDepartment Biochemistry and Molecular Biology
LaboratoryAgroforestry and Plant Biochemistry, Proteomics and Systems Biology
Last NameLópez Hidalgo
First NameCristina
AddressCampus de Rabanales; Edificio C6, Planta Baja
Emaillopezhcristina@uniovi.es
Phone626894948
Submit Date2022-02-25
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-05-09
Release Version1
Cristina López Hidalgo Cristina López Hidalgo
https://dx.doi.org/10.21228/M8SQ6J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001361
Project DOI:doi: 10.21228/M8SQ6J
Project Title:Untargeted metabolomics of Quercus ilex leaves in Drought
Project Type:LC-MS analysis
Project Summary:UPLC-MS analysis of samples from Quercus ilex leaves. The objective of the study is to characterize the leaf metabolome of Q. ilex in six-month-old seedlings and the changes that have taken place in response to drought stress by water withholding under high temperature and irradiance conditions.
Institute:Universidad de Córdoba
Department:Department Biochemistry and Molecular Biology
Laboratory:Agroforestry and Plant Biochemistry, Proteomics and Systems Biology
Last Name:López-Hidalgo
First Name:Cristina
Address:Campus de Rabanales; Edificio C6, Planta Baja
Email:lopezhcristina@uniovi.es
Phone:626894948
Funding Source:This work was supported by the University of Cordoba and financial support from the Spanish Ministry of Economy and Competitiveness (Project ENCINOMICS-2 PID2019-10908RB-100)
Publications:Untargeted MS-based metabolomics analysis of the responses to drought stress in Quercus ilex leaf seedlings, and identification of putative compounds related to tolerance
Contributors:Marta Tienda-Parrilla, Cristina López-Hidalgo, Víctor M. Guerrero-Sánchez, Álvaro Infantes-González, Rocío Valderrama, Jesús V. Jorrin-Novo, María-Dolores Rey

Subject:

Subject ID:SU002234
Subject Type:Plant
Subject Species:Quercus ilex
Taxonomy ID:58334

Factors:

Subject type: Plant; Subject species: Quercus ilex (Factor headings shown in green)

mb_sample_id local_sample_id Factor
SA205846190218_Blankneg4Blank
SA205847190218_Blankneg3Blank
SA205848190218_Blankneg2Blank
SA205849190218_Blankneg5Blank
SA205850190218_Blankneg7Blank
SA205851190218_Naringina_1ppm_negBlank
SA205852190218_Blankneg8Blank
SA205853190218_Blankneg1Blank
SA205854190218_Blankneg6Blank
SA205855190218_Blankpos1Blank
SA205856190218_Blankpos7Blank
SA205857190218_Blankpos8Blank
SA205858190218_Naringina_1ppm_posBlank
SA205859190218_Blankpos6Blank
SA205860190218_Blankpos5Blank
SA205861190218_Blankpos2Blank
SA205862190218_Blankpos3Blank
SA205863190218_Blankpos4Blank
SA205864190218_2_C_T1_R2_posC_T1
SA205865190218_1_C_T1_R1_negC_T1
SA205866190218_3_C_T1_R3_posC_T1
SA205867190218_1_C_T1_R1_posC_T1
SA205868190218_2_C_T1_R2_negC_T1
SA205869190218_3_C_T1_R3_negC_T1
SA205870190218_6_C_T2_R3_posC_T2
SA205871190218_4_C_T2_R1_posC_T2
SA205872190218_5_C_T2_R2_posC_T2
SA205873190218_6_C_T2_R3_negC_T2
SA205874190218_4_C_T2_R1_negC_T2
SA205875190218_5_C_T2_R2_negC_T2
SA205876190218_7_D_T1_R1_posD_T1
SA205877190218_8_D_T1_R2_posD_T1
SA205878190218_9_D_T1_R3_posD_T1
SA205879190218_9_D_T1_R3_negD_T1
SA205880190218_7_D_T1_R1_negD_T1
SA205881190218_8_D_T1_R2_negD_T1
SA205882190218_11_D_T2_R2_negD_T2
SA205883190218_11_D_T2_R2_posD_T2
SA205884190218_10_D_T2_R1_negD_T2
SA205885190218_12_D_T2_R3_posD_T2
SA205886190218_10_D_T2_R1_posD_T2
SA205887190218_12_D_T2_R3_negD_T2
SA205888190218_QCMIX_pos_FS_5Quality Control mixture
SA205889190218_QCMIX_pos_FS_4Quality Control mixture
SA205890190218_QCMIX_pos_FS_3Quality Control mixture
SA205891190218_QCMIX_pos_FS_6Quality Control mixture
SA205892190218_QCMIX_pos_TOP5_2Quality Control mixture
SA205893190218_QCMIX_neg_FS_4Quality Control mixture
SA205894190218_QCMIX_pos_TOP5_3Quality Control mixture
SA205895190218_QCMIX_pos_FS_2Quality Control mixture
SA205896190218_QCMIX_pos_TOP5_1Quality Control mixture
SA205897190218_QCMIX_neg_FS_5Quality Control mixture
SA205898190218_QCMIX_neg_TOP5_3Quality Control mixture
SA205899190218_QCMIX_neg_FS_2Quality Control mixture
SA205900190218_QCMIX_neg_FS_1Quality Control mixture
SA205901190218_QCMIX_neg_TOP5_2Quality Control mixture
SA205902190218_QCMIX_neg_TOP5_1Quality Control mixture
SA205903190218_QCMIX_neg_FS_3Quality Control mixture
SA205904190218_QCMIX_neg_FS_6Quality Control mixture
SA205905190218_QCMIX_pos_FS_1Quality Control mixture
Showing results 1 to 60 of 60

Collection:

Collection ID:CO002227
Collection Summary:Out of the biological replicates, three asymptomatic (non-damaged) non-irrigated seedlings were randomly selected for metabolomics. All leaves were collected when the chlorophyll fluorescence dropped by 20 and 45 % in the non-irrigated seedlings compared to irrigated ones (at days 17 and 24, respectively) [7]. After collection, leaves from the three biological replicates per treatment and sampling time were washed with tap water, blot dried with filter paper, shock-frozen in liquid nitrogen, and stored at -80 °C until metabolite extraction.
Sample Type:new
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002246
Treatment Summary:An experiment based on a completely randomized design was developed by using ten biological replicates per treatment [7]. Out of the biological replicates, three asymptomatic (non-damaged) non-irrigated seedlings were randomly selected for metabolomics. All leaves were collected when the chlorophyll fluorescence dropped by 20 and 45 % in the non-irrigated seedlings compared to irrigated ones (at days 17 and 24, respectively)
Treatment:Drought
Plant Plot Design:Randomized design
Plant Light Period:28 W m-2 solar irradiance
Plant Humidity:41% humidity
Plant Temp:37 °C temperature
Plant Growth Stage:Six-month-old seedlings
Plant Metab Quench Method:Liquid N2
Plant Storage:-80ºC

Sample Preparation:

Sampleprep ID:SP002240
Sampleprep Summary:Metabolites were extracted from leaves as described by Valledor et al., [41], with minor modifications. An extraction solution containing 600 µL of ice-cold methanol: chloroform: water (5:2:2) was added to 50 mg dry weight leaf tissue and vortexed for 10 sec. The mixture was sonicated (ultrasonic bath, 40 kHz for 10 min) and after centrifugation at 20,000 × g at 4°C for 4 mins, the supernatant was transferred to a new tube. Then, 200 µL of cold methanol: chloroform: water (5:2:2) was added to the pellets and the process was repeated once. After combining both supernatants, they were vacuum dried at 30°C (Speedvac, Eppendorf Vacuum Concentrator Plus/5301, Eppendorf, Leicestershire, UK). Dried extracts were reconstituted in methanol, centrifuged at 20,000×g for 10 min, and filtered through 0.22 μm PTPE membranes (Thermo Fisher Scientific, Courtaboeuf, France), and the filtrate was collected in 1.5 mL LC/MS certified sample vials.

Combined analysis:

Analysis ID AN003517 AN003518
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS
Column Waters Acquity BEH C8 (100 x 2.1mm, 1.7um) Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
MS Type ESI ESI
MS instrument type QTRAP QTRAP
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode NEGATIVE POSITIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH002597
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003275
Analysis ID:AN003517
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:QTRAP
MS Type:ESI
MS Comments:The operating parameters, in positive ion mode, were sheath gas flow rate at 60 kV, auxiliary gas flow rate at 25 kV, sweep gas flow rate at 2 kV, spray voltage at 3 kV, capillary temperature at 320 °C, S-lens RF level at 50 kV, and auxiliary gas heater temperature at 400 °C. The Xcalibur v3.1 software was used for instrument control and data acquisition. Spectra data were acquired in a full scan (FS) mode at a resolution of 70,000 (full width half maximum, FWHM at m/z 200) for MS1, and a data dependent (dd-MS2/dd-SIM) manner for MS2, fragmenting the five most abundant precursor ions per MS1 scan (TopN, 5), acquiring MS/MS data between 200 and 2000 m/z at a resolution of 17.500.
Ion Mode:NEGATIVE
  
MS ID:MS003276
Analysis ID:AN003518
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:QTRAP
MS Type:ESI
MS Comments:The operating parameters, in positive ion mode, were sheath gas flow rate at 60 kV, auxiliary gas flow rate at 25 kV, sweep gas flow rate at 2 kV, spray voltage at 3.5 kV, capillary temperature at 320 °C, S-lens RF level at 50 kV, and auxiliary gas heater temperature at 400 °C. The Xcalibur v3.1 software was used for instrument control and data acquisition. Spectra data were acquired in a full scan (FS) mode at a resolution of 70,000 (full width half maximum, FWHM at m/z 200) for MS1, and a data dependent (dd-MS2/dd-SIM) manner for MS2, fragmenting the five most abundant precursor ions per MS1 scan (TopN, 5), acquiring MS/MS data between 200 and 2000 m/z at a resolution of 17.500.
Ion Mode:POSITIVE
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