Summary of study ST000508

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 PR000381. The data can be accessed directly via it's Project DOI: 10.21228/M8SW34 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000508
Study TitleMetabolic Profiling of Date Palm Fruits
Study SummaryIn this study, two independent large cohorts of mature dates exhibiting substantial diversity in origin, varieties and fruit processing conditions were measured by metabolomics techniques in order to identify major determinants of the fruit metabotype. Additional samples reflecting different stages of date fruit ripening process has been included for 10 different fruit varieties.
Institute
Weill Cornell Medicine, Qatar
DepartmentBioinformatics Core
LaboratorySuhre Lab
Last NameSuhre
First NameKarsten
AddressEducation City
Emailnis2034@qatar-med.cornell.edu
Phone+97433888408
Submit Date2016-11-14
Analysis Type DetailGC/LC-MS
Release Date2017-01-14
Release Version1
Karsten Suhre Karsten Suhre
https://dx.doi.org/10.21228/M8SW34
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000381
Project DOI:doi: 10.21228/M8SW34
Project Title:Metabolic Profiling of Date Palm Fruits
Project Summary:The goal of this study was to investigate metabotypes of date palm fruits through global, non-targeted metabolomics of assorted date fruits varieties from different countries of origin.
Institute:Weill Cornell Medicine, Qatar
Department:Bioinformatics Core
Laboratory:Suhre Lab
Last Name:Suhre
First Name:Karsten
Address:Luqta Street, Education City, Doha, Qatar, 24144, Qatar
Email:nishastephan@gmail.com
Phone:+97444928281
Funding Source:Funding for this research was provided by Qatar National Research Fund, a member of Qatar Foundation under the National Priorities Research Program – Exceptional Award (NPRP-EP) NPRPX-014-4-001.

Subject:

Subject ID:SU000530
Subject Type:Date palm fruit
Subject Species:Phoenix dactylifera
Taxonomy ID:42345
Species Group:Plant

Factors:

Subject type: Date palm fruit; Subject species: Phoenix dactylifera (Factor headings shown in green)

mb_sample_id local_sample_id date_variety
SA02630432.1Abel
SA026305112Adam adaalee
SA026306129Adam admaan
SA026307120Adam bujamaa
SA026308101Admoo
SA02630980Agalid
SA02631036.3Ajwa medina
SA02631160.2Allig
SA02631260Allig
SA02631313.2Ambara
SA02631447.1Amber - medina
SA02631547.2Amber - medina
SA02631627.2Aseel
SA02631727Aseel
SA02631827.3Aseel
SA0263191.2Aseela
SA0263201.3Aseela
SA0263216.2Ayash
SA026322146Aydea Al Qaseem
SA02632385Azaghzaw
SA02632485AAzaghzaw
SA02632585CAzaghzaw
SA026326144Barakawi
SA02632725.2Barani
SA02632896Bekri-khder
SA02632991ABelahzit
SA02633091Belahzit
SA02633191FBelahzit
SA02633291HBelahzit
SA02633331.2Berni
SA02633431.3Berni
SA02633512.3Berni
SA02633612.1Berni
SA02633784Bid-djaj
SA02633893CBooserdoon
SA02633993DBooserdoon
SA02634093Booserdoon
SA026341104Boozekri
SA02634298Boufegous rqiq
SA02634379Boukhanda
SA02634486Bouslikh
SA026345100Boussakri
SA02634678Bouzagza
SA02634716.1BuMaan
SA02634816.2BuMaan
SA02634930Burmeel
SA02635030.3Burmeel
SA026351149Dabbas
SA026352125Ddagla
SA026353128Deglet
SA026354108Deglet Bayda
SA026355117Deglet Nour
SA02635664.3Deglet Nour
SA02635764.2Deglet Nour
SA026358109Deglet Nour Hourra
SA02635951.3Dried dates
SA02636051.2Dried dates
SA026361114Fegous
SA02636271Fegous-ghlid
SA02636319.3Gagee
SA026364124Gharss
SA02636520.3Ghazelee
SA02636620.2Ghazelee
SA02636728.3Gorakh
SA02636862.2Grenja
SA026369143Grundeela/Qundeil
SA02637077Hafs
SA026371131Hameera
SA02637261Hamrata
SA02637361.3Hamrata
SA02637461.1Hamrata
SA026375133Hamray
SA026376151Harmayi Sadrati
SA02637722.2Ibrahim ( Iraqi Ajwa)
SA02637822Ibrahim ( Iraqi Ajwa)
SA02637915.3Jabri
SA02638073Jihl
SA02649389Akhalt-lhammar
SA02649489Bkhalt-lhammar
SA02649589Dkhalt-lhammar
SA02649689Ckhalt-lhammar
SA02649789Ekhalt-lhammar
SA02649889khalt-lhammar
SA0263815.2Khasoy
SA0263825.3Khasoy
SA02638355.3Kheneizi
SA02638424.2Khiyara
SA02638524Khiyara
SA02638624.3Khiyara
SA02649943.3khlas
SA02638750Khudry
SA02638850.1Khudry
SA02638935.2Khudry
SA026390142Kulma soda
SA02639181Lakhal
SA026392137Lulu
SA02639399AMaajoun
SA02639499CMaajoun
SA02639599DMaajoun
SA02639699BMaajoun
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Collection:

Collection ID:CO000524
Collection Summary:In the present study, 123 unique date varieties (Phoenix dactylifera) from 14 countries were collected in two separate occasions: A first collection took part in 2012 (DS1) and the second one in 2013 (DS2). The term variety is used here to describe a distinct phenotypic class of dates and if the same variety was collected from different countries, a different sample ID was assigned to each collected sample per country. Overall, dates from the first sample collection were mostly from the Gulf region obtained in a fairly dried condition from shops and festivals whilst the second sample collection was dominated by North African dates obtained mostly fresh from the palm trees. For the second collection of dates, field work permissions were obtained verbally from owners of visited oases. The marketed versus fresh nature of dates between the two sample collections implies varying post-harvest conditions. All collected dates with homogenous brown color were further dried by exposing them to open air for two weeks before further processing. With the second sample collection, while harvesting ripened fruits from the palm trees, immature fruits still undergoing ripening activity and occasionally late green Kimri fruits from the pre-ripening stage were collected when available. In total, 37 immature date fruits, corresponding to 10 date samples, were collected. With each of the 10 samples, the immature fruits were ranked by their extent of ripening based on visual assessment of color change and skin wrinkling. Each fruit was given an ID based on a combination of the sample number and a letter reflecting the fruit rank within the sample. In general, dates were considered mature if the low moisture prevented any further change in their appearance. Notably, maturity is attained naturally with the dry class of dates but often artificially with the soft class of dates owing to intrinsically higher moisture levels.
Sample Type:Date palm fruit
Collection Location:Differnt locations specified in the
Collection Duration:2012 - 2013
Storage Conditions:-80C

Treatment:

Treatment ID:TR000544
Treatment Summary:The aim of this study was to determine metabolic phenotype of the date palm fruits without any treatment at the baseline.

Sample Preparation:

Sampleprep ID:SP000537
Sampleprep Summary:Sample pre-processing for DS1: 50 mg of the peel and flesh of the date fruits were flash frozen in liquid nitrogen and extracted as previously described (PMID:21699588). Sample pre-processing for DS2 The beads were added to the pre-weighed frozen samples together with water (8 µL of per mg of sample) for homogenisation. The samples were continuously stirred on the GenoGrinder (Glen Mills GenoGrinder 2000, Germany) at 1000 strokes per minute for five minutes, to ensure complete homogenization. 100 µL of aliquot from each sample was transferred to the plates. The samples were loaded on three plates. To each sample, 450 µL of extraction solvent (MeOH with 10 µL /ml chlorophenylalanine, 2.5 µL /ml 2-fluorophenylglycine, 25 µg/ml d-6 cholestrol and 25 µL /ml tridecanoic acid) was added. The samples were then shaken on the GenoGrinder (GenoGrinder, Spex, USA) at 675 strokes per min for two minutes and centrifuged at 2000 rpm for 5 minutes on a Beckman centrifuge (Beckman GS-6R Centrifuge, USA) at 40C. The extracted samples were divided into equal parts for metabolomics analysis on the Gas Chromatography Mass Spectrometry (GC/MS) and the Orbitrap Elite accurate Liquid Chromatography Mass Spectrometry2 (LC-MS-MS) platforms. Four sets of samples were prepared by the Hamilton robot (Hamilton Star, Germany) by transferring 110 µL aliquots from each well to three PCR plates, each for LC positive, LC negative, replicate set and one to 250 µL auto sampler vial inserts for GC. All samples were dried for 120 minutes by using a Zymark Turbovap 96 (Zymark Turbovap, USA) followed by overnight incubation in a drybox to ensure optimal dryness of the sample. Sample processing DS1 and DS2 Metabolite measurements with Ultrahigh Performance Liquid Chromatography/Mass Spectroscopy (UPLC/MS/MS): The UPLC/MS/MS analysis was based on the Waters ACUITY ultra performance liquid chromatography (Waters Corporation, USA) and the ThermoFischer Scientific Orbitrap Elite high-resolution accurate mass spectrometer (Thermo Fischer Scientific Inc., USA) equipped with a heated electrospray ionization (HESI) source and an Orbitrap mass analyzer. The dried sample extracts for the LC positive and LC negative mode were reconstituted in acidic and basic LC- compatible solvents. Two independent injections were performed on each sample using separate dedicated columns for optimized acidic positive ions and the other for optimized basic negative ions. The acidic samples were reconstituted by gradient elution of water and methanol containing 0.1 % formic acid whereas; the basic samples were reconstituted by gradient elution of water and methanol containing 6.5mM ammonium bicarbonate (PMID: 19624122). The mass spectra analysis alternated between MS and data dependent MS2 scans using dynamic exclusion. Metabolite measurements with GC/MS: The samples assigned for the GC/MS analysis were further dried under vacuum desiccation for an entire day and derivatized under dried nitrogen using bistrimethyl-silyl-trifluoroacetamide (BSTFA). The GS/MS analysis was based on a Thermo FinniganTM TRACETM DSQTM (ThermoFinnigan, USA) fast-scanning single –quadrupole mass spectrophotometer using electron impact ionization source. The GC column was 5% phenyl and the temperature ramp range was from 40 to 3000 C in a time span of 16 minutes.

Combined analysis:

Analysis ID AN000777 AN000778 AN000779
Analysis type MS MS MS
Chromatography type GC Reversed phase Reversed phase
Chromatography system Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer Waters Acquity Waters Acquity
Column 5% diphenyl/ 95% dimethyl polysiloxane GC column C18 reversed phase column C18 reversed phase column
MS Type EI ESI ESI
MS instrument type Single quadrupole Orbitrap Orbitrap
MS instrument name Thermo Trace DSQ Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE
Units Counts per second (cps) Counts per second (cps) Counts per second (cps)

Chromatography:

Chromatography ID:CH000557
Chromatography Summary:The 5% diphenyl/ 95% dimethyl polysiloxane GC column and the temperature ramp was from 40° to 300° C in a 16 minute period. Samples were analyzed on a Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer using electron impact ionization. The instrument was tuned and calibrated for mass resolution and mass accuracy on a daily basis.
Instrument Name:Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer
Column Name:5% diphenyl/ 95% dimethyl polysiloxane GC column
Chromatography Type:GC
  
Chromatography ID:CH000558
Chromatography Summary:The LC/MS portion of the platform was based on a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a ThermoFisher Scientific Orbitrap Elite high resolution/accurate mass spectrometer, which consisted of a heated electrospray ionization (HESI) source and orbitrap mass analyzer operated at 30,000 mass resolution. The MS analysis alternated between MS and data-dependent MS2 scans using dynamic exclusion.
Instrument Name:Waters Acquity
Column Name:C18 reversed phase column
Chromatography Type:Reversed phase

MS:

MS ID:MS000684
Analysis ID:AN000777
Instrument Name:Thermo Trace DSQ
Instrument Type:Single quadrupole
MS Type:EI
Ion Mode:POSITIVE
  
MS ID:MS000685
Analysis ID:AN000778
Instrument Name:Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000686
Analysis ID:AN000779
Instrument Name:Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
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