Summary of study ST000867

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

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 IDST000867
Study TitleMetabolic Profiling of Date Palm Fruits (part II)
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. This study includes updated date photographs and combined results data (GCMS/LCMS) and technical validation data, see downloadable files section to access this information.
Institute
Weill Cornell Medicine, Qatar
DepartmentBioinformatics Core
LaboratorySuhre Lab
Last NameSuhre
First NameKarsten
AddressEducation City
Emailnis2034@qatar-med.cornell.edu
Phone+97433888408
Submit Date2017-08-02
Analysis Type DetailGC/LC-MS
Release Date2017-10-03
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:SU000894
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
SA04814032.1Abel
SA048141112Adam adaalee
SA048142129Adam admaan
SA048143120Adam bujamaa
SA048144101Admoo
SA04814580Agalid
SA04814636.3Ajwa medina
SA04814760.2Allig
SA04814860Allig
SA04814913.2Ambara
SA04815047.2Amber - medina
SA04815147.1Amber - medina
SA04815227Aseel
SA04815327.2Aseel
SA04815427.3Aseel
SA0481551.3Aseela
SA0481561.2Aseela
SA0481576.2Ayash
SA048158146Aydea Al Qaseem
SA04815985Azaghzaw
SA04816085CAzaghzaw
SA04816185AAzaghzaw
SA048162144Barakawi
SA04816325.2Barani
SA04816496Bekri-khder
SA04816591Belahzit
SA04816691FBelahzit
SA04816791HBelahzit
SA04816891ABelahzit
SA04816912.3Berni
SA04817031.3Berni
SA04817131.2Berni
SA04817212.1Berni
SA04817384Bid-djaj
SA04817493Booserdoon
SA04817593DBooserdoon
SA04817693CBooserdoon
SA048177104Boozekri
SA04817898Boufegous rqiq
SA04817979Boukhanda
SA04818086Bouslikh
SA048181100Boussakri
SA04818278Bouzagza
SA04818316.2BuMaan
SA04818416.1BuMaan
SA04818530Burmeel
SA04818630.3Burmeel
SA048187149Dabbas
SA048188125Ddagla
SA048189128Deglet
SA048190108Deglet Bayda
SA048191117Deglet Nour
SA04819264.2Deglet Nour
SA04819364.3Deglet Nour
SA048194109Deglet Nour Hourra
SA04819551.2Dried dates
SA04819651.3Dried dates
SA048197114Fegous
SA04819871Fegous-ghlid
SA04819919.3Gagee
SA048200124Gharss
SA04820120.2Ghazelee
SA04820220.3Ghazelee
SA04820328.3Gorakh
SA04820462.2Grenja
SA048205143Grundeela/Qundeil
SA04820677Hafs
SA048207131Hameera
SA04820861.3Hamrata
SA04820961.1Hamrata
SA04821061Hamrata
SA048211133Hamray
SA048212151Harmayi Sadrati
SA04821322Ibrahim ( Iraqi Ajwa)
SA04821422.2Ibrahim ( Iraqi Ajwa)
SA04821515.3Jabri
SA04821673Jihl
SA04832989khalt-lhammar
SA04833089Ckhalt-lhammar
SA04833189Ekhalt-lhammar
SA04833289Bkhalt-lhammar
SA04833389Akhalt-lhammar
SA04833489Dkhalt-lhammar
SA0482175.3Khasoy
SA0482185.2Khasoy
SA04821955.3Kheneizi
SA04822024.3Khiyara
SA04822124.2Khiyara
SA04822224Khiyara
SA04833543.3khlas
SA04822350.1Khudry
SA04822450Khudry
SA04822535.2Khudry
SA048226142Kulma soda
SA04822781Lakhal
SA048228137Lulu
SA04822999CMaajoun
SA04823099DMaajoun
SA04823199BMaajoun
SA04823299AMaajoun
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Collection:

Collection ID:CO000888
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:TR000908
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:SP000901
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 AN001395 AN001396 AN001397
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:CH000977
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:CH000978
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:MS001287
Analysis ID:AN001395
Instrument Name:Thermo Trace DSQ
Instrument Type:Single quadrupole
MS Type:EI
Ion Mode:POSITIVE
  
MS ID:MS001288
Analysis ID:AN001396
Instrument Name:Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001289
Analysis ID:AN001397
Instrument Name:Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
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