Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA026393

Local Sample ID:	99A
Subject ID:	SU000530
Subject Type:	Date palm fruit
Subject Species:	Phoenix dactylifera
Taxonomy ID:	42345
Species Group:	Plant

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Subject:

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

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
99A	SA026393	FL006656	Maajoun	date_variety

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.

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	C18 reversed phase
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
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