Summary of Study ST000471

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 PR000361. The data can be accessed directly via it's Project DOI: 10.21228/M8CW21 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000471
Study TitleEffect of a complex matrix on the degradation of nucleotide triphosphates
Study TypeComparison of degradation kinetics
Study SummaryThe effect of a complex cellular matrix extracted from yeast (S. cerevisiae, strain YSBN6 (MATa; genotype: FY3 ho::HphMX4 derived from the S288C parental strain)) on the degradation profiles of nucleotide triphosphates extracted under typical boiling ethanol conditions was evaluated.
Institute
University of Groningen
DepartmentAnalytical Biochemistry
Last NameBischoff
First NameRainer
AddressAntonius Deusinglaan 1 (XB20), Building 3226, room 601, 9713 AV Groningen, The Netherlands
Emailr.p.h.bischoff@rug.nl
PhoneNA
Submit Date2016-09-13
Raw Data AvailableYes
Analysis Type DetailLC-MS
Release Date2016-10-10
Release Version1
Rainer Bischoff Rainer Bischoff
https://dx.doi.org/10.21228/M8CW21
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000361
Project DOI:doi: 10.21228/M8CW21
Project Title:Degradation of Nucleotides under different chemical environments
Project Summary:The degradation kinetics of nucleotide triphosphates (ATP, GTP, UTP and CTP) were evaluated under boiling ethanol extraction conditions (95°C) during 0 to 300 minutes.
Institute:University of Groningen
Department:Analytical Biochemistry
Last Name:Bischoff
First Name:Rainer
Address:Antonius Deusinglaan 1 (XB20), Building 3226, room 601, 9713 AV Groningen, The Netherlands
Email:r.p.h.bischoff@rug.nl
Phone:NA
Publications:Gil, A., Siegel, D., Bonsing-Vedelaar, S. et al. The degradation of nucleotide triphosphates extracted under boiling ethanol conditions is prevented by the yeast cellular matrix. Metabolomics (2017) 13:1. doi:10.1007/s11306-016-1140-4

Subject:

Subject ID:SU001170
Subject Type:Chemical
Subject Species:None
Subject Comments:Primary standards of nucleotide triphosphates (ATP, GTP, UTP and CTP).

Factors:

Subject type: Chemical; Subject species: None (Factor headings shown in green)

mb_sample_id local_sample_id Time (mins)
SA076807AG140814_2812 | Nucleotide:ATP | Yeast Matrix:No
SA076808AG140814_3012 | Nucleotide:ATP | Yeast Matrix:No
SA076809AG140814_2912 | Nucleotide:ATP | Yeast Matrix:No
SA076810AG140814_2712 | Nucleotide:ATP | Yeast Matrix:No
SA076811AG130814_6512 | Nucleotide:ATP | Yeast Matrix:Yes
SA076812AG130814_6212 | Nucleotide:ATP | Yeast Matrix:Yes
SA076813AG130814_6312 | Nucleotide:ATP | Yeast Matrix:Yes
SA076814AG130814_6412 | Nucleotide:ATP | Yeast Matrix:Yes
SA076815AG251114_2712 | Nucleotide:CTP | Yeast Matrix:No
SA076816AG251114_3012 | Nucleotide:CTP | Yeast Matrix:No
SA076817AG251114_2812 | Nucleotide:CTP | Yeast Matrix:No
SA076818AG251114_2912 | Nucleotide:CTP | Yeast Matrix:No
SA076819AG251114_6512 | Nucleotide:CTP | Yeast Matrix:Yes
SA076820AG251114_6412 | Nucleotide:CTP | Yeast Matrix:Yes
SA076821AG251114_6212 | Nucleotide:CTP | Yeast Matrix:Yes
SA076822AG251114_6312 | Nucleotide:CTP | Yeast Matrix:Yes
SA076823AG271014_3012 | Nucleotide:GTP | Yeast Matrix:No
SA076824AG271014_2712 | Nucleotide:GTP | Yeast Matrix:No
SA076825AG271014_2912 | Nucleotide:GTP | Yeast Matrix:No
SA076826AG271014_2812 | Nucleotide:GTP | Yeast Matrix:No
SA076827AG271014_6312 | Nucleotide:GTP | Yeast Matrix:Yes
SA076828AG271014_6512 | Nucleotide:GTP | Yeast Matrix:Yes
SA076829AG271014_6212 | Nucleotide:GTP | Yeast Matrix:Yes
SA076830AG271014_6412 | Nucleotide:GTP | Yeast Matrix:Yes
SA076831AG261114_2812 | Nucleotide:UTP | Yeast Matrix:No
SA076832AG261114_2712 | Nucleotide:UTP | Yeast Matrix:No
SA076833AG261114_3012 | Nucleotide:UTP | Yeast Matrix:No
SA076834AG261114_2912 | Nucleotide:UTP | Yeast Matrix:No
SA076835AG261114_6212 | Nucleotide:UTP | Yeast Matrix:Yes
SA076836AG261114_6412 | Nucleotide:UTP | Yeast Matrix:Yes
SA076837AG261114_6512 | Nucleotide:UTP | Yeast Matrix:Yes
SA076838AG261114_6312 | Nucleotide:UTP | Yeast Matrix:Yes
SA076839AG140814_3215 | Nucleotide:ATP | Yeast Matrix:No
SA076840AG140814_3315 | Nucleotide:ATP | Yeast Matrix:No
SA076841AG140814_3415 | Nucleotide:ATP | Yeast Matrix:No
SA076842AG140814_3515 | Nucleotide:ATP | Yeast Matrix:No
SA076843AG130814_7015 | Nucleotide:ATP | Yeast Matrix:Yes
SA076844AG130814_6915 | Nucleotide:ATP | Yeast Matrix:Yes
SA076845AG130814_6715 | Nucleotide:ATP | Yeast Matrix:Yes
SA076846AG130814_6815 | Nucleotide:ATP | Yeast Matrix:Yes
SA076847AG251114_3215 | Nucleotide:CTP | Yeast Matrix:No
SA076848AG251114_3415 | Nucleotide:CTP | Yeast Matrix:No
SA076849AG251114_3515 | Nucleotide:CTP | Yeast Matrix:No
SA076850AG251114_3315 | Nucleotide:CTP | Yeast Matrix:No
SA076851AG251114_6715 | Nucleotide:CTP | Yeast Matrix:Yes
SA076852AG251114_6815 | Nucleotide:CTP | Yeast Matrix:Yes
SA076853AG251114_6915 | Nucleotide:CTP | Yeast Matrix:Yes
SA076854AG251114_7015 | Nucleotide:CTP | Yeast Matrix:Yes
SA076855AG271014_3515 | Nucleotide:GTP | Yeast Matrix:No
SA076856AG271014_3415 | Nucleotide:GTP | Yeast Matrix:No
SA076857AG271014_3315 | Nucleotide:GTP | Yeast Matrix:No
SA076858AG271014_3215 | Nucleotide:GTP | Yeast Matrix:No
SA076859AG271014_6915 | Nucleotide:GTP | Yeast Matrix:Yes
SA076860AG271014_7015 | Nucleotide:GTP | Yeast Matrix:Yes
SA076861AG271014_6715 | Nucleotide:GTP | Yeast Matrix:Yes
SA076862AG271014_6815 | Nucleotide:GTP | Yeast Matrix:Yes
SA076863AG261114_3515 | Nucleotide:UTP | Yeast Matrix:No
SA076864AG261114_3415 | Nucleotide:UTP | Yeast Matrix:No
SA076865AG261114_3315 | Nucleotide:UTP | Yeast Matrix:No
SA076866AG261114_3215 | Nucleotide:UTP | Yeast Matrix:No
SA076867AG261114_6915 | Nucleotide:UTP | Yeast Matrix:Yes
SA076868AG261114_6815 | Nucleotide:UTP | Yeast Matrix:Yes
SA076869AG261114_7015 | Nucleotide:UTP | Yeast Matrix:Yes
SA076870AG261114_6715 | Nucleotide:UTP | Yeast Matrix:Yes
SA076871AG140814_123 | Nucleotide:ATP | Yeast Matrix:No
SA076872AG140814_153 | Nucleotide:ATP | Yeast Matrix:No
SA076873AG140814_133 | Nucleotide:ATP | Yeast Matrix:No
SA076874AG140814_143 | Nucleotide:ATP | Yeast Matrix:No
SA076875AG130814_493 | Nucleotide:ATP | Yeast Matrix:Yes
SA076876AG130814_503 | Nucleotide:ATP | Yeast Matrix:Yes
SA076877AG130814_473 | Nucleotide:ATP | Yeast Matrix:Yes
SA076878AG130814_483 | Nucleotide:ATP | Yeast Matrix:Yes
SA076879AG251114_153 | Nucleotide:CTP | Yeast Matrix:No
SA076880AG251114_143 | Nucleotide:CTP | Yeast Matrix:No
SA076881AG251114_133 | Nucleotide:CTP | Yeast Matrix:No
SA076882AG251114_123 | Nucleotide:CTP | Yeast Matrix:No
SA076883AG251114_503 | Nucleotide:CTP | Yeast Matrix:Yes
SA076884AG251114_493 | Nucleotide:CTP | Yeast Matrix:Yes
SA076885AG251114_483 | Nucleotide:CTP | Yeast Matrix:Yes
SA076886AG251114_473 | Nucleotide:CTP | Yeast Matrix:Yes
SA076887AG271014_123 | Nucleotide:GTP | Yeast Matrix:No
SA076888AG271014_153 | Nucleotide:GTP | Yeast Matrix:No
SA076889AG271014_133 | Nucleotide:GTP | Yeast Matrix:No
SA076890AG271014_143 | Nucleotide:GTP | Yeast Matrix:No
SA076891AG271014_493 | Nucleotide:GTP | Yeast Matrix:Yes
SA076892AG271014_473 | Nucleotide:GTP | Yeast Matrix:Yes
SA076893AG271014_483 | Nucleotide:GTP | Yeast Matrix:Yes
SA076894AG271014_503 | Nucleotide:GTP | Yeast Matrix:Yes
SA076895AG261114_123 | Nucleotide:UTP | Yeast Matrix:No
SA076896AG261114_133 | Nucleotide:UTP | Yeast Matrix:No
SA076897AG261114_153 | Nucleotide:UTP | Yeast Matrix:No
SA076898AG261114_143 | Nucleotide:UTP | Yeast Matrix:No
SA076899AG261114_493 | Nucleotide:UTP | Yeast Matrix:Yes
SA076900AG261114_503 | Nucleotide:UTP | Yeast Matrix:Yes
SA076901AG261114_483 | Nucleotide:UTP | Yeast Matrix:Yes
SA076902AG261114_473 | Nucleotide:UTP | Yeast Matrix:Yes
SA076903AG140814_206 | Nucleotide:ATP | Yeast Matrix:No
SA076904AG140814_196 | Nucleotide:ATP | Yeast Matrix:No
SA076905AG140814_176 | Nucleotide:ATP | Yeast Matrix:No
SA076906AG140814_186 | Nucleotide:ATP | Yeast Matrix:No
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Collection:

Collection ID:CO001164
Collection Summary:None

Treatment:

Treatment ID:TR001184
Treatment Summary:Pure solutions of nucleotide triphosphates (ATP, GTP, CTP and UTP) were incubated under boiling ethanol conditions (95°C) during 0, 5, 10, 20, 30, 60, 120, 180, 240 and 300 minutes.
Treatment:Abiotic

Sample Preparation:

Sampleprep ID:SP001177
Sampleprep Summary:Tubes containing 496 µL of 75% (aq) ethanol were preheated at 95°C for 5 min, followed by the addition of 4 µL of each nucleotide standard solution (500 µM) and vigorous mixing. 4 µL of solutions “A” to “H” were added to the reaction mixture and the samples were incubated at 95°C under shaking for 0 and 15 min. Reactions were stopped by snap-freezing in liquid nitrogen and samples were stored on dry ice. Subsequently, samples were thawed and 20 µL of the 13C15N-labeled internal standard solution were added for quantitative analysis. Excess solvent was evaporated under a stream of nitrogen without heating. Finally, samples were reconstituted in 200 µL of acetonitrile-water 70:30 and stored at –40°C until analysis by LC-MS. After the experimental procedure the final concentration of all components in solutions “A” to “H” was 10 µM. Compounds to be tested were divided into eight groups containing approximately ten compounds each, mainly comprising major central carbon metabolites including amino acids, organic acids, sugar phosphates, coenzymes, etc (Table 1).
Processing Method:Preparation of reagents, dilution, solvent removal under a stream of nitrogen without heating and reconstitution
Extraction Method:Boiling ethanol (95°C)
Extract Enrichment:Evaporation of excess of solvent under a stream of nitrogen without heating.
Extract Storage:-40C
Sample Resuspension:200 µL of acetonitrile-water 70:30

Combined analysis:

Analysis ID AN001822
Analysis type MS
Chromatography type HILIC
Chromatography system Waters Acquity
Column Phenomenex Luna NH2 (100 x 2.0mm,3um)
MS Type ESI
MS instrument type QTOF
MS instrument name Waters Synapt G2 Si QTOF
Ion Mode NEGATIVE
Units Peak area

Chromatography:

Chromatography ID:CH001291
Chromatography Summary:Untargeted HILIC Method
Instrument Name:Waters Acquity
Column Name:Phenomenex Luna NH2 (100 x 2.0mm,3um)
Column Temperature:20C
Flow Gradient:30% eluent A to 99% eluent A in 8 min, followed by isocratic elution at 99% eluent A until 14 min. A conditioning cycle of 6 min with the initial proportions of eluents A and B was performed prior to the next analysis.
Flow Rate:0.25 mL/min
Sample Injection:10 µL
Solvent A:100% water; 5 mM ammonium acetate, pH 9.9
Solvent B:100% acetonitrile
Analytical Time:20 min
Chromatography Type:HILIC

MS:

MS ID:MS001685
Analysis ID:AN001822
Instrument Name:Waters Synapt G2 Si QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:2KV
Collision Energy:2 V for the low-collision energy scan, and 10–30 V for the high-collision energy scan
Dry Gas Flow:Argon
Source Temperature:150C
Desolvation Temperature:400C
Scan Range Moverz:50 to 1200 Da
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