Summary of Study ST000473

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 IDST000473
Study TitleEffect of the chemical environment on the degradation of nucleotide triphosphates
Study TypeEndpoint measurement
Study SummaryThe influence of particular groups of compounds/metabolites, mainly comprising major central carbon metabolites including amino acids, organic acids, sugar phosphates, coenzymes, etc, 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 Date2016-09-10
PublicationsGil, 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
Raw Data AvailableYes
Analysis Type DetailLC-MS
Release Date2018-04-10
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:SU000494
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) Nucleotide Solution
SA024200AG290615_1515 ATP A
SA024201AG290615_1315 ATP A
SA024202AG290615_1415 ATP A
SA024203AG290615_1215 ATP A
SA024204AG290615_2315 ATP B
SA024205AG290615_2215 ATP B
SA024206AG290615_2415 ATP B
SA024207AG290615_2515 ATP B
SA024208AG290615_3415 ATP C
SA024209AG290615_3515 ATP C
SA024210AG290615_3315 ATP C
SA024211AG290615_3215 ATP C
SA024212AG290615_4415 ATP D
SA024213AG290615_4215 ATP D
SA024214AG290615_4515 ATP D
SA024215AG290615_4315 ATP D
SA024216AG290615_5415 ATP E
SA024217AG290615_5315 ATP E
SA024218AG290615_5515 ATP E
SA024219AG290615_5215 ATP E
SA024220AG290615_6415 ATP F
SA024221AG290615_6315 ATP F
SA024222AG290615_6515 ATP F
SA024223AG290615_6215 ATP F
SA024224AG290615_7215 ATP G
SA024225AG290615_7315 ATP G
SA024226AG290615_7415 ATP G
SA024227AG290615_7515 ATP G
SA024228AG290615_8315 ATP H
SA024229AG290615_8515 ATP H
SA024230AG290615_8415 ATP H
SA024231AG290615_8215 ATP H
SA024232AG050815_1315 CTP A
SA024233AG050815_1215 CTP A
SA024234AG050815_1415 CTP A
SA024235AG050815_1515 CTP A
SA024236AG050815_2315 CTP B
SA024237AG050815_2415 CTP B
SA024238AG050815_2215 CTP B
SA024239AG050815_2515 CTP B
SA024240AG050815_3215 CTP C
SA024241AG050815_3515 CTP C
SA024242AG050815_3415 CTP C
SA024243AG050815_3315 CTP C
SA024244AG050815_4315 CTP D
SA024245AG050815_4215 CTP D
SA024246AG050815_4515 CTP D
SA024247AG050815_4415 CTP D
SA024248AG050815_5515 CTP E
SA024249AG050815_5415 CTP E
SA024250AG050815_5215 CTP E
SA024251AG050815_5315 CTP E
SA024252AG050815_6515 CTP F
SA024253AG050815_6415 CTP F
SA024254AG050815_6315 CTP F
SA024255AG050815_6215 CTP F
SA024256AG050815_7515 CTP G
SA024257AG050815_7415 CTP G
SA024258AG050815_7215 CTP G
SA024259AG050815_7315 CTP G
SA024260AG050815_8215 CTP H
SA024261AG050815_8415 CTP H
SA024262AG050815_8515 CTP H
SA024263AG050815_8315 CTP H
SA024264AG300615_1215 GTP A
SA024265AG300615_1315 GTP A
SA024266AG300615_1415 GTP A
SA024267AG300615_1515 GTP A
SA024268AG300615_2515 GTP B
SA024269AG300615_2315 GTP B
SA024270AG300615_2415 GTP B
SA024271AG300615_2215 GTP B
SA024272AG300615_3515 GTP C
SA024273AG300615_3415 GTP C
SA024274AG300615_3315 GTP C
SA024275AG300615_3215 GTP C
SA024276AG300615_4415 GTP D
SA024277AG300615_4315 GTP D
SA024278AG300615_4515 GTP D
SA024279AG300615_4215 GTP D
SA024280AG300615_5515 GTP E
SA024281AG300615_5415 GTP E
SA024282AG300615_5215 GTP E
SA024283AG300615_5315 GTP E
SA024284AG300615_6315 GTP F
SA024285AG300615_6415 GTP F
SA024286AG300615_6215 GTP F
SA024287AG300615_6515 GTP F
SA024288AG300615_7215 GTP G
SA024289AG300615_7315 GTP G
SA024290AG300615_7415 GTP G
SA024291AG300615_7515 GTP G
SA024292AG300615_8215 GTP H
SA024293AG300615_8415 GTP H
SA024294AG300615_8515 GTP H
SA024295AG300615_8315 GTP H
SA024296AG111115_1415 UTP A
SA024297AG111115_1215 UTP A
SA024298AG111115_1315 UTP A
SA024299AG111115_1515 UTP A
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Collection:

Collection ID:CO000488
Collection Summary:None

Treatment:

Treatment ID:TR000508
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:SP000501
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 AN000737
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:CH000530
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:MS000654
Analysis ID:AN000737
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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