Summary of Study ST000470

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 IDST000470
Study TitleExahustive degradation of nucleotide triphosphates
Study TypeComparison of degradation kinetics
Study SummaryThe 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
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 Date2016-09-07
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:SU000491
Subject Type:Chemical
Subject Species:None
Subject Comments:Primary standards of nucleotide triphosphates (ATP, GTP, UTP and CTP).
Species Group:None

Factors:

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

mb_sample_id local_sample_id Time (mins) Nucleotide
SA023686AG070714_2210 ATP
SA023687AG070714_2010 ATP
SA023688AG070714_1810 ATP
SA023689AG070714_1710 ATP
SA023690AG070714_2110 ATP
SA023691AG070714_1910 ATP
SA023692AG260714_1110 CTP
SA023693AG260714_1310 CTP
SA023694AG260714_1410 CTP
SA023695AG260714_1210 CTP
SA023696AG220714_1710 GTP
SA023697AG220714_1910 GTP
SA023698AG220714_2010 GTP
SA023699AG220714_2210 GTP
SA023700AG240714_1310 UTP
SA023701AG240714_1410 UTP
SA023702AG240714_1610 UTP
SA023703AG240714_1510 UTP
SA023704AG070714_46120 ATP
SA023705AG070714_51120 ATP
SA023706AG070714_50120 ATP
SA023707AG070714_47120 ATP
SA023708AG070714_48120 ATP
SA023709AG070714_49120 ATP
SA023710AG260714_29120 CTP
SA023711AG260714_30120 CTP
SA023712AG260714_32120 CTP
SA023713AG260714_31120 CTP
SA023714AG220714_46120 GTP
SA023715AG220714_49120 GTP
SA023716AG220714_51120 GTP
SA023717AG220714_48120 GTP
SA023718AG240714_37120 UTP
SA023719AG240714_36120 UTP
SA023720AG240714_34120 UTP
SA023721AG240714_35120 UTP
SA023722AG070714_55180 ATP
SA023723AG070714_53180 ATP
SA023724AG070714_57180 ATP
SA023725AG070714_54180 ATP
SA023726AG070714_56180 ATP
SA023727AG070714_58180 ATP
SA023728AG260714_35180 CTP
SA023729AG260714_36180 CTP
SA023730AG260714_34180 CTP
SA023731AG260714_33180 CTP
SA023732AG220714_53180 GTP
SA023733AG220714_58180 GTP
SA023734AG220714_55180 GTP
SA023735AG220714_56180 GTP
SA023736AG240714_41180 UTP
SA023737AG240714_42180 UTP
SA023738AG240714_40180 UTP
SA023739AG240714_39180 UTP
SA023740AG070714_2920 ATP
SA023741AG070714_2820 ATP
SA023742AG070714_2520 ATP
SA023743AG070714_2420 ATP
SA023744AG070714_2620 ATP
SA023745AG070714_2720 ATP
SA023746AG260714_1520 CTP
SA023747AG260714_1820 CTP
SA023748AG260714_1720 CTP
SA023749AG260714_1620 CTP
SA023750AG220714_2420 GTP
SA023751AG220714_2620 GTP
SA023752AG220714_2920 GTP
SA023753AG220714_2720 GTP
SA023754AG240714_1920 UTP
SA023755AG240714_1820 UTP
SA023756AG240714_2020 UTP
SA023757AG240714_2120 UTP
SA023758AG070714_62240 ATP
SA023759AG070714_61240 ATP
SA023760AG070714_65240 ATP
SA023761AG070714_60240 ATP
SA023762AG070714_64240 ATP
SA023763AG070714_63240 ATP
SA023764AG260714_37240 CTP
SA023765AG260714_40240 CTP
SA023766AG260714_38240 CTP
SA023767AG260714_39240 CTP
SA023768AG220714_60240 GTP
SA023769AG220714_62240 GTP
SA023770AG220714_63240 GTP
SA023771AG220714_65240 GTP
SA023772AG240714_44240 UTP
SA023773AG240714_47240 UTP
SA023774AG240714_46240 UTP
SA023775AG240714_45240 UTP
SA023776AG070714_69300 ATP
SA023777AG070714_72300 ATP
SA023778AG070714_68300 ATP
SA023779AG070714_71300 ATP
SA023780AG070714_70300 ATP
SA023781AG070714_67300 ATP
SA023782AG260714_42300 CTP
SA023783AG260714_43300 CTP
SA023784AG260714_41300 CTP
SA023785AG260714_44300 CTP
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Collection:

Collection ID:CO000485
Collection Summary:None

Treatment:

Treatment ID:TR000505
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:SP000498
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 AN000734
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
Ion Mode NEGATIVE
Units Peak area

Chromatography:

Chromatography ID:CH000527
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:MS000651
Analysis ID:AN000734
Instrument Name:Waters Synapt-G2-Si
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:2KV
Dry Gas Flow:Argon
Source Temperature:SOURCE_TEMPERATURE
Desolvation Temperature:DESOLVATION_TEMPERATURE
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