Summary of Study ST000472

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 IDST000472
Study TitleEffect of the culture medium on the degradation of nucleotide triphosphates
Study TypeEndpoint measurement
Study SummaryThe effect of the Verduyn culture medium 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:SU001171
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
SA076983AG250615_2415 ATP
SA076984AG250615_2615 ATP
SA076985AG250615_2515 ATP
SA076986AG250615_2315 ATP
SA076987AG150715_6615 CTP
SA076988AG150715_7015 CTP
SA076989AG150715_7215 CTP
SA076990AG150715_6815 CTP
SA076991AG150715_3715 GTP
SA076992AG150715_4015 GTP
SA076993AG150715_3815 GTP
SA076994AG150715_3915 GTP
SA076995AG200715_1515 UTP
SA076996AG200715_1715 UTP
SA076997AG200715_2115 UTP
SA076998AG200715_1915 UTP
SA076967AG250615_21- ATP
SA076968AG250615_20- ATP
SA076969AG250615_18- ATP
SA076970AG250615_19- ATP
SA076971AG150715_58- CTP
SA076972AG150715_60- CTP
SA076973AG150715_62- CTP
SA076974AG150715_64- CTP
SA076975AG150715_34- GTP
SA076976AG150715_35- GTP
SA076977AG150715_33- GTP
SA076978AG150715_32- GTP
SA076979AG200715_9- UTP
SA076980AG200715_13- UTP
SA076981AG200715_11- UTP
SA076982AG200715_7- UTP
Showing results 1 to 32 of 32

Collection:

Collection ID:CO001165
Collection Summary:None

Treatment:

Treatment ID:TR001185
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:SP001178
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 AN001823
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:CH001292
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:MS001686
Analysis ID:AN001823
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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