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
Raw Data File Type(s).raw
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) Nucleotide Yeast Matrix
SA076807AG140814_2812 ATP No
SA076808AG140814_3012 ATP No
SA076809AG140814_2912 ATP No
SA076810AG140814_2712 ATP No
SA076811AG130814_6512 ATP Yes
SA076812AG130814_6212 ATP Yes
SA076813AG130814_6312 ATP Yes
SA076814AG130814_6412 ATP Yes
SA076815AG251114_2712 CTP No
SA076816AG251114_3012 CTP No
SA076817AG251114_2812 CTP No
SA076818AG251114_2912 CTP No
SA076819AG251114_6512 CTP Yes
SA076820AG251114_6412 CTP Yes
SA076821AG251114_6212 CTP Yes
SA076822AG251114_6312 CTP Yes
SA076823AG271014_3012 GTP No
SA076824AG271014_2712 GTP No
SA076825AG271014_2912 GTP No
SA076826AG271014_2812 GTP No
SA076827AG271014_6312 GTP Yes
SA076828AG271014_6512 GTP Yes
SA076829AG271014_6212 GTP Yes
SA076830AG271014_6412 GTP Yes
SA076831AG261114_2812 UTP No
SA076832AG261114_2712 UTP No
SA076833AG261114_3012 UTP No
SA076834AG261114_2912 UTP No
SA076835AG261114_6212 UTP Yes
SA076836AG261114_6412 UTP Yes
SA076837AG261114_6512 UTP Yes
SA076838AG261114_6312 UTP Yes
SA076839AG140814_3215 ATP No
SA076840AG140814_3315 ATP No
SA076841AG140814_3415 ATP No
SA076842AG140814_3515 ATP No
SA076843AG130814_7015 ATP Yes
SA076844AG130814_6915 ATP Yes
SA076845AG130814_6715 ATP Yes
SA076846AG130814_6815 ATP Yes
SA076847AG251114_3215 CTP No
SA076848AG251114_3415 CTP No
SA076849AG251114_3515 CTP No
SA076850AG251114_3315 CTP No
SA076851AG251114_6715 CTP Yes
SA076852AG251114_6815 CTP Yes
SA076853AG251114_6915 CTP Yes
SA076854AG251114_7015 CTP Yes
SA076855AG271014_3515 GTP No
SA076856AG271014_3415 GTP No
SA076857AG271014_3315 GTP No
SA076858AG271014_3215 GTP No
SA076859AG271014_6915 GTP Yes
SA076860AG271014_7015 GTP Yes
SA076861AG271014_6715 GTP Yes
SA076862AG271014_6815 GTP Yes
SA076863AG261114_3515 UTP No
SA076864AG261114_3415 UTP No
SA076865AG261114_3315 UTP No
SA076866AG261114_3215 UTP No
SA076867AG261114_6915 UTP Yes
SA076868AG261114_6815 UTP Yes
SA076869AG261114_7015 UTP Yes
SA076870AG261114_6715 UTP Yes
SA076871AG140814_123 ATP No
SA076872AG140814_153 ATP No
SA076873AG140814_133 ATP No
SA076874AG140814_143 ATP No
SA076875AG130814_493 ATP Yes
SA076876AG130814_503 ATP Yes
SA076877AG130814_473 ATP Yes
SA076878AG130814_483 ATP Yes
SA076879AG251114_153 CTP No
SA076880AG251114_143 CTP No
SA076881AG251114_133 CTP No
SA076882AG251114_123 CTP No
SA076883AG251114_503 CTP Yes
SA076884AG251114_493 CTP Yes
SA076885AG251114_483 CTP Yes
SA076886AG251114_473 CTP Yes
SA076887AG271014_123 GTP No
SA076888AG271014_153 GTP No
SA076889AG271014_133 GTP No
SA076890AG271014_143 GTP No
SA076891AG271014_493 GTP Yes
SA076892AG271014_473 GTP Yes
SA076893AG271014_483 GTP Yes
SA076894AG271014_503 GTP Yes
SA076895AG261114_123 UTP No
SA076896AG261114_133 UTP No
SA076897AG261114_153 UTP No
SA076898AG261114_143 UTP No
SA076899AG261114_493 UTP Yes
SA076900AG261114_503 UTP Yes
SA076901AG261114_483 UTP Yes
SA076902AG261114_473 UTP Yes
SA076903AG140814_206 ATP No
SA076904AG140814_196 ATP No
SA076905AG140814_176 ATP No
SA076906AG140814_186 ATP 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:5 mM ammonium acetate in water at pH 9.9
Solvent B: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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