Analysis of mononucleotides by tandem mass spectrometry: investigation of fragmentation pathways for phosphate- and ribose-modified nucleotide analogues.
Dominika StrzeleckaSebastian ChmielinskiSylwia BednarekJacek JemielityJoanna KowalskaPublished in: Scientific reports (2017)
Synthetic nucleotide and nucleic acid analogues are useful research tools and modern therapeutics. Hence, methods for the rapid and unambiguous identification of mononucleotides derived from organic syntheses or biological materials are of broad interest. Here, we analysed over 150 mononucleotides (mostly nucleoside 5'-mono-, 5'-di-, and 5'-triphosphates) and their structurally related nucleobase-, phosphate-, and ribose-modified analogues by electrospray tandem mass spectrometry (ESI/MS/MS), identifying characteristic fragmentation ions that may be helpful in structure determination. While positive-ion mode yielded fragments derived mainly from nucleobases, negative-ion mode provided insight into the structures of phosphoryl and phosphoribosyl moieties, enabling the determination of structural features such as the number of phosphate groups and the presence of ribose or phosphate substitutions. Based on these data, we proposed fragmentation pathways that were confirmed by experiments with [18O]-isotopologues. We demonstrated the utility of ESI(-)/MS/MS in the analysis of structurally related compounds by analysing isomeric and isobaric nucleotides and applying ESI(-)/MS/MS to rapid identification of nucleotide synthesis products. We formulated general rules regarding nucleotide structure-fragmentation pattern relationships and indicating characteristic fragmentation ions for the interpretation of ESI(-)/MS/MS spectra of nucleotides and their analogues. The ESI(-)/MS/MS spectra of all nucleotides are available in an on-line database, msTide, at www.msTide-db.com.
Keyphrases
- ms ms
- ultra high performance liquid chromatography
- tandem mass spectrometry
- high performance liquid chromatography
- liquid chromatography
- solid phase extraction
- gas chromatography
- liquid chromatography tandem mass spectrometry
- molecular docking
- simultaneous determination
- mass spectrometry
- nucleic acid
- high resolution mass spectrometry
- molecularly imprinted
- quantum dots
- big data
- emergency department
- electronic health record
- small molecule
- machine learning
- artificial intelligence
- escherichia coli
- molecular dynamics simulations
- biofilm formation
- pseudomonas aeruginosa
- loop mediated isothermal amplification