Mass spectrometry of small nucleotides

Our laboratory generates hundreds of novel nucleotide structures every year. Some of the syntheses are performed at a very low scale, which is not sufficient for structure confirmation by traditional analytical techniques (NMR). We have found that tandem mass spectrometry in negative ion mode (ESI(−)/MS/MS) is a very useful technique with low sample consumption, enabling the determination of nucleotide structural features such as the number of phosphate groups and the presence of ribose or phosphate substitutions. ESI(−)/MS/MS is useful in the analysis of structurally related compounds e.g. isomeric and isobaric nucleotides and rapid identification of nucleotide synthesis products. Based on the analysis of 150+ nucleotides we formulated general rules regarding nucleotide structure–fragmentation pattern relationships and indicating characteristic fragmentation ions to facilitate the interpretation of ESI(−)/MS/MS spectra of nucleotides and their analogues. To share this knowledge in the best possible way we created an on-line database of nucleotide fragmentation spectra, msTide, available at:

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