Nanoelectrospray mass spectrometry/mass spectrometry for the analysis of modified oligoribonucleotides

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Abstract
Tandem mass spectrometry offers a fast and sensitive method to study the primary structure of oligonucleotides. 2′-O-methyl modified oligoribonucleotides, which are used as highly effective drugs in the antisense and ribozyme approach, were chosen to test the performance of mass spectrometry within these fields. Measurements were carried out on a triple quadrupole mass spectrometer equipped with a nanoelectrospray source. The collision energy was optimised for each sample to give relatively low energy settings. Mass spectrometry/mass spectrometry collision-induced decomposition spectra can give extensive information on the sequence, types of the modifications and their locations of oligonucleotides up to 20 units long. The mass differences between the ion series allow the modification sites to be localised. The w-series is dominant and allows the sequences and reading frames to be determined. For the same chain length wi-fragments dominate di-fragments and yi-fragments dominate bi-fragments. xi, zi and ci fragments were not observed.

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