Study of the mass spectrometric fragmentation of pseudouridine: comparison of fragmentation data obtained by matrix-assisted laser desorption/ionisation post-source decay, electrospray ion trap multistage mass spectrometry, and by a method utilising electrospray quadrupole time-of-flight tandem mass spectrometry and in-source fragmentation.

Many nucleosides and their modified forms have been studied by mass spectrometry elaborating the detailed fragmentation pathways under MS2 and MS(n) conditions. Although the C-nucleoside pseudouridine has been fragmented and studied briefly, usually amongst many other nucleosides, it has not been investigated to the same extent as other nucleosides. In this report a number of different mass spectrometric techniques are applied to obtain a fuller picture of pseudouridine fragmentation. At the same time this study is used to compare different tandem mass spectrometric techniques, including a novel methodology utilising a quadrupole time-of-flight (Q-ToF) instrument for MS(n) analysis comparable with that available with an ion trap mass spectrometer. (c) 2005 John Wiley & Sons, Ltd.