Tandem mass spectrometry is a powerful analytical tool for the structural characterization of oligonucleotides. Highly charged oligonucleotides with a pyrimidine nucleobase in a terminal position were found to show a unique dissociation pattern.
The product ion spectra give evidence for the predominant release of a NCO^- moiety via a Retro-Diels-Alder mechanism. Knowledge about the origin of fragment ions is a prerequisite for the unambiguous interpretation of tandem mass spectra.

This work was carried out by Rahel Eberle and Adrien Nyakas in the group of PD Dr. Stefan Schürch.

References:

• A. Nyakas, R. Eberle, S. R. Stucki, S. Schürch;
  "More Than Charged Base Loss - Revisiting the Fragmentation of Highly Charged Oligonucleotides"
  J. Am. Soc. Mass. Spectrom., 25, 1155-1166, (2014); doi:10.1007/s13361-014-0873-4.