Location of the Na+ cation in negative ions of DNA evidenced by using MS2 experiments in ion trap mass spectrometry

Collision-induced dissociation (CID) spectra of deprotonated molecules prepared from a variety of monocationized homonucleotides and heteronucleotides, using an external nanoelectrospray source with an ion trap mass spectrometer, are described. Under such conditions, the achieved sensitivity in the negative ion mode is sufficient to obtain useful CID mass spectra of deprotonated oligonucleotides from doubly or triply charged negative ions. Results from the analysis of the daughter ions show that the negative charges are located on 5'- or 3'-terminal sites whereas the salt group is at a central position. The cation appears to remain stationary during the CID process. Moreover, evidence exists that the central cation site is neither influenced by the size of the oligonucleotide nor by the nature of the 5'- or 3'-terminus base, which indicates particular stability for the doubly or triply charged quasimolecular anion. (Int J Mass Spectrom 190/191 (1999) 303-312) (C) 1999 Elsevier Science B.V.