Fragmentation reactions of all 64 protonated trimer oligodeoxynucleotides and 16 mixed base tetramer oligodeoxynucleotides via tandem mass spectrometry in an ion trap

The gas phase fragmentation reactions of the [M + H](+) ions derived from a ll 64 trimer oligodeoxynucleotides and 16 isomeric tetramer oligodeoxynucle otides each containing adenine, thymine, guanine, and cytosine were examine d by electrospray ionization using multistage tandem mass spectrometry in a quadrupole ion trap. The MS/MS and MS3 spectra of the [M + 2H](2+) ions of 16 isomeric tetramer oligodeoxynucleotides were also examined. The initial collisionally induced dissociation (CID) reaction mechanism for [M + nH](n +) ions involves neutral base loss. The relative abundance of each of these neutral losses is dependent on the relative proton affinity (where C appro ximate to G > A >> T), and position within the oligodeoxynucleotide sequenc e (5' > 3' > internal). These non-sequence [M + H - BnH](+) ions (where B-n denotes the nucleobase in the nth position from the 5' position), provide information on the identity but not the position of the base. MS3 experimen ts were carried out to demonstrate that these ions can provide further sequ ence information. It is proposed that intramolecular proton transfer follow ing base loss leads to cleavage of the 3' - C-a phosphodiester bond (relati ve to the site of base loss) to yield an ion-molecule complex, which then u ndergoes either proton transfer or direct dissociation to yield complementa ry w- and (a - B)-type ions. For the trimer oligodeoxynucleotides, loss of the 5' base yields w(2)(+)-type ions, loss of the 3' base yields results in neutral water loss with formation of (a(3) - B-3)(+)-type ions and loss of the internal base yields w(1)(+) and (a(2) - B-2)(+)-type ions. The MS/MS and MS3 spectra of the [M + H](+) and [M + 2H](2+) ions of 16 isomeric tetr amers were examined and found to follow the trends observed for the trimers . (Int J Mass Spectrom 194 (2000) 145-164) (C) 2000 Elsevier Science B.V.