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

摘要

The gas phase fragmentation reactions of the [M + H]~+ ions derived from all 64 trimer oligodeoxynucleotides and 16 isomeric tetramer oligodeoxynucleotides each containing adenine, thymine, guanine, and cytosine were examined by electrospray ionization using multistage tandem mass spectrometry in a quadrupole ion trap. The MS/MS and MS~3 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 ≈ G > A 》 T), and position within the oligodeoxynucleotide sequence (5' > 3' > internal). These non-sequence [M + H - B_nH]~+ 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. MS~3 experiments were carried out to demonstrate that these ions can provide further sequence information. It is proposed that intramolecular proton transfer following base loss leads to cleavage of the 3' - C-O phosphodiester bond (relative to the site of base loss) to yield an ion-molecule complex, which then undergoes either proton transfer or direct dissociation to yield complementary w- and (a - B)-type ions. For the trimer oligodeoxynucleotides, loss of the 5' base yield 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 MS~3 spectra of the [M + H]~+ and [M + 2H]~(2+) ions of 16 isomeric tetramers were examined and found to follow the trends observed for the trimers.