Fragmentation reactions of all 64 deprotonated trinucleotide and 16 mixed base tetranucleotide anions via tandem mass spectrometry in an ion trap

Abstract

The gas-phase fragmentation reactions of the [M-H]- ions derived from all 64 trinucleotides and 16 isomeric tetranucleotides each containing adenine, thymine, guanine and cytosine were examined using multistage mass spectrometry (MS/MS and MS3) collision-induced dissociation in an ion trap mass spectrometer. The initial fragmentation pathway involved neutral base loss predominantly from the 5′ terminus, along with minor 3′ and internal base loss in the order A > T > G > C to form [M-H-BH]- 'non-sequence' ions. The resultant [M-H-BH]-ions often fragment via intramolecular proton transfer with concomitant cleavage of the 3′ C-O phosphodiester bond to yield an ion-molecule complex, which underg..