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

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 spectro metry (MS/MS and MS3) collision-induced dissociation in an ion trap mass sp ectrometer. The initial fragmentation pathway involved neutral base loss pr edominantly from the 5' terminus, along with minor 3' and internal base los s in the order A > T > G > C to form [M-H-BH](-) 'non-sequence' ions. The r esultant [M-H-BH](-) ions often fragment via intramolecular proton transfer with concomitant cleavage of the 3' C-O phosphodiester bond to yield an io n-molecule complex, which undergoes either direct dissociation or proton tr ansfer to yield the w-type or (a-B)-type 'sequence' ions respectively.