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 undergoes either direct dissociation or proton transfer to yield the w-type or (a–B)-type ‘sequence’ ions respectively.