Effect of oligonucleotide structural difference on matrix‐assisted laser desorption/ionization in‐source decay in comparison with collision‐induced dissociation fragmentation

Abstract

Mass spectrometry (MS) is an effective tool for the structural analysis of oligonucleotides. Currently, various modifications of oligonucleotides have been proposed to increase the efficacy and safety of oligonucleotide therapeutics. For MS-based structural characterization, the fragmentation behavior of modified oligonucleotides by MS must first be determined. The impact of the oligonucleotide structure on the in-source decay (ISD) of matrix-assisted laser desorption/ionization (MALDI) was examined using a new matrix and compared with collision-induced dissociation (CID) fragmentation behavior. When a part of the oligonucleotide structure was replaced, an impact was observed at the 3' side of the replaced structure. Among the oligonucleotide components considered herein, nucleobases most significantly impacted both ISD and CID fragmentation patterns. Compared with CID, ISD was less sensitive to structural differences. Because ISD fragmentation was less affected by various oligonucleotide modifications, MALDI is a useful and applicable method for the structural characterization or identification of various modified oligonucleotide therapeutics.