Sequence Analysis of Antisense Oligonucleotides Using a MALDI-8030 Benchtop MALDI-TOF Mass Spectrometer

User Benefits

- MALDI-ISD enables simple and reliable sequencing of antisense oligonucleotide. - There is no need to interpret complicated MS/MS spectra, which saves labor and time. - Oligonucleotide therapeutics can be analyzed using a simple and affordable benchtop instrument.

Introduction

Oligonucleotidetherapeutics have recently attracted particular attention as a new pharmaceutical modality. Unlike biopharmaceuticals, oligonucleotide therapeutics can be produced by cost-effective chemical synthesis. The development and standardization of analytical methods for quality control are still in progress, with efforts being made in collaboration with industry and academia. Mass spectrometry (MS) has now become an established analytical tool for analyzing biopolymers, such as oligonucleotides, proteins, and glycans, thanks to the development of various soft ionization methods and instrument performance improvements. Although tandem mass spectrometry (MS/MS) is generally used to sequence oligonucleotide, collision-induced dissociation (CID), the technique typically used for conventional ion cleavage, has been problematic because of the difficulty in producing fragments that suggest particularly internal sequences. Matrix-assisted laser desorption/ionization (MALDI) is used as a technique for ionizing various biopolymers, including oligonucleotides. MALDI can softly ionize a sample without causing unwanted fragmentation. However, by using a specific MALDI matrix with increased laser irradiation, it is possible to cause ionization and fragmentation at the same time. Then the resulting in-source decay (ISD) fragment ions can be used for structural analysis. MALDI-ISD fragmentation of oligonucleotides provides successive fragment ions by simple cleavages and is therefore highly useful for simple sequencing of oligonucleotides. This Application News describes an example in which synthetic antisense oligonucleotides were subjected to ISD fragmentation using the Shimadzu MALDI-8030 benchtop linear MALDI-TOF mass spectrometer, and the resulting mass spectra were analyzed for sequence assignment with LabSolutions Insight Biologics, a software designed for oligonucleotide sequence characterization.

December 25, 2022 GMT