Rapid identification of short oligonucleotide impurities using lithium adduct consolidated MALDI-TOF mass spectrometry

Published

August 8, 2022

Author(s)

Owen Becette, Anh Tran, Jace Jones, John Marino, Robert Brinson

Abstract

Nucleic acids are an increasingly popular platform for the development of pharmaceuticals to treat and prevent multiple diseases including those where traditional small molecule and protein-based drug development efforts have failed. Short oligonucleotide therapeutics, which consist of antisense oligonucleotides (ASOs) and short interfering ribonucleic acids (siRNAs), are prepared by solid phase chemical synthesis, which can generate various impuriies that have the potential to lower drug safety and efficacy. Drug substance-related impurities can be especially difficult to identify and characterize. To address this short coming, here we apply lithium adduct consolidation with matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) to afford a simplified, quick, and facile method for identification of a known drug substance impurity, isobutyryl (iBu) groups arising from incomplete deprotection during solid phase synthesis. We further employ high-resolution nuclear magnetic resonance (NMR) spectroscopy to confirm assessment of the iBu impurity. This lithium adduction consolidation method should find general applicability for routine quality assessment of synthetic oligonucleotides in both academic and industrial laboratories.

Citation

International Journal of Mass Spectrometry

Volume

481

Pub Type

Journals

Download Paper

https://doi.org/10.1016/j.ijms.2022.116913

Local Download

Keywords

MALDI TOF MS, NMR fingerprinting, oligonucleotide therapeutics, drug development, impurities, quality attributes, siRNA

Citation

Becette, O. , Tran, A. , Jones, J. , Marino, J. and Brinson, R. (2022), Rapid identification of short oligonucleotide impurities using lithium adduct consolidated MALDI-TOF mass spectrometry, International Journal of Mass Spectrometry, [online], https://doi.org/10.1016/j.ijms.2022.116913, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=934156 (Accessed October 13, 2025)