Decoding Complexity in Synthetic Oligonucleotides: Unraveling Coeluting Isobaric Impurity Ions by High Resolution Mass Spectrometry

Abdullah, A. M.; Sommers, Cynthia; Rodriguez, Jason D.; Zhang, Deyi; Kozak, Darby; Hawes, Jessica; Sapru, Mohan; Yang, Kui

doi:10.1021/acs.analchem.3c05016

Title: Decoding Complexity in Synthetic Oligonucleotides: Unraveling Coeluting Isobaric Impurity Ions by High Resolution Mass Spectrometry

Journal Article · 28 December 2023 · Analytical Chemistry

DOI: https://doi.org/10.1021/acs.analchem.3c05016 · OSTI ID:2274719

Abdullah, A. M. ^[1]; Sommers, Cynthia ^[1]; Rodriguez, Jason D. ^[1]; Zhang, Deyi ^[2]; Kozak, Darby ^[2]; Hawes, Jessica ^[3]; Sapru, Mohan ^[4];

^[1]

Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri 63110, United States
Division of Therapeutic Performance I, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, United States
Division of New Drug Product III, Office of New Drug Product, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States

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Sponsoring Organization:: USDOE

OSTI ID:: 2274719

Alternate ID(s):: OSTI ID: 2471323

Journal Information:: Analytical Chemistry, Journal Name: Analytical Chemistry Journal Issue: 2 Vol. 96; ISSN 0003-2700

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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Analytical techniques currently used in the pharmaceutical industry for the quality control of RNA-based therapeutics and ongoing developments Demelenne, Alice; Servais, Anne-Catherine; Crommen, Jacques Journal of Chromatography A, Vol. 1651 https://doi.org/10.1016/j.chroma.2021.462283	journal	August 2021
Physicochemical property evaluation of modified oligonucleotides by traveling‐wave ion mobility mass spectrometry Omuro, Shogo; Yamaguchi, Takao; Kawase, Taiji Rapid Communications in Mass Spectrometry, Vol. 36, Issue 10 https://doi.org/10.1002/rcm.9279	journal	March 2022
Small alkyl amines as ion-pair reagents for the separation of positional isomers of impurities in phosphate diester oligonucleotides Roussis, Stilianos G.; Pearce, Megan; Rentel, Claus Journal of Chromatography A, Vol. 1594 https://doi.org/10.1016/j.chroma.2019.02.026	journal	June 2019
Antisense technology: an overview and prospectus Crooke, Stanley T.; Baker, Brenda F.; Crooke, Rosanne M. Nature Reviews Drug Discovery, Vol. 20, Issue 6 https://doi.org/10.1038/s41573-021-00162-z	journal	March 2021
Advancements in the characterisation of oligonucleotides by high performance liquid chromatography‐mass spectrometry in 2021: A short review Hannauer, Fabien; Black, Rachelle; Ray, Andrew D. Analytical Science Advances, Vol. 3, Issue 3-4 https://doi.org/10.1002/ansa.202100066	journal	April 2022
Tandem mass spectrometric sequence characterization of synthetic thymidine‐rich oligonucleotides Abdullah, A. M.; Sommers, Cynthia; Hawes, Jessica Journal of Mass Spectrometry, Vol. 57, Issue 4 https://doi.org/10.1002/jms.4819	journal	March 2022
Chromatographic approaches for the characterization and quality control of therapeutic oligonucleotide impurities El Zahar, N. M.; Magdy, N.; El‐Kosasy, A. M. Biomedical Chromatography, Vol. 32, Issue 1 https://doi.org/10.1002/bmc.4088	journal	October 2017
Determination of oligonucleotide deamination by high resolution mass spectrometry Rentel, Claus; DaCosta, Jaimie; Roussis, Stilianos Journal of Pharmaceutical and Biomedical Analysis, Vol. 173 https://doi.org/10.1016/j.jpba.2019.05.012	journal	September 2019
Challenges and Opportunities for Nucleic Acid Therapeutics Corey, David R.; Damha, Masad J.; Manoharan, Muthiah Nucleic Acid Therapeutics, Vol. 32, Issue 1 https://doi.org/10.1089/nat.2021.0085	journal	February 2022
Recent developments in the characterization of nucleic acids by liquid chromatography, capillary electrophoresis, ion mobility, and mass spectrometry (2010–2020) Santos, Inês C.; Brodbelt, Jennifer S. Journal of Separation Science, Vol. 44, Issue 1 https://doi.org/10.1002/jssc.202000833	journal	October 2020
The Limitless Future of RNA Therapeutics Damase, Tulsi Ram; Sukhovershin, Roman; Boada, Christian Frontiers in Bioengineering and Biotechnology, Vol. 9 https://doi.org/10.3389/fbioe.2021.628137	journal	March 2021
Determination of individual oligonucleotide impurities by small amine ion pair-RP HPLC MS and MS/MS: n − 1 impurities Roussis, Stilianos G.; Rodriguez, Andrew A.; Rentel, Claus Journal of Chromatography B, Vol. 1169 https://doi.org/10.1016/j.jchromb.2021.122611	journal	April 2021
High-resolution ion mobility spectrometry-mass spectrometry of isomeric/isobaric ribonucleotide variants Kenderdine, Thomas; Nemati, Reza; Baker, Andrew Journal of Mass Spectrometry, Vol. 55, Issue 2 https://doi.org/10.1002/jms.4465	journal	January 2020
Separation of phosphorothioated oligonucleotide diastereomers using multiplexed drift tube ion mobility mass spectrometry Demelenne, Alice; Nys, Gwenael; Nix, Cindy Analytica Chimica Acta, Vol. 1191 https://doi.org/10.1016/j.aca.2021.339297	journal	January 2022
RNA therapeutics on the rise Wang, Feng; Zuroske, Travis; Watts, Jonathan K. Nature Reviews Drug Discovery, Vol. 19, Issue 7 https://doi.org/10.1038/d41573-020-00078-0	journal	April 2020
Impurities in Oligonucleotide Drug Substances and Drug Products Capaldi, Daniel; Teasdale, Andy; Henry, Scott Nucleic Acid Therapeutics, Vol. 27, Issue 6 https://doi.org/10.1089/nat.2017.0691	journal	December 2017
Current State of Oligonucleotide Characterization Using Liquid Chromatography–Mass Spectrometry: Insight into Critical Issues Sutton, J. Michael; Guimaraes, Guilherme J.; Annavarapu, Vidya Journal of the American Society for Mass Spectrometry, Vol. 31, Issue 9 https://doi.org/10.1021/jasms.0c00179	journal	July 2020
Therapeutic Oligonucleotides, Impurities, Degradants, and Their Characterization by mass Spectrometry Pourshahian, Soheil Mass Spectrometry Reviews, Vol. 40, Issue 2 https://doi.org/10.1002/mas.21615	journal	December 2019
Assay, Purity, and Impurity Profile of Phosphorothioate Oligonucleotide Therapeutics by Ion Pair–HPLC–MS Rentel, Claus; Gaus, Hans; Bradley, Kym Nucleic Acid Therapeutics, Vol. 32, Issue 3 https://doi.org/10.1089/nat.2021.0056	journal	June 2022

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