Analysis of Oligonucleotide Impurities on the BioAccord System with ACQUITY Premier

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Catalin E. Doneanu, Chris Knowles, Jonathan Fox, Emma Harry, Ying Qing Yu, Joseph Fredette, Weibin Chen
Note applicative
Note applicative
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Oligonucleotide therapeutics have emerged in recent years as a powerful alternative to small molecule and protein therapeutics. Manufacturing and quality control of oligonucleotide therapeutics requires highly selective and sensitive LC-MS methods. One of the well-accepted mass spectrometry-based methods for oligonucleotide analysis is ion-pairing reversed-phase chromatography (IP-RP) separation followed by ESI-MS detection in negative ion mode. Using this method, an automated workflow for oligonucleotide analysis employing the BioAccord System – operating under compliance-ready waters_connect data acquisition and processing software – was recently described. A fully integrated LC-MS system comprised of an ACQUITY Premier UPLC BSM System, a Tunable Ultraviolet (TUV) Detector, and an ESI-Tof ACQUITY RDa Mass Detector (system shown in Figure 1) was used in this application note for the analysis of low-level oligonucleotide impurities. Here we investigated the capabilities of this UPLC system for intact mass confirmation of oligonucleotides and their associated impurities. All datasets were acquired in full scan MS mode on the BioAccord System with ACQUITY Premier and processed in waters_connect using the BayesSpray mass spectral charge deconvolution algorithm to produce accurate intact mass measurements for each compound.

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