Multilevel─Intact, Subunits, and Peptides─Characterization of Antibody-Based Therapeutics by a Single-Column LC–MS Setup

A comprehensive characterization of biotherapeutics, mandated by regulatory authorities, requires analyses of a protein drug at multiple structure levels. Such multilevel characterization can be performed by mass spectrometry (MS), with established conventional MS-based assays of product quality attributes (PQAs) comprising intact protein and subunit middle-up MS with analytes resolved on a C4 column, and bottom-up peptide mapping with analytes resolved on a C18 column. Recent advances in MS have facilitated the increasing use of middle-down analysis, expanding the qualitative analytical capability of MS for protein characterization. Recent studies using less-retentive reversed-phase LC in bottom-up MS also offer an opportunity for streamlining equipment configuration to a single-column LC–MS setup for multilevel characterization of therapeutic proteins. In this study, we developed a robust middle-down LC–MS method on a ZenoTOF 7600 and evaluated a C4 LC–MS setup for the characterization of NISTmAb, RG7221 bispecific antibody (bsAb), and Fc-fusion etanercept by intact protein, subunit middle-up/down, and bottom-up analyses. Successful multilevel characterization of the analytes using C4 LC–MS was demonstrated; notably, high sequence coverage and comprehensive post-translational modification profiling, including the mapping of all 13 O- and 3 N-glycosylation sites on etanercept in a single run, were obtained by bottom-up C4 LC–MS. This is also the first report on middle-down analysis of the major etanercept TNFR and Fc subunit glycoforms. A streamlined single-column LC–MS setup will enable more robust and efficient MS workflows for PQA assessment and simplify the integration of an LC–MS analyzer as a process analytical technology instrument for biopharma applications.