A landscape of sequence variants in 51 commercial antibody therapeutics

Abstract Background Sequence variants (SVs), unintended amino acid substitutions, represent a quality attribute of antibody therapeutics with potential safety and efficacy implications. Although control strategies are evolving, a comprehensive landscape of SVs in commercial antibody products, including biosimilars, innovators, and those from different expression systems or geographical origins, remains largely unexplored. Methods We systematically analyzed SVs in 51 commercial antibody therapeutics via optimized high-sensitivity LC-MS/MS peptide mapping. The panel encompassed originators and biosimilars from Chinese and multinational firms, eukaryotic (CHO, NS0) and prokaryotic (E. coli) expression systems, and diverse formats (mAbs, bispecifics, ADCs) and subclasses (IgG1, IgG2, IgG4). Results Across all products, 3006 SV occurrences were identified. The vast majority (92.5%) were ≤0.1% per site. Only 7.5% (226 SV occurrences) exceeded 0.1%, 2.4% (72 SV occurrences) exceeded 0.2%, and a minimal 0.4% (12 SV occurrences) exceeded 0.5%. SV levels of Chinese biosimilars and innovators were comparable to international counterparts. While prokaryotic-derived products showed more SVs above 0.2%, SV levels showed no significant correlation with antibody subclasses or formats. Batch-to-batch consistency was excellent across all products. Conclusions This study provides the largest empirical SV dataset for marketed antibody therapeutics to date. It demonstrates manufacturing processes maintain SV levels below 0.2% per site and reveals no inherent SV disparity across product origin, subclass, or format. Empirically, this 0.2% threshold serves as a pragmatic benchmark for commercial antibody quality control. These findings provide a science-based reference for establishing cell line screening in-process limits, refining industrial SV control strategies, and guiding regulatory science.