Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery

• DOI: 10.1007/s13361-016-1580-0
• Publication Date: 2017-01-20T02:02:27Z
• Authors: K. Ilker Sen; Wilfred H Tang; Shruti Nayak; Yong J Kil; Marshall Bern; Berk Ozoglu; Beatrix Ueberheide; Darryl Davis; Christopher Becker
• Keywords: 0301 basic medicine; Biological Products; 0303 health sciences; Antibodies, Monoclonal; 3. Good health; Mice; 03 medical and health sciences; Sequence Analysis, Protein; Tandem Mass Spectrometry; Drug Discovery; Animals; Humans; Amino Acid Sequence; Databases, Protein

Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis. Here, we present a novel method to automatically de novo sequence antibodies using mass spectrometry and the Supernovo software. The robustness of the algorithm is demonstrated through a series of stress tests. Graphical Abstract ᅟ.