title: Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery.
abstract: 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.
authors.affiliation: Protein Metrics Inc, 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA. sen@proteinmetrics.com.
authors.forename: K Ilker
authors.identifier: 0000-0003-0756-9518
authors.initials: KI
authors.lastname: Sen
authors.affiliation: Protein Metrics Inc, 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA.
authors.forename: Wilfred H
authors.initials: WH
authors.lastname: Tang
authors.affiliation: Langone Medical Center, New York University, 430 East 29th street, 8th floor room 860, New York, NY, 10016, USA.
authors.forename: Shruti
authors.initials: S
authors.lastname: Nayak
authors.affiliation: Protein Metrics Inc, 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA.
authors.forename: Yong J
authors.initials: YJ
authors.lastname: Kil
authors.affiliation: Protein Metrics Inc, 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA.
authors.forename: Marshall
authors.initials: M
authors.lastname: Bern
authors.affiliation: Janssen Research and Development, LLC, 1400 McKean Road, Spring House, PA, 19477, USA.
authors.forename: Berk
authors.initials: B
authors.lastname: Ozoglu
authors.affiliation: Langone Medical Center, New York University, 430 East 29th street, 8th floor room 860, New York, NY, 10016, USA.
authors.forename: Beatrix
authors.initials: B
authors.lastname: Ueberheide
authors.affiliation: Janssen Research and Development, LLC, 1400 McKean Road, Spring House, PA, 19477, USA.
authors.forename: Darryl
authors.initials: D
authors.lastname: Davis
authors.affiliation: Protein Metrics Inc, 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Becker
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000911:Antibodies, Monoclonal / Q000737:chemistry*; D001688:Biological Products / Q000737:chemistry; D030562:Databases, Protein; D055808:Drug Discovery / Q000379:methods*; D006801:Humans; D051379:Mice; D020539:Sequence Analysis, Protein / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D000911:Antibodies, Monoclonal; D001688:Biological Products
keywords: Antibody; Byonic; De novo sequencing; Mass spectrometry; Supernovo; mAb