title: Advantages of extended bottom-up proteomics using Sap9 for analysis of monoclonal antibodies.
abstract: Despite the recent advances in structural analysis of monoclonal antibodies with bottom-up, middle-down, and top-down mass spectrometry (MS), further improvements in analysis accuracy, depth, and speed are needed. The remaining challenges include quantitatively accurate assignment of post-translational modifications, reduction of artifacts introduced during sample preparation, increased sequence coverage per liquid chromatography (LC) MS experiment, and ability to extend the detailed characterization to simple antibody cocktails and more complex antibody mixtures. Here, we evaluate the recently introduced extended bottom-up proteomics (eBUP) approach based on proteolysis with secreted aspartic protease 9, Sap9, for analysis of monoclonal antibodies. Key findings of the Sap9-based proteomics analysis of a single antibody include: (i) extensive antibody sequence coverage with up to 100% for the light chain and up to 99-100% for the heavy chain in a single LC-MS run; (ii) connectivity of complementarity-determining regions (CDRs) via Sap9-produced large proteolytic peptides (3.4 kDa on average) containing up to two CDRs per peptide; (iii) reduced artifact introduction (e. g., deamidation) during proteolysis with Sap9 compared to conventional bottom-up proteomics workflows. The analysis of a mixture of six antibodies via Sap9-based eBUP produced comparable results. Due to the reasons specified above, Sap9-produced proteolytic peptides improve the identification confidence of antibodies from the mixtures compared to conventional bottom-up proteomics dealing with shorter proteolytic peptides.
authors.affiliation: Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland.
authors.forename: Kristina
authors.initials: K
authors.lastname: Srzentić
authors.forename: Luca
authors.initials: L
authors.lastname: Fornelli
authors.forename: Ünige A
authors.initials: ÜA
authors.lastname: Laskay
authors.forename: Michel
authors.initials: M
authors.lastname: Monod
authors.forename: Alain
authors.initials: A
authors.lastname: Beck
authors.forename: Daniel
authors.initials: D
authors.lastname: Ayoub
authors.forename: Yury O
authors.initials: YO
authors.lastname: Tsybin
mesh_terms: D000911:Antibodies, Monoclonal / Q000737:chemistry*; D016282:Aspartic Acid Endopeptidases / Q000737:chemistry* / Q000302:isolation & purification; D002176:Candida albicans / Q000737:chemistry / Q000201:enzymology; D002853:Chromatography, Liquid; D022801:Complementarity Determining Regions; D005656:Fungal Proteins / Q000737:chemistry* / Q000302:isolation & purification; D006801:Humans; D007074:Immunoglobulin G / Q000737:chemistry*; D013058:Mass Spectrometry; D010455:Peptides / Q000302:isolation & purification*; D059748:Proteolysis; D040901:Proteomics / Q000379:methods*
chemical_list: D000911:Antibodies, Monoclonal; D022801:Complementarity Determining Regions; D005656:Fungal Proteins; D007074:Immunoglobulin G; D010455:Peptides; D016282:Aspartic Acid Endopeptidases; C116371:Sap9 protein, Candida albicans