Summary
De novo sequencing of monoclonal antibodies is an important step in the drug discovery process in when the cDNA or original cell line are not available, or when the characterization of unexpected post translational modifications is needed to verify the integrity of the antibody. Despite being time-consuming, the fifty year old technique of Edman degradation has remained the primary tool for de novo protein sequencing. Here we demonstrate that Shotgun Protein Sequencing (SPS), a recently developed approach employing tandem mass spectrometry, represents a fast and accurate protein analysis technique with the potential to dramatically reduce the reliance on Edman degradation in the studies of unknown proteins. We illustrate the application of SPS for sequencing monoclonal antibodies and introduce Comparative Shotgun Protein Sequencing (CSPS) to assemble multiple protein contigs into complete antibodies using related antibodies as templates. We estimate that CSPS leads to one-two orders of magnitude reduction in protein sequencing effort as compared to conventional Edman degradation approaches. Furthermore, rather than being hindered by post-translational modifications, this approach allows one to automatically discover unexpected modifications.
cSPS is included in the currently included in the latest release of MetaSPS, an extension of Shotgun Protein Sequencing (SPS) that improves de novo sequencing length and accuracy.