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Automated de novo protein sequencing of monoclonal antibodies

Nature Biotechnology volume 26, pages 1336–1338 (2008)Cite this article

To the editor:

De novo protein sequencing of monoclonal antibodies (mAbs) is required when cDNA or the original cell line is not available, or when characterization of post-translational modifications is needed to verify antibody integrity and effectiveness. Here, we demonstrate that comparative shotgun protein sequencing (CSPS) based on tandem mass spectrometry can reduce the time required to sequence a mAb to 36 h, a dramatic reduction as compared to the classic Edman degradation. We therefore argue that CSPS has the potential to be a disruptive technology for all protein sequencing applications.

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Figure 1: Protein contigs resulting from shotgun protein sequencing of aBTLA tandem mass spectra.
Figure 2: CSPS methodology.

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Acknowledgements

The authors are grateful to Dan Eaton, Jill Calemine-Fenaux, Ari Frank, Richard Vandlen, Oleg Borisov and Bao-Jen Shyong for help with various aspects of this manuscript. This project was supported by National Institutes of Health grants NIGMS 1-R01-RR16522 and 1-P41-RR024851-01.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, University of California, San Diego, 92093, California, USA

    Nuno Bandeira & Pavel Pevzner

  2. Protein Chemistry Department, Genentech Inc., 1 DNA Way, South San Francisco, 94080, California, USA

    Victoria Pham, David Arnott & Jennie R Lill

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  1. Nuno Bandeira
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  2. Victoria Pham
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  3. Pavel Pevzner
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Competing interests

D.A., V.P. and J.R.L. are employed by Genentech, Inc., a pharmaceutical company.

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Bandeira, N., Pham, V., Pevzner, P. et al. Automated de novo protein sequencing of monoclonal antibodies. Nat Biotechnol 26, 1336–1338 (2008). https://doi.org/10.1038/nbt1208-1336

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