UC San Diego and Genentech scientists develop potentially disruptive antibody sequencing ...( Bioinformatics researchers at the Un...)

Bioinformatics researchers at the University of California, San Diego and Genentech have developed a new, quicker way to sequence monoclonal antibodies a process that is many times faster than the sequencing technology typically used by academic and industry researchers today.

The breakthrough is detailed in the December 2008 issue of Nature Biotechnology, in an article titled, "Automated de novo protein sequencing of monoclonal antibodies." In it, the authors propose a new shotgun protein sequencing method, which reduces the time required to sequence an unknown antibody to under 36 hours a "dramatic reduction" compared to the most widely used technique today, which can take weeks or even months The technique is also faster than the complementary DNA (cDNA) sequencing approach commonly used in many laboratories.

While DNA sequencing technologies witnessed dramatic progress in recent years, protein sequencing has hardly changed in 50 years. As a result, today nearly all proteins are discovered using DNA rather than protein sequencing technology. While it works for most proteins (that are coded by DNA), it does not work for some important proteins, such as antibodies, that are not directly inscribed in genomes.

"Our new approach has the potential to be a disruptive technology for all protein sequencing applications," said Nuno Bandeira, lead author on the paper and director of the new Center for Computational Mass Spectrometry (CCMS) at UC San Diego. "This project is a collaboration with Genentech, the leader in development of antibody-based drugs, and it illustrates the potential impact that this center and this technology can have on the biotech industry in California and around the world."

CCMS is a joint effort between the Computer Science and Engineering (CSE) department of the Jacobs School of Engineering, and the UCSD division of the California Institute for Telecommunications and Information Technology (Cal
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