Friday, October 17, 2008

Proteins...Putting them Back Together (Algorithmically)

UC San Diego computer scientists just received an NIH grant to help clean up "the mass spec data mess". (San Diego Untion Tribune clip here)

It's easy to blast apart proteins with mass spectrometers and generate huge amounts of data comprised of all the little protein pieces. It is much harder to put those pieces back together in order to figure out what proteins (and protein modifications) are present in biological samples such as blood and tumors.) UCSD engineers are doing just that...using computational tools, and they just secured an almost $5M NIH grant to keep up the good work and create the software and cyberinfrastructure to enable scientists around the world to take advantage of their algorithmic breakthroughs. More info below and at the links provided.

UC San Diego engineers and scientists have received a five-year $4.94M grant from the National Center for Research Resources (NCRR), a part of NIH, to develop algorithms and software for deciphering all the proteins that are present in biological samples. This “proteomics” work promises to revolutionize routine blood tests, vaccine development, cancer diagnostics, and many other
important biomedical challenges, says Pavel Pevzner, the UC San Diego Jacobs School of Engineering computer science professor leading the project. (Read the UCSD release here and the NIH press release here)

"Unanalyzed data from mass spectrometers is piling up in laboratories around the world. Our algorithms can turn much of these ‘dark’ data into the lists of modified proteins that researchers are looking for,” says Nuno Bandeira, the first executive director of the Center for Computational Mass Spectrometry at UCSD’s Jacobs School of Engineering.

Key collaborators on the new grant are Jacobs School of Engineering computer science professors Vineet Bafna and Ingolf Krueger as well as Steven Briggs, a professor of biology at UCSD’s Division of Biological Sciences.

Genetic Engineering News also picked up the story.