Proteomics Breakthrough

Photo: Courtesy of Pacific Northwest National Laboratory Measuring the faint expression of a low-level protein in a complex biological system is a bit like playing Where's Waldo in a moving picture with tens of thousands of extras. Without technology that can process the system quickly, accurately, and repeatedly, there's no telling how long each investigation will take. Scientists at the US Department of Energy's (DOE) Pacific Northwest National Laboratory (PNNL) in Richland, Wash., report they have an instrument that can do the job. Their protein mass spectrometer (PROMS) is the first high-throughput MS built expressly for proteomics. Richard D. Smith and his colleagues fashioned the prototype out of a 9.4-tesla Fourier-transform ion cyclotron resonance (FTICR) MS manufactured by Bruker Daltonics in Billerica, Mass. As much as 100 times more sensitive than other methods for identifying proteins, PROMS can analyze results 10 to 100 times faster than a tandem MS, according to a PNNL announcement. "We're making measurements that are right on the edge of what it takes to measure a single cell," says Smith, who continues to tinker and predicts that characterizing proteomes at the single-cell level is "not far away." The new design incorporates an invention by Smith and his team, called dynamic range enhancement applied to mass spectrometry (DREAMS). Overcoming limits imposed by the number of molecules an MS can measure at any one time, DREAMS allows researchers to exclude the largest, most abundant proteins and focus on low-level proteins. The smaller, less-common players are often more important to biological processes, Smith says, citing for example the messengers involved in cell signaling. PNNL researchers have used the system to investigate a cytomegalovirus known to cause retinitis, and three microbes that interest the DOE. In August, they reported identifying more than 1,900 proteins (61% of nearly 3,200) of the predicted proteome for Deinococcus radiodurans, a radiation-resistant bacterium. This achievement is the broadest proteome analysis for any organism to date, according to the paper.1 "We are going to have to increase the capability to deal effectively and to deal equally well with mammalian systems," Smith says. One of the challenges, he notes, is that the complexity to be found in mammalian cells is still largely unknown. John Wronka, vice president and general manager for life systems at Bruker, says PROMS is ready for proteomics with mammalian cells--and for "metabolomics," a newer catchword for profiling metabolites. Bruker already has two PROMS instruments on order, says Wronka; one customer is a private lab, the other an academic center. PROMS' price tag is between $1.2 million and $1.5 million (US). For labs not ready to spend that kind of money, the prototype is a limited option. As a user facility, PNNL must make it available to the scientific community--the D. radiodurans project was done in collaboration with scientists from Louisiana and Maryland. Smith says he already has commitments to other collaborators in the near future, and he is working to increase the instrument's availability. Where does this leave the two- dimensional gel? Not only is MS far more expensive, but it also requires a significant investment in bioinformatics technology and expertise: PROMS spews forth 1.8 terabytes of data each month. Nonetheless, says Smith, the switch from 2-D gels is becoming a significant trend. Wronka suggests that while MS will open up new experiments, the gels will survive as a less-expensive workhorse for simpler research. "You can use a Cadillac to haul manure," he observes, "but why would you?" Jane Salodof MacNeil (macneiljs@earthlink.net) is a freelance writer in Groveland, Mass. 1. M.S. Lipton et al., "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags," Proceedings of the National Academy of Sciences, 99:11049-54, Aug. 20, 2002.

Proteomics Breakthrough

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