ANN ARBOR—If you think you finally understand the human genome and why it’s important, get ready for proteomics. Discovering how cells respond to genetic instructions by creating millions of protein variations and figuring out what all those proteins do will be the next frontier of biomedical research.

The ability to identify cellular proteins will be especially valuable in cancer research, because each type of cancer produces its own protein biomarkers, according to Samir M. Hanash, M.D., Ph.D., a professor of pediatrics and communicable diseases in the University of Michigan Medical School. Unfortunately, current technology is neither accurate nor sensitive enough to detect most of these proteins, which often exist only in trace amounts.

A new liquid-phase protein separation technology under development at the U-M could help scientists solve the proteomics puzzle. The system eliminates the difficult, time-consuming 2-D gel electrophoresis method scientists now use to separate cells into individual proteins—the critical first step in proteomics analysis.

In the U-M system, proteins remain in a liquid phase throughout the separation process. According to David Lubman, Ph.D., a U-M professor of chemistry, liquid phase has many advantages over gels. “The process takes hours instead of days. It can handle large quantities of protein and detect trace amounts of protein,” Lubman says. “It is easily interfaced for mass spectrometry detection, data are automatically digitized online and the entire process has the potential to be fully automated.”

Hanash presented data from studies of the U-M protein separation method compared to traditional 2-D PAGE techniques on
“Everyone dreams about putting a cell sample into a machine and having the proteins instantly appear on a computer screen,” says Hanash. “We’re not there yet, but we have created a proof-of-concept for this new technology and have demonstrated its potential.”

U-M scientists dissolve cell tissue in liquids and then use a two-stage process to separate proteins by isoelectric point and hydrophobicity. Once separated and digested, the proteins are identified with mass spectrometry, which provides information on their molecular weight. Software developed at U-M converts the mass spectrometry data into a two-dimensional image of the protein map making it easy to compare images and see differences.

Although custom-designed equipment still must be developed, Hanash says the U-M team is working on ways to combine the protein separation and mass spectrometry stages into one fully automated system. “Automation will make it possible to avoid human variability in processing,” he says.

In addition to cancer research, Lubman adds, there are potential applications for the new technology in many other areas of science including toxicology, bacteriology, and protein chemistry.

The U-M has applied for a patent on the new liquid-phase separation technology. The research is funded by the National Institutes of Health. Other researchers involved in the project include U-M graduate students Daniel B. Wall, Maureen T. Kachman and Siyuan Gong; and U-M research assistants Robert Hinderer, Stephen Parus and David E. Misek.

pediatrics and communicable diseasesDavid LubmanNational Institutes of Health