Purdue Instrument To Fashion Custom-made Proteomics Chips

The instrument makes use of a new method to remove and isolate the tangle of proteins found within cells, a process necessary to reveal protein function within an organism. In contrast to other, more labor-intensive separation methods, the Purdue team's technique allows proteins with similar chemical properties to be separated in the gas phase based on their mass so that analysis can be accomplished in far fewer steps than previously required.

"This technique, when fully developed, will allow us to take hundreds of proteins from a cell without damaging them," said R. Graham Cooks, the Henry Bohn Hass Distinguished Professor of Analytical Chemistry in Purdue's School of Science. "We can then deposit these proteins in specific locations on a chip, where their functions can be analyzed quickly. We hope this chip-making instrument will streamline proteomics research."

The research involving the separation technique appears in this week's (8/13) online edition of Science.

Proteins are well known as the building blocks for all living things, but within plants and animals there are thousands of varieties of these complex molecules. Each performs a different task - transporting chemicals within cells, for example, or facilitating the transfer of energy.

Categorizing protein function is a young and promising field of biology called proteomics, which many scientists believe will provide untold medical advances over the next few decades. To make such advances, however, scientists must sift through the jumble of proteins inside a cell and isolate each one, which has not been an easy job.

"Proteins form a kind of complex soup inside your cells," said Zheng Ouyang, research scientist and co-author of the paper. "It has only been recently that we have had any technology capable of sorting through them. And even those methods have been difficult and time-consuming."

Adding to the difficulty is that once scientists isolate proteins by current methods, the process can destroy the proteins' biological activity. This renders them unusable for drug testing, for example, which is one of the main reasons scientists want to isolate proteins in the first place.

"Current methods essentially demand that we overhandle our proteins," Cooks said. "Just as you can ruin food's flavor by overhandling it while you cook, proteins can lose their reactivity to potential drugs by too violent an isolation process. Current methods do generate valuable data, but isolating and purifying thousands of proteins is costly in both time and money."

The solution Cooks' team devised was to separate the proteins in a single step using a mass spectrometer, an instrument chemists routinely use to analyze a sample of various materials by ionizing the sample's molecules and separating them in the gas phase so they can be detected individually. Cooks' team modified the spectrometer so it could collect the material after the separation by depositing the ions onto different locations on a chip's surface, a process called ion soft-landing. The comparatively gentle process produces highly pure protein samples that retain their ability to react with potential drugs.

"To continue the soup metaphor, our process allows you to separate the peas, carrots and potatoes from each other, while still allowing each to remain flavorful," Ouyang said. "People can use these separated, pure proteins to find out what function each performs for the body."

The chips themselves are a few centimeters square, and depositing proteins onto them takes a matter of hours. Once the surface is prepared, scientists expose it to a solution containing chemical or biological reagents that might react with those on the chip. They then examine the surface visually or with other analytical techniques to determine which of the hundreds of protein "spots" have reacted.

"By this process, we should be able to create custom-made chips, each with different sets of proteins," Cooks said. "There is a wealth of potential basic knowledge about the body which experiments using these chips could reveal. A practical application for them would be as disease markers, for example for certain types of cancer."

One challenge still facing Cooks' team is determining how to maximize the number of proteins that remain biologically active through the process.

"Some proteins do survive the trip from cell to chip with their properties intact, but we want to minimize our losses," Cooks said. "Our process puts energy into these molecules, which can change their conformations and render them inactive. We'd like to reduce the heating and phase changes that are necessary to our method so we can reduce this possibility."

This research has been supported in part by Inproteo (formerly the Indiana Proteomics Consortium), an Indianapolis company that unites researchers from Purdue, Indiana University and Eli Lilly and Co. Inproteo's goal is to develop novel instrumentation and methodologies to unleash proteomics' potential to improve human health.

Cooks is associated with Bindley Bioscience Center, one of five interdisciplinary centers in Purdue's Discovery Park. The center encourages and supports interdisciplinary research initiatives between life sciences and engineering, both within and beyond Purdue.