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Source: Wired: Protein and the Lean Machines Sep. 23, 2000 by Kristen Philipkoski  

Proteins are the workhorses in the human body, and a better understanding of exactly how they work could lead to better health care. But one of the stiffest challenges facing the new science of proteomics is developing tools to analyze proteins much more quickly than the current technology -- and making those tools economically viable.

Applied Biosystems , with its ABI Prism 3700 machine, changed the way genes were analyzed and spurred the race to map the human genome. The company hopes for a repeat performance with its Maldi Tof Tof mass spectrometer.

"It's not unlike DNA sequencing five years ago, when no one was in a hurry. All of a sudden Craig (Venter, president of Celera Genomics) wakes up and says, 'I can do it faster,' then everyone wakes up and says, 'I can do it faster, too,'" said Steve Martin, director of the proteomics research center at Applied, Celera's parent company and creator of its own human genome map.

The mass spectrometer increased protein analysis significantly when it was first introduced in the 70s. But now, with the entire human genome map ready to be analyzed, researchers need something even faster.

If Applied's Tof Tof machines are as successful as Martin believes they will be, health care could see the benefits of proteomics -- the study of proteins -- in as little as three to five years.

"The challenge is that although the human genome was complicated, it pales in comparison to what we need to do in proteomics," Martin said. "The reason people want to take the challenge is because although the human genome sequence is the basis of human biology, it doesn't tell you what's happening in the cell at any given time. Proteins do."

If researchers can look at a sample of a patient's blood and immediately see what the proteins are doing and what those proteins represent, researchers can predict disease on the spot with 100 percent accuracy.

"The proteome is largely where the genome hits the road," said Elbert Branscomb, director of the Joint Genome Sequencing Institute in Walnut Creek, California. "But it's much richer and harder to characterize than the genome."

To know the function of proteins is no simple task. In fact, it's a job about 1,000 times more complicated than decoding the human genome, Martin said, a task that took the government-funded Human Genome Project 10 years and about $3 billion.

While humans have approximately 100,000 genes, researchers say there are probably at least 10 times that number of proteins, the molecules that carry out the instructions of genes. Plus, proteins can behave in wildly different ways depending on whether they're acting on their own or in cooperation with other proteins.

Proteomics is suddenly a burgeoning business for life science companies. About one proteomics startup surfaces every week, according to Martin.

Scimagix, Oxford GlycoSciences and MDS Proteomics are just a few of the key players. With the incredible amount of information presented in the human proteome, there should be room for everyone.

Applied announced on Tuesday that it had agreed to ship Oxford GlycoSciences its brand new machine, the Tof Tof, in exchange for feedback on its performance.

Oxford will receive its first machine in early 2001, and Celera will get its own machine to test out in about a month.

Other researchers agree that studying proteins will impact health care much more than studying genes.

"DNA just stores the information that tells the cell what to do," Branscomb said. "Proteins are the engine, the catalyst, the detectors ... they do not quite everything but pretty damn close.

"Just staring at DNA we learn close to bunk," he said. "We need to go understand the engines themselves rather than the blueprint for the engines."