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Experts Say Proteomics Tools Not Ready for Clinical Setting

SAN DIEGO — Until instruments used for proteomics research become cheaper and more user-friendly, proteomics may always play second fiddle to genomic technologies in the clinical setting, according to participants in a panel discussion at the annual meeting of the US Human Proteome Organization, held here this week.

One panelist, Patrick Brown, a professor of biochemistry at the Stanford University School of Medicine, said to date the cost of instruments such as mass spectrometers, and the special training needed to run them, have meant that proteomics has poorly served the medical field, and, as a result, the discipline has become marginalized compared to genomics.

Brown, who has worked extensively with DNA microarrays, made his remarks during a panel discussion originally meant to address the challenges facing proteogenomics. But as none of the panelists could define proteogenomics, the conversation instead turned into an evaluation of proteomics, its highs and lows, and what kind of future may be laying ahead for the field.

Another panelist, Ruedi Aebersold, a professor of systems biology at the Swiss Federal Institute of Technology, was critical of the direction some research has taken, and decried what he said was the science's lack of clear objectives.

A fundamental problem, Aebersold said, is that proteomics continues to "operate in a perpetual-discovery mode" when a more targeted approach would provide greater benefits.

"If we continue in this perpetual discovery mode, the high-performance application of the [the tools] will remain in specialized labs," and the potential impact of proteomics will be lost, he said.

The field also needs to better define the issues it wants to address, including narrowing down what the discipline wants to achieve and how it will do it, he said. According to Aebersold, proteomics "has to define achievable goals," such as creating a basic human proteome map in which one protein would be mapped for every gene, an approach that HUPO first threw out last year when it proposed the Human Proteome Project.

This week, the panelists and some audience members, mindful of the criticism and financial challenges the discipline has had to weather in recent years, were quick to point out the progress that it has made.

Several panelists said that one of the key accomplishments of proteomics has been the delineation of complex biological components and organisms, which have in turn led to insight into diseases.

For his part, Aebersold said a sometimes-overlooked benefit of proteomics has been its success in developing tools and instruments that address questions about biomarkers while also shedding light on more basic biological mechanisms and processes such as interaction networks and signaling pathways.

"So I don't think we can underestimate the degree to which proteomics has driven that part of science," said Aebersold.

But the discipline has a good deal of work ahead of it before it can elbow its way into the clinic — or before other tools elbow it out of its own field. For instance, Stanford's Brown suggested that despite their advances in recent years, mass specs may be holding the field back, especially in translating the science to the clinic, because of the special skills needed to operate them.

Aebersold agreed, saying that neither proteomics in general nor the technology in particular had reached the level of maturity that would be required for the discipline to enter the clinic. Trying to push the science into the clinic prematurely, he added, "may do a disservice to the field."

A more comprehensive version of this article appears in this week's issue of ProteoMonitor.