The complete gene sequence of humans has been solved, but the genome is just a recipe for proteins, the building blocks that are crucial to the structure and function of every cell in our bodies. To truly understand the body in both health and disease, scientists must learn which proteins appear, disappear or become more or less abundant under different conditions. Discovering how individual proteins behave differently in cancer cells than in normal cells, for example, could lead to new diagnostic tests and more precisely targeted treatments.

Deciphering this “protein code,” which is the domain of a new field of study known as proteomics, has proved to be a much tougher proposition than sequencing the human genome. Unlike genes, which all possess the uniform structure of the DNA double helix, each protein has a unique chemical makeup, and thus displays its own three-dimensional structure and quirky behavior. In addition, proteins are frequently modified during their lifespan: the 10,000 or so genes in the human genome that are active within each cell type give rise to many times that number of ever-changing protein variants. Comprehensively cataloging this diversity is an art as well as a science, requiring expensive equipment and specialized expertise far beyond the reach of most individual laboratories.

Tackling the proteomics puzzle is the job of Walter J. McMurray, Ph.D., and Kathryn Stone, co-directors of the Protein Chemistry and Mass Spectrometry (PCMS) Resource, one of 12 research services in the School of Medicine’s W.M. Keck Foundation Biotechnology Resource Laboratory.

Using the latest analytical techniques, McMurray, Stone and their colleagues sort, identify and quantify thousands of proteins in samples of cells, tissues and blood on behalf of researchers at Yale and around the world. The lab’s state-of-the-art equipment in the basement of 300 George Street in New Haven churns out protein profile data 24 hours a day, seven days a week, bringing researchers closer to the medical promise of the postgenomic era.

Kenneth R. Williams, Ph.D., director of the Keck Laboratory, the medical school’s outstanding and often-copied shared research resource, recognized the importance of protein profiling and the growing demand among researchers for cutting-edge proteomics techniques several years ago. What followed—a concerted effort by Williams, Stone and McMurray to bring the latest and greatest large-scale protein analysis technologies to the medical school—is now paying off for Yale researchers, who have access to one of the best academic proteomics facilities anywhere in the nation. “To our knowledge,” says Williams, “no other academic core lab in the U.S. provides such a wide array of proteomic technologies.”

At the heart of protein profiling lies the analytic technique of mass spectrometry (MS), a separation and detection tool that uses high voltages and strong magnets to sort molecules, which can then be identified based on their size and electric charge.

McMurray has logged more than 40 years in the field, dating from his postdoctoral work in the early days of the technique in the 1960s. He set up the first MS analyzer at Yale in 1965 and, in an example of the method’s versatility, and later used it to analyze the chemical composition of moon rocks brought back by the Apollo 11 mission. In 1984, he was named director of an MS facility launched by Alan C. Sartorelli, Ph.D., the Alfred Gilman Professor of Pharmacology, who was then director of the Yale Cancer Center.

Stone came from a completely different direction. With a brand-new bachelor’s degree in chemistry in hand, she arrived at the medical school’s fledgling core research facility in 1982, intending to stay for two years. Five years later she was directing a protein chemistry facility, which eventually grew into the Keck Laboratory’s Mass Spectrometry Resource. No stranger to the vagaries of protein behavior, during her 24 years at Yale Stone has identified the “unknown” proteins in more than 5,500 samples—without making a single mistake, to her knowledge.

In 1998, Stone and McMurray merged their MS efforts into one center under the Keck umbrella. Since then, the PCMS has grown to include seven MS analyzers, and has seen the adoption of several advanced protein profiling methodologies. With names like MudPIT and iTRAQ, these separation and identification techniques offer researchers the chance to learn more about proteins of interest than was previously possible in a single experiment, a competitive advantage that pays off in times of tight research funding.

The excellence of the PCMS has attracted top-dollar grant support for new equipment. The latest addition, a $1.5 million high-sensitivity, high-resolution mass spectrometer—“the Cadillac of MS machines,” Stone calls it—was funded by the National Institutes of Health, as was a new supercomputer to process the massive quantities of protein profiling data the lab produces.

Funding for research projects at the center is also robust. Stone’s group does the proteomics work for large NIH-funded studies of blood vessel disease and drug addiction and provides support to the Northeast Biodefense Center, earning operating expenses by accepting samples on a fee-for-service basis from scientists around the world.

Stone and McMurray recently oversaw the resettling of the PCMS in 5,500 square feet of renovated space provided by the School of Medicine in 300 George Street, a building overlooking the medical and central campuses that is home to several biotechnology companies and medical school departments.

The result is a lab that never sleeps—as profiling techniques get better, the demand from medical school scientists continues to mount, keeping lab robots working night and day to feed the MS machines, and the staff streaming useful data out to researchers.

Stone says the biggest challenge at the PCMS is keeping the work flowing while juggling “45 different projects for different people”—not to mention the daily phone calls from eager researchers asking, “Is it done yet?”