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The day will come when people will be screened for hundreds of diseases through a simple blood test if the vision of the newest faculty recruit under the Strategic Plan for Research at Weill Cornell Medical College is fulfilled. Through new technology in "proteomics," which he is developing, conditions like pancreatic cancer will be diagnosed at a stage early enough so that there will be a good chance they can be treated and cured.

Dr. Samie R. Jaffrey, 29 years old and now an assistant professor in the Department of Pharmacology at Weill Cornell, says that the word "proteomics" is used in different ways, but, he says, "The aspect that I am interested in is the global profiling of protein expression. I see it as the study of all the proteins in a cell, or in blood, or in some other biological sample. Proteins are the mediators of all biological functions. Proteins are responsible for metabolism, for growth, for the differentiation of cells, for the way cells communicate with other cells."

In addition to this basic science challenge, Dr. Jaffrey sees in proteomics a practical medical opportunity in possibly identifying markers for early stages of diseases like pancreatic cancer, lupus, and Parkinson's. This will allow drugs for the treatment of early stages of diseases to be developed. He points out that some early-detection technology—like the Pap test for cervical cancer—already exists, and, in the case of the Pap test, has done wonders in reducing mortality from cervical cancer. He says that if he can perfect his own new technique for identifying and measuring all the proteins in a specimen—a technique he calls MPACT (for Mass Spectrometric Proteome Analysis Using C-terminal Tags)—he will be able to achieve similar successes in the management of other diseases.

Dr. Jaffrey, a product of the Massachusetts Institute of Technology and Johns Hopkins University School of Medicine, and the winner of many honors and awards for young scientists, first made a name for himself with his research into the signaling function of nitric oxide in the cardiovascular, immune, and nervous systems. But when he is asked what is most interesting about his current work, he speaks about the work that he expects will consume his time for the next couple of decades: work in proteomics.

"Nitric oxide we're interested in," says Dr. Jaffrey, "but it's only a topic for the next two or three years. Proteomics is something for the next 10 or 20 years."

From Genomics to Proteomics

"The problem is that the technology for detecting proteins in a complex mixture is rudimentary, in an embryonic state," he says. It is unlike the technology for the analysis of genetic material, in which, "If you want to know if any RNA is present, you can create a reagent that can detect it"—and, through such means as fluorescence, make it show up smartly in a device.

"There is one tool which lends itself to proteomics," Dr. Jaffrey says, "and that is the mass spectrometer. Mass spectrometry is a technique by which one can determine with exquisite precision the molecular weight of peptides." Peptides are sequences of amino acids, usually less than 100 amino acids in length. By determining their molecular weight, you can generally determine their identity. Proteins may be too large to be measured directly through mass spectrometry, so, he says, "My goal is to convert every protein to one unique peptide. So if I can determine the molecular weight of the peptide, I should be able to determine what protein was its parent."

From Proteins to Peptides

The problem is there are 30,000 proteins in the human body (for the 30,000 genes in the genome). And when you break down proteins into peptides, you produce an enormous number of peptides. Dr. Jaffrey has been doing preliminary work in yeast, which has 6,000 proteins, and which, when processed, yields no fewer than 344,000 peptides.

So, to identify just one peptide for each protein, Dr. Jaffrey puts a tag on one end of it, the carboxy terminus. Each protein has two ends, an amino (NH2) end and a C, or carboxy (COO-), end. He adds a tag called biotin to each C end. Then he recovers all the biotinylated peptides with a naturally occurring protein called avidin, which is found in egg whites. From this, he can derive one unique peptide from each of the original proteins.

To go further: Dr. Jaffrey will have to find ways to load as many as 30,000 peptides onto the mass spectrometer. "There are ways to load the peptides onto the column in a graded system," he says, "so that the more oily peptides, or hydrophobic peptides, get loaded on first, then others sequentially. That allows us to have smaller loads, many scans. With maybe 20 different loads, we may be able to scan only 1,500 peptides at a time."

Dr. Jaffrey is also trying to improve the quantitative powers of the technique. "We have been working on a synthetic biotin, which has a slightly higher molecular weight." With that, he can compare the readings for the yeast-derived peptides produced under baseline conditions with the readings for the peptides after they have been, say, exposed to ethanol. Eventually, this method might lead to the measurement of a significant difference of a level of a protein in a person.

Dr. Jaffrey has compared his MPACT technique with possible alternatives and predicts that his method "will one day become a standard approach in solving proteomic questions."

Basic Science as Well as Practical Diagnostics

He says that proteomics lends itself to basic science applications as well as practical diagnostic ones. "For example, in learning or memory, how do neurons change after the animal has learned?" he asks. "How are synapses different after neurotransmitter stimulation? What proteins are present before and after neuronal stimulation? So we can find out more about learning and memory, and much else."