Imagine you had to break a secret code, but you could see only part of the message. That's the kind of frustration researchers face when trying to identify proteins and characterize how those proteins are modified in cells by biological processes.

But now, Cornell researchers have extended a powerful technique to increase by fourfold the size of a protein that can be analyzed, to those containing more than 2,000 amino acids, up from about 500.

Called a "top-down" approach, the technique uses a mass spectrometer, which measures the masses of ions or charged particles. Researchers break up the protein into pieces and weigh both the masses of the whole protein and of the individual pieces. By matching the weight of the whole protein and its pieces with those of known protein sequences in a database, they can identify the protein. Any differences in mass with known proteins can help researchers also find where and how proteins have been modified in cells.

For example, if a section of a protein has an increased weight of 16, researchers can tell that the protein has been oxidized within that section, which means that an oxygen atom (with an atomic weight of 16) was added.

"When you isolate a protein from a mixture, your first problem is to know which one it is," said Fred McLafferty, Cornell's Peter J.W. Debye Professor Emeritus of Chemistry and Chemical Biology and senior author of the paper published in the Oct. 6 issue of the journal Science. "Mass spectrometry characterizes a protein by measuring the masses produced from it."

The new technique provides a far more efficient way to break down proteins inside the mass spectrometer -- sprayed, heated and then bashed with gas molecules -- to obtain their pieces for the mass analysis. They are sprayed in an electric field where they pick up charges and are vaporized as they pass through a heated capillary. Then they are hit by air molecules in low-energy collisions to keep the protein from foldi
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5-Oct-2006