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So many proteins, so much promise

r peptides often do not map cleanly to single human genes. The study will be published Oct. 30 by the journal Nature.

The top-down method can accurately identify which gene produced which protein. The bottom-up method is only 60 to 90 percent accurate in identifying proteins precisely.

"We need to define all the protein molecules in the human body," Kelleher said. "First, we need a map of healthy protein forms, which will become a highly valuable reference list for understanding damaged and diseased forms of proteins. Our technology should allow us to get farther down this road faster."

In the first large-scale demonstration of the top-down method, the researchers were able to identify more than 3,000 protein forms created from 1,043 genes from human HeLa cells.

Their goal was to identify which gene each protein comes from -- to provide a one-to-one picture. They were able to produce this accurate map of thousands of proteins in just a few months.

The researchers also can produce the complete atomic composition for each protein. "If a proton is missing, we know about it," Kelleher said.

One gene they studied, the HMGA1 gene associated with premature aging of cells, produces about 20 different protein forms.

Kelleher's team developed a four-dimensional separation system that uses separations and mass spectrometry to measure the charge, mass and weight of each protein as well as how "greasy" a protein is. The software the researchers developed to analyze the data during years of work prior to the study proved critical to the success of the top-down method.

"If you want to know how the proteins in cancer really work and change, top-down mass spectrometry is getting to the point where it can be part of the discussion," Kelleher said.

"Analyzing the entire set of proteins expressed in a cell presents a continuing and significant technical challenge to the field of proteomics," said

Contact: Megan Fellman
Northwestern University

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