Pandey says the original goal of the research was to identify accurately as many protein changes as possible using the new technology. “But to see how well we measured up, we had to compare our findings to what already was published, and there was just no clean, easy way of doing that because there were reports all over the place.
“That’s when we decided to go through and consolidate just about everything on phosphorylation that was out there.?
Working with human kidney cells, the researchers fished out the thousands of different proteins and analyzed them by ETD, resulting in a net total of 1,435 phosphorylations. Comparing these 1,435 to the 20 years?of published data, they discovered that about 80 percent of what they found never had been reported.
The team then constructed an online search tool, PhosphoMotif Finder, which was incorporated into their previously established Human Protein Reference Database. Human Protein Reference Database now contains about 16,000 phosphorylation sites described in the literature and the PhosphoMotif Finder tool allows any researcher to find potential phosphorylation sites in any protein of interest.
“The power of this technique is not just in the numbers,?says Pandey. “Rather, we’ve found what you might call new information about old proteins, and we hope the new data will help researchers study their favorite proteins in greater depth. After all, there’s no sense in reinventing the wheel.?
Pandey and his team now are curious about other chemical modifications of proteins, which are the “business-end?products of our genes. “There is evidence of other, more fragile modifications that until now no one has been able to get a handle on because they’re way too hard to work with. Now we have the tools to probe further,?he says.
Source:Johns Hopkins Medical Institutions