When scientists reported 2 years ago that they had discovered intact protein fragments from a 68-million-year-old Tyrannosaurus rex, the skeptics pounced. They argued that one of the main lines of evidence, signatures of the protein fragments taken by mass spectrometry, was flawed. But now a reanalysis of that mass-spec data from an independent group of researchers backs up the original claim that dinosaur proteins have indeed survived the assault of time.
In 2005, a team led by Mary Schweitzer of North Carolina State University in Raleigh reported  in Science that it had discovered an unusual T. rex fossil, in which some of the soft tissues, including blood vessels and other fibrous tissue, seemed to have been preserved. Two years later, Schweitzer teamed with mass-spec expert John Asara of Harvard Medical School in Boston and colleagues to report  that mass-spec studies identified seven peptide fragments that appeared to come from dinosaur collagen and that those sequences were closely related to analogous sequences from the chicken and other modern birds, as would be expected given the many lines of evidence that birds evolved from dinosaurs . But skeptics argued that the mass-spec signals barely hovered above the data's background noise. And Schweitzer and Asara, they argued, couldn't rule out that the signals were caused by contaminants.
The controversy has continued in letters and follow-up papers. It also prompted Asara to release his complete mass-spec data set to other experts to allow them to judge for themselves. So researchers from the Palo Alto Research Center in California and the University of California, Davis, decided to do just that. They reanalyzed Asara's mass-spec data using a different set of bioinformatics tools and statistical tests.
In a paper published this month in the Journal of Proteome Research, the California researchers report that three of the peptides are a strong match to what looks to be an ancient form of collagen, whereas others matched with less statistical significance. "In summary, we find nothing obviously wrong with the T. rex mass spectra: the identified peptides seem consistent with a sample containing old, quite possibly very ancient, bird-like bone, contaminated with only fairly explicable proteins," they conclude.
"That's pretty good news," says Asara. He doubts that the new result will put the entire controversy to rest, because soft tissue from dinosaur is such an extraordinary find. However, he argues, "I think it puts the mass-spectrometry interpretation to rest." The case for T. rex proteins is also helped by the fact that it is no longer a unique discovery. In May, Schweitzer, Asara, and colleagues reported  a similar result from an 80-million-year-old dinosaur and raised further hopes that scientists may soon have a window into the molecular makeup of dinosaurs.