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Reanalysis of T. rex Spectra Confirms Findings of 2007 Study

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A new study lends support to a 2007 study in which researchers said they discovered proteins in a 68-million-year-old Tyrannosaurus rex fossil.

In the study, published July 15 in the online edition of the Journal of Proteome Research, researchers in California reanalyzed the original mass spectra generated from the T. rex sample, and, using different bioinformatics tools and statistical sets, "found nothing obviously wrong with 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 wrote.

The findings are the latest addition to a controversy that arose with the publication two years ago of a study in which its authors claimed to have uncovered and sequenced a set of proteins belonging to the dinosaur and genetically linking T. rex to modern day chickens [see PM 04/12/07].

That study became the target of much criticism aimed at its scientific techniques, and in a reanalysis of the data, Martin McIntosh, a full member of the Fred Hutchinson Cancer Research Center found peptides that were an exact match to ostrich, raising the possibility that the original findings were contaminated and spectra attributed to T. rex may actually belong to ostrich.

In the current JPR study, the researchers from the Palo Alto Research Center and the Genome Center at the University of California, Davis reevaluated the entire T. rex data set containing 31.367 MS/MS data and 48,216 combinations of spectrum and precursor charge assignment, and searched the spectra against the database using ByOnic tool. They then compiled a protein list using the program ComByne.

Based on their results, the researchers concluded that "the identification of bird-like collagen at the protein level is clearly significant."

One of the criticisms raised against the 2007 study was that among the proteins that were detected in the T. rex fossil was collagen, which is believed to be too fragile to survive millions of years.

But in a study published in May, John Asara, one of the authors of the 2007 study and director of the Beth Israel Deaconess Medical Center Mass Spectrometry core in Boston, and his colleagues sequenced proteins, including collagen, belonging to an 80-million-year-old duck-billed hadrosaur [see PM 05/07/09].

That study, in which the authors took great pains to make sure their methods were unassailable as possible, also detected traces of hemoglobin.

In the JPR study, the authors said that hemoglobin and collagen are "plausible proteins to find in fossil bone," because they are two of the most abundant proteins in bone and bone marrow.

"Contamination remains a tricky and possibly unresolvable issue for this particular sample," they add. "Perhaps a bird died on top of the T. rex excavation in the filed; perhaps ostrich bone lingered in the mass spectrometry facility for a year; or perhaps avian collagen from a cosmetic or medical product found its way into the T. rex sample.'

One way to dispel one contamination scenario would be to sequence ostrich collagen completely. In the meantime, though, the scientific community is still developing sample handling standards and data analysis for fossil protein, they said.

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