Such comparisons are commonly used by biologists to construct evolutionary "family trees," since similar protein structure is a sign of shared genetic makeup.
Until very recently, however, protein sequences have not been available for ancient organisms such as dinosaurs, since most fossils do not yield proteins or DNA.
The family trees of dinosaurs and other ancient vertebrates are instead known largely by comparing many fine details of skeletal anatomy.
If molecular data become more widely available for dinosaurs, Asara noted, researchers will be able to fill in gaps and overcome possible errors in existing classification based on physical features.
To illustrate his point, he noted that the shared ancestry of two present-day groups—elephants and shrew-like tenrecs—is known solely from DNA and protein comparisons.
"Nobody could make that connection based on bones," he noted.
"The amazing part of this study is that we could establish the dinosaur-bird connection using only 89 total amino acids [the building blocks of proteins]," Asara said.
With only a small amount of sequence data, he continued, "we can take an unidentified or fragmented fossil bone and not only identify the species but also help place it in evolution."
It remains to be seen whether even small sequences can be extracted from ancient fossils with any regularity, experts say.
Mary Schweitzer of North Carolina State University is a co-author of the new study and made the initial discovery of the T. rex soft tissue remains.
She has argued that such remains may be relatively common in well-preserved fossils but are often overlooked.
Others have said that protein preservation over tens of millions of years should not be possible. Some scientists have continued to question whether Asara's and Schweitzer's sequences really came from an ancient T. rex.
Proteins from some other biological source could have somehow contaminated the dinosaur remains, the skeptics note.
The new finding that the proteins are most similar to those of birds, Asara said, helps rule out the possibility of contamination from other sources such as mammals.
But doubts remain. Peggy Ostrom is a biologist at Michigan State University in East Lansing and an expert on fossil proteins.
Many have remained skeptical about the T. rex protein findings, she said, because of the small size of the sequences.
"They have a very tiny bit of data relative to the size of the collagen molecule," Ostrom said.
"What's going to be really convincing is to actually see some more sequences," she added.
"If [preservation of dinosaur proteins] is a ubiquitous occurrence, then that should be forthcoming."
Ostrom also noted that many recent findings, including the mastodon remains dated to nearly half a million years ago, have greatly pushed back previously accepted time limits for protein molecule preservation.
"In 2000, there probably wasn't one biochemist around who would tell you we'd find a protein over 40 thousand years old," she said.
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