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Re-analysis of T. rex Spectra Confirms Findings

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A new study lends support to findings from 2007 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 re-analyzed 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 write.

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.

That study became the target of much criticism aimed at its scientific techniques, and in a re-analysis 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, re-evaluated 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 conclude 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.

— Tony Fong

Proteomics Notes

Satoris will be distributing Rules-Based Medicine's panel of 189 protein biomarkers for neurology research. The panel, called DiscoveryMAP, launched in June around the same time as Satoris' own neurological panels for Alzheimer's disease, neurodegeneration, and neuroinflammation.

Bruker Daltonics and Boston University's Mass Spectrometry Resource will be using high-performance ion trap mass spectrometry and Fourier transform mass spec for glycomics and proteomics research. They will use Bruker's solariX FTMS with a 12 Tesla magnet, electron transfer dissociation, and electron capture dissociation capabilities.

The National Institute of General Medical Sciences will be funding a new Protein Structure Initiative program that will be supported by five grant programs.

Datapoint

$179 Thousand
Amount of cash on hand Vermillion had in June, according to a report filed with a US Bankruptcy Court

Funded Grants

$210,000/FY 2009
Comparative and functional proteomics of germline chromatin in C. elegans
Grantee: Kenneth Hillers, California Polytechnic State University, San Luis Obispo
Began: Jun. 1, 2009; Ends: Mar. 31, 2011
Hillers and his colleagues will use proteomic analysis to study germline chromatin in C. elegans, particularly to find proteins involved in meiosis. Then using bioinformatic and functional analyses they will determine the role of those candidate proteins to learn about meiosis and gametogenesis.

$228,300/FY 2009
Proteomics of Auditory Brainstem Circuitry During Development and in Deafness
Grantee: Raphael Pinaud, University of Rochester
Began: Jun. 15, 2009; Ends: May 31, 2011
Pinaud and his colleagues will use high-throughput quantitative proteomics and mass spectrometry-based approaches to determine the series of protein regulatory events involved in the development of the medial nucleus of the trapezoid body of the auditory pathway. They will use 2DIGE to find age- and experience-regulated proteins before and after hearing onset.

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