Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry"

Abstract

We use authentication tests developed for ancient DNA to evaluate claims by Asara et al. of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon passes, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of the α1(I) peptide sequences with amphibians not birds, suggests that T. rex does not. CommentEarly reports of DNA preservation in multi-million year old bones (i.e. dinosaurs) have been largely dismissed (see 1 and SOM T1, 2) but reports of protein recovery are persistent (see 3 for review). Most of these studies used secondary methods of detection, but protein sequence, arguably the gold standard for molecular palaeontology, has now been claimed for the first time (2). Following initial optimism generated by reports of dinosaur DNA, there arose a gradual awareness of the problems and pitfalls which bedevil analysis of ancient samples (1), leading to a series of recommendations for future analysis (1, 4). As yet, there are no equivalent standards for fossil protein, so here we apply the recommended tests for DNA (4) to the authentication of the reported protein sequences (2) ( Table 1).* To whom correspondence should be addressed. E-mail: mc80@york.ac.uk. Europe PMC Funders Group Likelihood of collagen survivalThe extremely hierarchical structure of collagen results in unusual, catastrophic degradation (5) as a consequence of fibril collapse. The rate of collagen degradation in bone is slow because the mineral 'locks' the components of the matrix together, preventing helical expansion which is a pre-requisite of fibril collapse (6). The packing which stabilises collagen fibrils (6) also increases the temperature sensitivity of degradation (E a 173 kJ mol -1 ; Fig. 1). Collagen decomposition would be much faster in the T. rex buried in the then megathermal (>20 °C) (7) environment of the Hell Creek formation (collagen t ½ ~ 2 ka) than it would have been in the mastodon lying within the Doeden Gravel Beds (present day mean temperature 7.5 °C; collagen t ½ 130 ka; Fig. 1).

Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen

“…The results hinted at the potential of identifying peptides from proteolytic digest of well-preserved bone samples. This work also highlighted the importance of minimizing sources of protein contamination and adhering to data publication guidelines (20,21). In the past few years, a very well-preserved juvenile mammoth referred to as Lyuba was discovered in the Siberian permafrost and analyzed using high-resolution tandem mass spectrometry (29).…”

Evolutionary Proteomics: Empowering Tandem Mass Spectrometry and Bioinformatics Tools for the Study of Evolution

“…In the same Science issue, Schweitzer et al (2007) provided evidence of collagen I in T. rex's cortical and medullary bone, using multiple techniques, atomic force microscopy (AFM), in situ immunohistochemisty, and TOF-SIMS, validating the results obtained by Asara et al (2007). Both articles were subjected to an intense scrutiny and public debate within the scientific community (Buckley et al 2008;Pevzner et al 2008). Part of the scrutiny is valuable as it pushes researchers to ensure the integrity of their sample preparation and analysis, while other part hinders progress, with obstacles difficult to overcome.…”

“…Although unlikely due to fast rate decomposition of soft tissue in comparison to bone, no one questioned if the keratin was actually a conserved peptide from the well preserved dinosaur's sample. There were three major concerns in accepting the tandem mass spectrometry data published by Asara et al (2007), namely: sample preparation, database search, and validation of the results (Buckley et al 2008;Pevzner et al 2008). The bioinformatics component in tandem mass spectrometry is a bottleneck and the most quietly accepted limitation.…”

Exploring the potential of public proteomics data

“…The initial publications by Asara et al 74, 75 proved controversial in the proteomics community (see, e.g. 76, 77). As a consequence, the authors decided to make their data publicly available (PRD000074 in PRIDE), such that other researchers could inspect and reprocess the data themselves.…”