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A Fossil Protein Chimera; Difficulties in Discriminating Dinosaur Peptide Sequences From Modern Cross-Contamination

ABSTRACT: Proteome analyses of ostrich bone using Orbitrap Elite mass spectrometry

INSTRUMENT(S):

ORGANISM(S): Struthio Camelus (ostrich)

TISSUE(S): Long Bone

SUBMITTER: Michael Buckley

LAB HEAD: Michael Buckley

PROVIDER: PXD006360 | Pride | 2020-04-20

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20130301_SD1.raw.mgf	Mgf
	20130301_SD1.raw.pride.mgf.gz	Mgf
	20130621_MB21.raw.mgf	Mgf
	20130621_MB21.raw.pride.mgf.gz	Mgf
	20141104_NP11_1in50.raw.mgf	Mgf

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Publications

A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination.

Buckley Michael M Warwood Stacey S van Dongen Bart B Kitchener Andrew C AC Manning Phillip L PL

Proceedings. Biological sciences 20170501 1855

A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68 Myr <i>Tyrannosaurus rex</i> fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequ ...[more]

PMID: 28566488

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A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination.

Project description:A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68 Myr Tyrannosaurus rex fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr Brachylophosaurus canadensis fossil were reported that have remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, Struthio camelus The resulting LC-MS/MS data were found to match all of the proposed sequences for both the original Tyrannosaurus and Brachylophosaurus studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.

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Proteome variation with collagen yield in ancient bone

Project description:Isotope analyses are some of the most common analytical methods applied to ancient bone, aiding the interpretation of past diets and chronology. For this, the evaluation of “collagen” yield is a routine step that allows for the selection of the specimens that are adequate for subsequent analyses, and samples with below ~1% yield normally discarded. Additionally, during the “collagen extraction” procedure, several sample fractions are generated and subsequently discarded but could contain proteins of analytical interest. In this study we evaluated the proteome variability of different fractions generated during the “collagen extraction” process of 29 samples, and their correlation with the collagen yield. We found that these fractions contained a significant amount of both collagenous and non-collagenous protein (NCP) spectra and that these were not correlated with the collagen yield. The variety of the extracted NCPs was comparable with that normally obtained from ancient samples, and the information obtained can be used to conduct species identification, phylogenetic studies, isotopic analyses and may be used to perform radiocarbon dating on the specimens. Overall, these findings suggest that not only is there value in retaining the fractions typically discarded as waste, but that low collagen yield specimens can still yield useful information.

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