Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein.

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Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the previous study with substantially less sample material. Data are available via ProteomeXchange with identifier PXD005087.", "claims": [{"id": "claim-target-result", "statement": "The study recovered eight collagen I peptide sequences from Brachylophosaurus canadensis (MOR 2598), evaluated their phylogenetic placement using Bayesian analysis in MrBayes, and made the underlying proteomics data available through ProteomeXchange under identifier PXD005087.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28111950", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides."}, {"asset": "source:pmid:28111950", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Phylogenetic analyses place the recovered sequences within basal archosauria."}, {"asset": "source:pmid:28111950", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD005087."}, {"asset": "source:pmid:28111950", "locator": "sections[11] \"Phylogenetic Analysis\" paragraph 2", "quote": "Using MrBayes v 3.2.2 x64,51 the collagen I matrix was searched with the following parameters: outgroup Thamnophis sirtalis, prset aamodelpr = mixed, 1 250 000 generations with sampling frequency 200, and burnin of 312 500 generations."}, {"asset": "source:pmid:28111950", "locator": "sections[19] \"fn-group\" paragraph 1", "quote": "Raw data, including MS acquisition files (.RAW files), PEAKS, and Byonic raw export files (.MZID files), have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD005087."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study recovered eight collagen I peptide sequences from Brachylophosaurus canadensis (MOR 2598), evaluated their phylogenetic placement using Bayesian analysis in MrBayes, and made the underlying proteomics data available through ProteomeXchange under identifier PXD005087.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:28111950"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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