Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics

Abstract

Vertebrate fossils have been collected for hundreds of years and are stored in museum collections around the world. These remains provide a readily available resource to search for preserved proteins; however, the vast majority of palaeoproteomic studies have focused on relatively recently collected bones with a well-known handling history. Here, we characterize proteins from the nasal turbinates of the first Castoroides ohioensis skull ever discovered. Collected in 1845, this is the oldest museum-curated specimen characterized using palaeoproteomic tools. Our mass spectrometry analysis detected many collagen I peptides, a peptide from haemoglobin beta, and in vivo and diagenetic post-translational modifications. Additionally, the identified collagen I sequences provide enough resolution to place C. ohioensis within Rodentia. This study illustrates the utility of archived museum specimens for both the recovery of preserved proteins and phylogenetic analyses.

Expansion for theBrachylophosaurus canadensisCollagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein

“…Silver stains of ancient protein extracts have typically shown a higher degree of smearing than observed here, 27,28,52,53 and it has been hypothesized that such smearing was the result of peptide breakages at various locations, producing a cascade of fragments rather than peptides of uniform length that converge in tight bands. 54,55 However, we suggest the possibility that smearing of these extracts in electrophoresis may be reduced relative to other reports from fossils because the protocol that we employed resulted in a steep reduction of residual EDTA in the GuHCl extracts when compared with previous studies. EDTA has been shown to cause smearing in SDS-PAGE gels of extant bone extractions 53 and is difficult to remove by dialysis.…”

“…To be consistent with previous studies, 13,31,55 we have used the sequences as they are identified by bioinformatics software in our phylogenetic analyses. However, it must be noted that without detection of a complete ion series, the identity of certain residues in poorly fragmented regions may be ambiguous.…”

Bone protein “extractomics”: comparing the efficiency of bone protein extractions ofGallus gallusin tandem mass spectrometry, with an eye towards paleoproteomics

“…Because the extant chicken bones used for these analyses were not subject to the diagenetic factors that can cause chemical alterations in fossil proteins (e.g., deamidation, carboxymethylation of lysine, loss of hydroxylations to proline (Cleland et al, 2016; Cleland, Schroeter & Schweitzer, 2015; Hill et al, 2015)), it is unclear whether the disparity of efficiencies between protocols observed here would be similar if conducted on a fossil sample. Indeed, given the chemical differences in depositional environments experienced by fossils from different localities, it is possible that similar comparison analyses of 10 different fossil specimens would yield 10 different results.…”

Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting

“…Unrelated to UV damage,P TMs on OS6 and OS7 revealed ah igh prevalence of mass shifts on lysine (Lys) and arginine (Arg) side chains corresponding to PTMs described in the literature as advanced glycation end products (AGEs,F igure 3), caused by carbohydrate excess [36] and ascribed to diagenesis in archaeological bones. [37,38] The degradation of carbohydrates can produce glyoxal and methylglyoxal in vitro,which react with Lysand Arg residues to form carboxymethyl or carboxyethyl Lysa nd (methyl-) imidazolone Arg. [39] Combined, AGEs were at least four times more abundant in the painting samples than in the controls.I nasemi-quantitative analysis (Supporting Information, Table S9), we found at least 1g lyoxal or methylglyoxal modification for 102 of all 608 Lysr esidues in both OS6 and OS7 (17 %).…”