Proteome variation with collagen yield in ancient bone

Procopio, Noemi, Hopkins, Rachel, Harvey, Virginia and Buckley, Michael (2021) Proteome variation with collagen yield in ancient bone. Journal of Proteome Research, 20 (3). pp. 1754-1769. ISSN 1535-3893

[img]
Preview
Text (Final published version)
acs.jproteome.0c01014.pdf - Published Version
Available under License Creative Commons Attribution 4.0.

Download (3MB) | Preview
[img]
Preview
Text (Advance online version)
acs.jproteome.0c01014.pdf - Published Version
Available under License Creative Commons Attribution 4.0.

Download (3MB) | Preview
Official URL: https://doi.org/10.1021/acs.jproteome.0c01014

Abstract

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” (as defined in radiocarbon dating and stable isotope research) is a routine step that allows for the selection of specimens that are deemed adequate for subsequent analyses, with samples containing less than ∼1% “collagen yield” normally being used for isotopic analysis but discounted for radiocarbon dating. The aims of this study were to use proteomic methods of MALDI–TOF (matrix assisted laser desorption ionization time-of-fligh mass spectrometry) and LC−ESI−MS/MS (liquid chromatography electrospray ionization tandem mass spectrometry) to investigate the endogeneity of the dominant proteinaceous biomolecules within samples that are typically considered to contain poorly preserved protein. Taking 29 archaeological samples, we evaluated the proteome variability between different acid-soluble fractions removed prior to protein gelatinization and considered waste as part of the radiocarbon dating process. We then correlated these proteomes against the commonly used “collagen yield” proxy for preservation. We found that these waste fractions contained a significant amount of both collagenous and noncollagenous proteins (NCPs) but that the abundance of these was not correlated with the acquired “collagen yield”. Rather than a depleted protein load as would be expected from a low “collagen yield”, the variety of the extracted NCPs was comparable with that commonly obtained from ancient samples and included informative proteins useful for species identification, phylogenetic studies, and potentially even for isotopic analyses, given further method developments. Additionally, we did not observe any correlation between “collagen yield” and peptide mass fingerprint success or between the different fractions taken from the same sample but at different radiocarbon pretreatment stages. Overall, these findings highlight the value in retaining and analyzing sample fractions that are otherwise discarded as waste during the radiocarbon dating process but more importantly, that low “collagen yield” specimens that are often misinterpreted by archaeologists as being devoid of protein can still yield useful molecular sequence-based information.

Item Type: Article
Additional Information: The mass spectrometry proteomics data have been deposited to the PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) via the PRIDE partner repository with the data set identifiers PXD020516 and 10.6019/PXD020516. Funding information: The authors would like to acknowledge financial support from the Royal Society for funding a fellowship to M.B. (UF120473) and the UKRI for funding a Future Leaders Fellowship to N.P. (MR/S032878/1). Many thanks also go to the University of Manchester for a Dean’s Award to V.L.H. This research has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007−2013)/ERC grant agreement no. 324139 PalaeoChron awarded to Tom Higham. The publication process was supported by the Hunt Fellowship granted to R.J.A.H. by the Wenner Gren Foundation (Gr. 9881). We also acknowledge the support of Nikolay Sirakov (National Institute of Archaeology of the Bulgarian Academy of Sciences), Jean-Luc Guadelli (UMR5199 CNRS PACEA/ PPP), and Aleta Guadelli (UMR PACEA, Université Bordeaux I), who granted us access to the material from Kozarnika, Temnata, and Manastira, which were excavated as part of the Franco-Bulgarian Prehistoric Mission in Northern Bulgaria. Their work was financially supported by the Advisory Committee of the Archaeological Researches abroad (MAEE, France)−DGRCST, by CNRS (Centre National de la Reserche Scientifique), by the Region Aquitaine, by the University of Bordeaux I, and by the Bulgarian Academy of Sciences. Furthermore, we thank Klára Palotás and László Makádi (Geological Institute Budapest) for giving us permission to sample the bones from Máriaremete in Hungary.
Subjects: C700 Molecular Biology, Biophysics and Biochemistry
F100 Chemistry
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: Elena Carlaw
Date Deposited: 13 Jan 2021 12:12
Last Modified: 31 May 2021 14:41
URI: http://nrl.northumbria.ac.uk/id/eprint/45209

Actions (login required)

View Item View Item

Downloads

Downloads per month over past year

View more statistics