Proteome Variation with Collagen Yield in Ancient Bone
dc.contributor.author | Harvey, Virginia L. | |
dc.contributor.author | Procopio, Noemi | |
dc.contributor.author | Hopkins, Rachel J. A. | |
dc.contributor.author | Buckley, Michael | |
dc.date.accessioned | 2022-06-07T09:24:15Z | |
dc.date.available | 2022-06-07T09:24:15Z | |
dc.date.issued | 2021-02-02 | |
dc.identifier | https://chesterrep.openrepository.com/bitstream/handle/10034/626925/collagen-yield-paper_AAM.pdf?sequence=3 | |
dc.identifier.citation | Procopio, N., Hopkins, R. J., Harvey, V. L., & Buckley, M. (2021). Proteome variation with collagen yield in ancient bone. Journal of proteome research, 20(3), 1754-1769. https://doi.org/10.1021/acs.jproteome.0c01014 | en_US |
dc.identifier.issn | 1535-3893 | |
dc.identifier.doi | 10.1021/acs.jproteome.0c01014 | |
dc.identifier.uri | http://hdl.handle.net/10034/626925 | |
dc.description | “This document is the Accepted Manuscript version of a Published Work that appeared in final form in [Journal of Proteome Research], copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see [https://pubs.acs.org/doi/full/10.1021/acs.jproteome.0c01014].” | en_US |
dc.description.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-flight 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. | en_US |
dc.publisher | American Chemical Society | en_US |
dc.relation.url | https://pubs.acs.org/doi/full/10.1021/acs.jproteome.0c01014 | en_US |
dc.rights.uri | https://creativecommons.org/licenses/by-nc-nd/4.0/ | en_US |
dc.subject | Proteomics | en_US |
dc.subject | Ancient bone | en_US |
dc.subject | Collagen | en_US |
dc.subject | NCPs | en_US |
dc.subject | Radiocarbon dating | en_US |
dc.subject | Stable isotopes | en_US |
dc.title | Proteome Variation with Collagen Yield in Ancient Bone | en_US |
dc.type | Article | en_US |
dc.identifier.eissn | 1535-3907 | en_US |
dc.contributor.department | Northumbria University; University of Manchester; University of New Mexico | en_US |
dc.identifier.journal | Journal of Proteome Research | en_US |
or.grant.openaccess | Yes | en_US |
rioxxterms.funder | Royal Society UF120473; UKRI MR/S032878/1; ERC (FP7/2007–2013)/ERC grant agreement no. 324139 PalaeoChron; Wenner Gren Foundation (Gr. 9881) | en_US |
rioxxterms.identifier.project | Royal Society fellowship (UF120473) to MB | en_US |
rioxxterms.identifier.project | UKRI for funding a Future Leaders Fellowship (MR/S032878/1) to NP | en_US |
rioxxterms.identifier.project | University of Manchester for a Dean’s Award to VLH | en_US |
rioxxterms.identifier.project | Hunt Fellowship granted to RJAH. by the Wenner Gren Foundation (Gr. 9881) | en_US |
rioxxterms.identifier.project | 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. | en_US |
rioxxterms.version | AM | en_US |
rioxxterms.versionofrecord | 10.1021/acs.jproteome.0c01014 | en_US |
rioxxterms.licenseref.startdate | 2022-02-02 | |
dcterms.dateAccepted | 2020-12-14 | |
rioxxterms.publicationdate | 2021-02-02 | |
dc.date.deposited | 2022-06-07 | en_US |
dc.indentifier.issn | 1535-3893 | en_US |