Testing the efficacy and comparability of ZooMS protocols on archaeological bone

Wang Naihui, Brown Samantha, Ditchfield Peter, Hebestreit Sandra, Kozilikin Maxim, Luu Sindy, Wedage Oshan, Grimaldi Stefano, Chazan Michael, Horwitz Kolska Liora, Spriggs Matthew, Summerhayes Glenn, Shunkov Michael, Richter Korzow Kristine, Douka Katerina

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

Collagen peptide mass fingerprinting, best known as Zooarchaeology by Mass Spectrometry (or ZooMS) when applied to archaeology, has become invaluable for the taxonomic identification of archaeological collagenous materials, in particular fragmentary and modified bone remains. Prior to MALDI-based spectrometric analysis, collagen needs to be extracted from the bone's inorganic matrix, isolated and purified. Several protocols are currently employed for ZooMS analysis, however their efficacy and comparability has not been directly tested. Here, we use four different ZooMS protocols to analyze 400 bone samples from seven archaeological sites, dating to between ~500,000–2000 years ago. One of them, single-pot solid-phase-enhance sample preparation (SP3), is used for the first time as a ZooMS protocol. Our results indicate that the least-destructive ZooMS protocol which uses an ammonium bicarbonate buffer as a means of extracting collagen is most suitable for bones with good collagen preservation, whereas the acid-based methodologies can improve success rates for bones with low-to-medium collagen preservation. Since preservation of biomolecules in archaeological bones is highly variable due to age and environmental conditions, we use the percent nitrogen by weight (%N) value as an independent semi-quantitative proxy for assessing collagen content and for predicting which bones will likely result in a successful ZooMS-based identification. We find that 0.26%N as a threshold for screening material could optimize the number of spectra which produce identifications using ZooMS. Significance statement: We present a direct comparison of three previously published ZooMS protocols for the analyses of archaeological bones, and the first use of an SP3-based approach to ZooMS analysis. Our results show that the acid-based ZooMS protocols increase the success rate for bones with low-medium collagen preservation. We identify 0.26%N as a threshold for optimizing the number of samples with enough collagen for successful peptide mass fingerprinting.

Original languageEnglish
Article number104078
JournalJournal of Proteomics
Volume233
DOIs
StatePublished - 20 Feb 2021
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2020

Funding

Data Availability Statement is included in the manuscript. This work received support from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program, grant agreement 715069-FINDER-ERC-2016-STG, awarded to Katerina Douka. We would like to thank the Max Planck Society and the staff of the Department of Archaeology, Max Planck Institute for the Science of Human History, for facilitating this work and providing training and access to equipment, in particular, Patrick Roberts, Jana Zech and Nicole Boivin; and the Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford for providing access to their stable isotope facilities. The Wonderwerk Cave project is funded by grants from the Canadian Social Sciences and Humanities Research Council, and The Leakey Foundation. The Denisova Cave excavation is supported by grants from the Russian Foundation for Basic Research (RFBR), project No. 18-09-40100. The MALDI spectrometric data and the nitrogen values are publicly available (https://zenodo.org/deposit/3784979#). The LC-MS/MS data from Connochaetes taurinus can be found at PXD020810 through MassIVE (doi:10.25345/C5TJ3M password: reviewer), sample OM 20A, DA383 and from Ovis aries at PXD020809 through MassIVE (doi:10.25345/C5Z75H password: reviewer), sample DA157 and DA327. All of the protocols are available on protocols.io. The AmBic, acid soluble, and acid insoluble protocols can be found at dx.doi.org/10.17504/protocols.io.bf5djq26. The SP3 protocol for ZooMS used here can be found at dx.doi.org/10.17504/protocols.io.bf6pjrdn. The Wonderwerk Cave project is funded by grants from the Canadian Social Sciences and Humanities Research Council , and The Leakey Foundation . This work received support from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program, grant agreement 715069-FINDER-ERC-2016-STG , awarded to Katerina Douka. We would like to thank the Max Planck Society and the staff of the Department of Archaeology, Max Planck Institute for the Science of Human History, for facilitating this work and providing training and access to equipment, in particular, Patrick Roberts, Jana Zech and Nicole Boivin; and the Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford for providing access to their stable isotope facilities. The Denisova Cave excavation is supported by grants from the Russian Foundation for Basic Research (RFBR) , project No. 18-09-40100 .

FundersFunder number
Canadian Social Sciences and Humanities Research Council
Department of Archaeology
European Union's Horizon 2020 research and innovation program
Research Laboratory for Archaeology
Leakey Foundation
Social Sciences and Humanities Research Council of Canada
European Research Council
Russian Foundation for Basic Research18-09-40100, DA327, DA157, DA383
Max-Planck-Gesellschaft
Horizon 2020715069-FINDER-ERC-2016-STG
Max-Planck-Institut für Menschheitsgeschichte

    Keywords

    • Bone
    • Collagen
    • Nitrogen
    • Palaeoproteomics
    • ZooMS

    Fingerprint

    Dive into the research topics of 'Testing the efficacy and comparability of ZooMS protocols on archaeological bone'. Together they form a unique fingerprint.

    Cite this