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A guide to ancient protein studies
Open accessAbstract
Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.
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“However, our results here suggest that techniques like Py-GC-MS or HPLC that give more general information on protein presence versus absence or general amino acid composition should be considered frontline approaches when dealing with samples of significant age and/or thermal maturity (e.g. Demarchi et al., 2016; Hendy et al., 2018; Cappellini et al., 2018).”
From Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities (2019) · cites this paper as Hendy et al., 2018
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“These studies demonstrate the importance of strategies discriminating endogenous and modern sources of protein in archeological investigation—a major research strategy and concern that remains in present-day research (1).”
From Ancient protein analysis in archaeology (2021) · cites this paper as [1]
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“When it comes to analyzing ancient human remains, most studies work with historic dental calculus [11, 15, 22-26], as it is a stable, long-term reservoir of proteins [27].”
From Metaproteomic analysis of King Ghezo tomb wall (Abomey, Benin) confirms 19th century voodoo sacrifices (2024) · cites this paper as [11]
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Metadata
- Authors
- Hendy, J., Welker, F., Demarchi, B., Speller, C., Warinner, C., & Collins, M. J.
- Affiliations
- Max Planck Institute of Geoanthropology (DE)
- University of Copenhagen (DK)
- University of York (GB)
- University of Zurich (CH)
- Corresponding author
- Hendy, Jessica
- Welker, Frido
- ORCID
- Venue
- Nature Ecology & Evolution
- Published
- 2018-03-26
- Volume
- 2
- Issue
- 5
- Pages
- 791-799
- ISSN
- 2397-334X (ISSN-L)
- OpenAlex
- W2794613307
- Semantic Scholar
- b379d0e4bbfe1aafe5dd599e2112fc851af4925d
- Cited by
- 291
- References
- 98
- Citations by year
- 2026: 50 · 2025: 31 · 2024: 30 · 2023: 42 · 2022: 27 · 2021: 25 · 2020: 30 · 2019: 47 · 2018: 9
- FWCI
- 4.99
- Type
- journal article
- Language
- en
- Update notices
- correction (2018-06-04)
- Open access
- green
- orcid.org
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, other-oa)
- Max Planck Digital Library (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- National Science Foundation (1516633, 1643318, 1523264)
- Villum Fonden (00017649)
- Wellcome Trust (108375, 108375/Z/15/Z)
- European Commission (677576)
- Danmarks Grundforskningsfond
- Max-Planck-Gesellschaft
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM089886)
- Topics
- Social Sciences › Archeology › Archaeology and ancient environmental studies
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Social Sciences › Arts and Humanities › Archeology (arts and humanities) › Paleopathology and ancient diseases
- Keywords
- palaeoproteomics, ancient proteins, research guidelines, data reporting standards, data validation, contamination control, sample selection, reproducibility, ancient DNA, ancient diseases
- MeSH terms
- Archaeology, Paleontology, Proteomics
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