A guide to ancient protein studies

Abstract

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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Fig. 1
Fig. 2: Schematic depiction of ancient proteome compositional changes through time.
Fig. 3: Injection blanks in LC–MS/MS.
Fig. 4: Damage-induced sequence ambiguity affects peptide taxonomic assignment for the whey protein beta-lactoglobulin.

Change history

  • 04 June 2018

    In the version of this Perspective originally published, in the third paragraph of the section ‘Selection and sampling’, the sentence beginning ‘Pyrolysis–gas chromatography’ should have also referred to high-performance liquid chromatography; the sentence has now been amended to read ‘Pyrolysis–gas chromatography/mass spectrometry (py–GC/MS) and high-performance liquid chromatography (HPLC) can be used to detect the presence of amino acids62 in any putative proteinaceous sample.’

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Acknowledgements

We thank E. Cappellini for valuable comments on a previous version of the manuscript. We are grateful to K. Penkman, J. Thomas-Oates, J. Wilson and R. Fischer, as well as C. Trachsel and J. Grossmann (Functional Genomics Center Zürich) for support and helpful discussions. This research was supported by the Max Planck Society (J.H., F.W. and C.W.) and its Donation Award (to J.H. and C.W.), the US National Science Foundation BCS-1516633, BCS-1523264, and BCS-1643318 (to C.W.), the European Research Council under the European Union’s Horizon 2020 research and innovation programme under grant agreement numbers STG 678901-FOODTRANSFORMS and STG-677576-HARVEST, the ‘Rita Levi-Montalcini Young Researchers Programme’ (to B.D.), the Wellcome Trust (grant no 108375/Z/15/Z), the Leverhulme Trust (Philip Leverhulme Prize) (to C.S.), the VILLUM FONDEN (grant no 17649), a Danish National Research Foundation Niels Bohr Professorship and ERC Investigator Grant 295729-CodeX (to M.J.C) and the US National Institutes of Health R01GM089886 (to C.W.).

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J.H. and F.W. conceived the manuscript. All authors wrote and contributed to the main text.

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Correspondence to Jessica Hendy or Frido Welker.

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Supplementary Data 1

FASTA formatted file containing proteins (in)frequently identified as likely contaminants in standard palaeoproteomic research

Supplementary Table 1

Reporting of extraction blanks, injection blanks, evidence of protein degradation and MS data reporting in MS/MS-based ancient protein analysis publications

Supplementary Table 2

Demonstration of misleading species assignments in Mascot outputs

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Hendy, J., Welker, F., Demarchi, B. et al. A guide to ancient protein studies. Nat Ecol Evol 2, 791–799 (2018). https://doi.org/10.1038/s41559-018-0510-x

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