How can proteins survive when DNA does not?

Some proteins, especially structural ones bound within bone and enamel, are more chemically stable than DNA, so they can persist in older or harsher-preserved material and still be identified by mass spectrometry.

ZooMS, or zooarchaeology by mass spectrometry, identifies the animal species of a bone fragment from the masses of its collagen peptides, allowing identification of fragments too small or broken to recognize by shape.

Ancient Proteins and Paleoproteomics

Paleoproteomics analyzes ancient proteins preserved in bones, teeth, dental calculus, and artifacts, recovering information about species, diet, disease, and sex—sometimes far beyond the survival limits of DNA.

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Definition

The study of ancient proteins surviving in archaeological remains, using mass spectrometry to identify species, reconstruct diet and disease, estimate sex, and recover biological information when DNA is absent.

Scope

This topic covers mass-spectrometry-based study of ancient proteins: species identification from collagen peptides (ZooMS), reconstruction of diet and disease from dental calculus proteomes, sex estimation from enamel amelogenin peptides, and the use of proteins in deep-time contexts where DNA does not survive. It addresses preservation, contamination, and the complementarity of proteins and DNA.

Core questions

How are ancient proteins recovered and identified by mass spectrometry?
How does collagen peptide mass fingerprinting identify species from fragmentary bone?
What do dental calculus proteomes reveal about diet and the oral microbiome?
When do proteins outlast DNA, and what can they recover in deep time?

Key theories

Proteins as a deep-time biomolecular archive: The principle that proteins, especially structural ones such as collagen and enamel proteins, can survive longer than DNA, extending biomolecular inference into time periods and conditions where ancient DNA does not preserve.
Dental calculus as a proteomic reservoir: Warinner and colleagues' demonstration that mineralized dental plaque traps host, microbial, and dietary proteins, making calculus a rich archive of past diet, oral pathogens, and immune response.

History

Ancient protein study grew from amino-acid and collagen work into modern paleoproteomics with the spread of high-sensitivity mass spectrometry after about 2010. Collagen peptide fingerprinting (ZooMS) became a routine tool for species identification, dental calculus emerged as a major proteomic archive, and proteins were used to recover information in contexts where DNA had degraded.

Debates

Reliability and reach of ancient protein claims: How to authenticate ancient proteins against modern contamination and degradation artifacts, and how far very old protein sequences can support phylogenetic and dietary inference relative to better-validated DNA evidence.

Key figures

Christina Warinner
Matthew J. Collins
Enrico Cappellini
Jessica Hendy

Seminal works

hendyetal2018
warinneretal2014
cappellinietal2018

Frequently asked questions

How can proteins survive when DNA does not?: Some proteins, especially structural ones bound within bone and enamel, are more chemically stable than DNA, so they can persist in older or harsher-preserved material and still be identified by mass spectrometry.
What is ZooMS?: ZooMS, or zooarchaeology by mass spectrometry, identifies the animal species of a bone fragment from the masses of its collagen peptides, allowing identification of fragments too small or broken to recognize by shape.