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Digging deeper into ancient skeletal proteomes through consecutive digestion with multiple proteases.

Zandra Fagernäs1, Gaudry Troché1, Jesper V Olsen2

  • 1Globe Institute, University of Copenhagen, Copenhagen, Denmark.

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|February 29, 2024
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Summary

Recovering ancient skeletal proteomes for evolutionary studies is enhanced by using multiple proteases. Sequential digestion with proteases like Glu-C or chymotrypsin followed by trypsin significantly increases proteome size and protein coverage from fossil specimens.

Keywords:
ArchaeologyPalaeoproteomicsProteasesSkeletal proteomes

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Area of Science:

  • Paleoproteomics
  • Evolutionary Biology
  • Archaeological Science

Background:

  • Ancient skeletal proteome recovery is crucial for phylogenetic and evolutionary analyses.
  • Current methods often yield small proteomes with limited protein sequence coverage.

Purpose of the Study:

  • To investigate methods for increasing proteome size and protein sequence coverage from ancient skeletal specimens.
  • To explore the efficacy of parallel and consecutive protease digestion protocols.

Main Methods:

  • Applied parallel and consecutive digestion techniques using proteases such as Glu-C, chymotrypsin, and trypsin on Pleistocene skeletal samples.
  • Analyzed recovered peptides to assess proteome size and protein sequence coverage.

Main Results:

  • Consecutive digestion, particularly Glu-C or chymotrypsin followed by trypsin, recovered alternative proteome components missed by trypsin alone.
  • Both parallel and consecutive multi-protease digestion improved proteome size and coverage for Holocene and Pleistocene bone specimens.

Conclusions:

  • Optimized extraction and digestion protocols are necessary to unlock protein sequence information from degraded ancient specimens.
  • Sequential protease digestion is a promising strategy for maximizing data recovery from unique hominin proteomes for phylogenetic studies.