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Optimizing ancient protein extraction from skeletal remains is crucial. Simple acid-insoluble methods best recover degraded proteomes, while EDTA demineralization suits well-preserved samples for species identification.

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Area of Science:

  • Paleoproteomics
  • Archaeological Science
  • Biogeochemistry

Background:

  • High-throughput proteomic analysis of ancient skeletal remains offers insights into past fauna and species dispersal.
  • Archaeological skeletal remains are a finite resource, necessitating optimized proteome extraction methods.
  • Ancient proteins are often degraded, making standard extraction protocols unsuitable.

Purpose of the Study:

  • To compare six proteomic extraction methods for Late Pleistocene skeletal remains.
  • To evaluate method performance based on species identification accuracy, protein sequence coverage, deamidation, and post-translational modifications.
  • To identify optimal protocols for extracting ancient proteins from bone with varying preservation states.

Main Methods:

  • Tested six distinct proteomic extraction protocols on Late Pleistocene skeletal samples.
  • Assessed species identification accuracy, protein sequence coverage, deamidation levels, and post-translational modifications.
  • Focused on methods with minimal steps and equipment, yielding results within three working days.

Main Results:

  • Significant differences observed in proteome complexity and sequence coverage across methods.
  • Simple acid-insoluble proteome extraction methods demonstrated superior performance for highly degraded samples.
  • EDTA demineralization and protease-mix proteolysis yielded more identified peptides for well-preserved specimens.

Conclusions:

  • Method choice critically impacts proteomic data quality from ancient bone.
  • Acid-insoluble extraction is recommended for degraded skeletal remains, while EDTA demineralization is effective for well-preserved samples.
  • Developed protocols are efficient, suitable for large-scale screening in archaeological and human evolution research.