Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing

Area of Science:

• Paleoproteomics
• Geochemistry
• Analytical Chemistry

Background:

• Ancient proteomics analyzes ancient proteins in paleontological specimens for phylogenetic and degradation studies.
• Proteomic analysis of fossils is destructive, costly, and time-consuming.
• Reliable screening methods are needed to maximize proteomic information recovery from precious fossil samples.

Purpose of the Study:

• To evaluate three techniques (ATR-FTIR, MALDI-ToF MS, chiral AA analysis) for screening fossil material for protein preservation.
• To identify reliable and minimally destructive methods for predicting protein survival in fossils.
• To enhance the efficiency and success rate of ancient proteomics research.

Main Methods:

• Fourier-transform infrared spectroscopy (ATR-FTIR) was used to assess splitting factor and C/P indices.
• Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) was employed for protein identification.
• Chiral amino acid (AA) analysis was performed to assess the preservation state of amino acids.

Main Results:

• ATR-FTIR splitting factor and C/P indices were unreliable indicators of protein survival due to secondary mineralization.
• Both MALDI-ToF MS and chiral AA analysis successfully identified samples with surviving proteins.
• These methods are quick, inexpensive, and minimally destructive, requiring minimal sample mass.

Conclusions:

• Chiral amino acid analysis and MALDI-ToF MS are reliable screening methods for predicting protein survival in fossils.
• These methods provide crucial information on the endogeneity of surviving proteins.
• Adoption of these screening techniques will facilitate broader examination of paleontological specimens for ancient proteomic analysis, improving understanding of long-term protein preservation.