Multi-protease analysis of Pleistocene bone proteomes.

Area of Science:

• Paleoproteomics
• Evolutionary Biology
• Biochemistry

Background:

• Ancient protein analysis offers insights into hominin evolution during the Pleistocene.
• Current methods predominantly use trypsin for protein identification, potentially limiting data recovery.

Purpose of the Study:

• To investigate the impact of using multiple proteases on ancient bone proteome size and protein sequence recovery.
• To enhance phylogenetic information retrieval from Pleistocene hominin and Equidae specimens.

Main Methods:

• Identified 18 new hominin bone specimens using MALDI-TOF MS.
• Compared proteome size and sequence recovery using nanoLC-MS/MS with six different proteases (including trypsin) on Pleistocene bone samples.

Main Results:

• Trypsin alone recovers only a fraction of the preserved bone proteome.
• Combining data from multiple proteases significantly increases protein sequence coverage.
• The majority of the Pleistocene bone proteome is inaccessible to trypsin.

Conclusions:

• Employing multiple proteases alongside trypsin is advantageous for palaeoproteomics.
• This approach maximizes proteome and protein sequence recovery for evolutionary studies of ancient hominins.