Exploring Palaeoproteomics in the Philippines: Ancient Proteins from Human Archaeological Bones in Tropical Environments

John Paulo Austria* and Michelle S. Eusebio

The application of biomolecular archaeological techniques, particularly palaeoproteomics, has emerged as a critical tool for elucidating taxonomic identification, phylogeny, health, and disease in contexts where ancient DNA degrades rapidly. Collagen, for example, covers 80-90% of bone proteome from which the majority of phylogenetic analyses are conducted. The rest are composed of Non-Collagenous Proteins (NCPs), which are used in describing the physiological condition of the individual to infer health and disease. While the recovery of ancient proteins through palaeoproteomics is positioned to answer these critical archaeological questions, the severe diagenesis of tropical environments remains a pressing issue. This could be the reason why despite its growing application, palaeoproteomics remains largely underutilized in tropical areas, such as in Southeast Asia. To assess and contribute to this field, this paper develops a pilot study by establishing the baseline criteria in the preservation screening of ancient proteins before subjecting the samples to expensive palaeoproteomic runs. Consequently, the use of Liquid Chromatography High-Resolution Mass Spectrometry (LC-HRMS) aims to characterize these surviving collagen and NCPs from human archaeological bones. This establishes the protein biomarkers that are likely to survive in tropical environments. Ultimately, the success of this pilot study will contribute to the growing field of biomolecular archaeological techniques in the Philippines.