Applications of mass spectrometry-based proteomics in archaeology and palaeoanthropology

Abstract

This review aims to provide an overview of recent palaeoproteomic studies for Japanese researchers. Compared to mass spectrometry-based proteomics, conventional immunological methods to detect protein suffer from lower sensitivity and specificity, and the target proteins need to be determined before the analysis. In contrast, mass spectrometry enables high-throughput sequencing of any protein residue present in femtomolar quantities, with no need to pre-define a target. Palaeoproteomics, the high-throughput analysis of protein residues in archaeological or palaeoanthropological materials, has been developed and expanded since the 2010s. Mass spectrometry-based palaeoproteomics can be divided into two methodological categories: peptide mass fingerprinting (e.g., ZooMS) and shotgun proteomics. The former mainly aims to identify the taxa of bioarchaeological materials by comparing the spectra of digested peptides of a specific protein, such as collagen and keratin, to spectra of known species. The later aims to comprehensively identify different proteins present in the analyzed sample by sequencing all digested peptides. Major topics in recent palaeoproteomic studies are taxonomic identification and phylogenetic reconstruction, estimation of genetic information, identification of unknown proteinaceous materials, reconstruction of physiological status, and dietary reconstruction. Although there are limitations and concerns, such as quantification and degradation of ancient proteins, palaeoproteomics has provided, and will continue to provide, unique and useful applications in archaeology and palaeoanthropology.