Spatial analysis of the ancient proteome of archeological teeth using mass spectrometry imaging

Abstract

Rationale: Proteins extracted from archaeological bone and teeth are utilised for investigating the phylogeny of extinct and extant species, the biological sex and age of past individuals, as well as ancient health and physiology. However, variable preservation of proteins in archaeological materials represents a major challenge.Methods: To better understand the spatial distribution of ancient proteins preserved within teeth, we applied matrix assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for the first time to bioarchaeological samples to visualise the intensity of proteins in archaeological teeth thin sections. We specifically explored the spatial distribution of four proteins (collagen type I, of which the chains alpha-1 and alpha-2, alpha-2-HS-glycoprotein, haemoglobin subunit alpha and myosin light polypeptide 6).Results: We successfully identified ancient proteins in archaeological teeth thin sections using mass spectrometry imaging. The data are available via ProteomeXchange with identifier PXD038114. However, we observed that peptides did not always follow our hypotheses for their spatial distribution, with distinct differences observed in the spatial distribution of several proteins, and occasionally between peptides of the same protein.Conclusions: While it remains unclear what causes these differences in protein intensity distribution within teeth, as revealed by MALDI-MSI in this study, we have demonstrated that MALDI-MSI can be successfully applied to mineralised bioarchaeological tissues to detect ancient peptides. In future applications, this technique could be particularly fruitful not just for understanding the preservation of proteins in a range of archaeological materials, but making informed decisions on sampling strategies and the targeting of key proteins of archaeological and biological interest.

COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics

“…In fact, our analysis of the raw data obtained by Ruẗher et al 20 from three human bone samples resulted in the BC042586 entry receiving the highest score for all samples (Table S7k−m). In addition, analysis of the raw data obtained from human teeth by Dekker et al 60 also yielded similar results (Table S9). In contrast, for the raw data by Cleland 61 opposite results to these were obtained (Table S10).…”

Bone of contention: Intra-element variability in remodelling of human femora based on histomorphometric and isotope analyses

“…Proteomic investigations have highlighted the prevalence of non-collagenous proteins (NCPs) obtained from the 'collagen' extraction method used in stable isotope and radiocarbon analysis, and their distribution varies spatially within an element [46,[58][59][60]. Depending on their amino acid structure, these proteins may vary in isotope composition, particularly those with a higher proportion of non-essential amino acids, which fractionate across trophic levels [61].…”