Composition variations in archaeological human bone proteomes

Abstract

12 Sampling strategies within the field of skeletal palaeoproteomics are often based on specimen 13 availability. Knowledge of bone biology might assist in improving sample selection strategies 14 and minimise unnecessary sampling of precious (hominin) material. We study ten bone sample 15 locations across four bone elements, for a total of 10 adult, archaeological human skeletons. 16 We compare bone proteome composition and modification for skeletal elements formed 17 through endochondral and intramembranous ossification, as well as cortical-trabecular bone 18 pairs of three skeletal locations. We observe minimal differences in bones formed through the 19 two ossification processes, outside of the exclusive presence of cartilage-related proteins in 20 endochondral bone samples. We observe higher protein concentrations, a larger number of 21 protein groups and peptides, and lower rates of deamidation in cortical bone compared to 22 trabecular bone proteomes, this indicates that cortical bone provides a better preservation 23 environment compared to trabecular bone. Throughout our analysis, the petrous bone stands 24 out, with the largest and most complex proteomes recovered for all studied individuals. Formed 25 through endochondral ossification, the petrous bone undergoes minimal turnover during life. 26 Our observations indicate that the petrous bone is the ideal source of ancient protein sequence 27 information. 1. Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. 2. Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Faculty of Archaeology, Leiden University, Leiden, the Netherlands. 3. 1 bioRxiv preprint doi: https://doi.org/10.1101/2025.06.02.657369; this version posted June 3, 2025. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. 28