Ancient DNA (aDNA) is themost informative biomolecule extracted fromskeletal remains at archaeological sites,
but its survival is unpredictable and its extraction and analysis is time consuming, expensive and often fails. Several
proposed methods for better understanding aDNA survival are based upon the characterisation of some aspect
of protein survival, but these are typically non-specific; proteomic analyses may offer an attractive method
for understanding preservation processes. In this study, in-depth proteomic (LC-Orbitrap-MS/MS) analyseswere
carried out on 69 archaeological bovine bone and dentine samples from multiple European archaeological sites
and comparedwith mitochondrial aDNA and amino acid racemisation (AAR) data. Comparisons of these data, including
estimations of the relative abundances for seven selected non-collagenous proteins, indicate that the survival
of aDNA in bone or dentine may correlatewith the survival of some proteins, and that proteome complexity
is a more useful predictor of aDNA survival than protein abundance or AAR. The lack of a strong correlation between
the recovery of aDNA and the proteome abundance may indicate that the survival of aDNA is more closely
linked to its ability to associate with bone hydroxyapatite crystals rather than to associate with proteins.
Significance: Ancient biomolecule survival remains poorly understood, even with great advancements in ‘omics’
technologies, both in genomics and proteomics. This study investigates the survival of ancient DNA in relation to
that of proteins, taking into account proteome complexity and the relative protein abundances to improve our
understanding of survival mechanisms. The results show that although protein abundance is not necessarily directly
related to aDNA survival, proteome complexity appears to be.
