Decontamination enhances palaeoproteomic analysis of a Pleistocene hominin tooth from Khudji, Tajikistan

Contamination is a potential issue in palaeoproteomic studies of human evolution, as it may mask low-abundance endogenous proteins and introduce modern variation into the reconstructed ancient proteome. This contamination may stem from many sources, such as the burial environment, storage facilities, and subsequent handling. Here, we apply a bleach decontamination protocol to a Pleistocene hominin tooth from the archaeological site of Khudji, Tajikistan, which was found to be heavily contaminated with skin-derived proteins during initial analysis. Bleach treatment removed nearly all contaminating proteins from the dentine proteome, without damaging endogenous proteins. Finally, phylogenetic analysis of the reconstructed proteome showed that the tooth likely stems from a Neanderthal.