Evaluation of decontamination methods for palaeoproteomic analysis of Pleistocene skeletal proteomes

Palaeoproteomic analysis of skeletal elements is increasingly used to study topics such as human evolution. However, many of the skeletal elements that are analysed have been stored and handled over long time periods, and have therefore accumulated contaminating proteins, which may complicate analysis of the endogenous ancient proteome. In this study, we evaluate five commonly used approaches for decontamination in palaeoproteomics, using a Pleistocene Equus sp. bone that was artificially contaminated with modern dog saliva and fur. First, we show that contamination affects reconstruction of the ancient proteome, even when the potential for contamination is not taken into account. Thereafter, our results show that although most decontamination methods reduce contamination, only a brief bleach wash seemingly returns the proteome to its original composition. None of the decontamination approaches are found to damage the endogenous proteome. Decontamination may, however, significantly improve recovery of low-abundance proteins.