Hominid Palaeoproteomic Reference Dataset

This dataset contains the 'Hominid Palaeoproteomic Reference Dataset'.

We used PaleoProPhyler ( https://github.com/johnpatramanis/Proteomic_Pipeline )  to generate a palaeoproteomic reference dataset of protein sequences from ancient and present-day hominids. Using the first two modules of PaleoProPhyler, we translated 195 publicly available whole genomes from extant hominid groups. Details on the processing of the sequences can be found in the supplementary materials of PaleoProPhyler (https://github.com/johnpatramanis/Proteomic_Pipeline/blob/main/GitHub_Tutorial/Supplementary.pdf). We also translated 8 ancient hominin genomes from VCF files, including those of several Neanderthals and one Denisovan. Since the dataset is tailored for palaeoproteomic analyses, we chose  to translate proteins that have previously been reported as present in either teeth or bone tissue. We compiled a list of 1,696 proteins from previous works and successfully translated 1,543 of them. For each protein, both the canonical and all alternative protein coding isoforms were translated, leading to a total of 10,058 protein sequences for each individual in the dataset.