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. Content: The zipped file contains 4 files, two fasta files as well as two additional folders: - PalaeoProPhyler_Publication_Data_for_Tree.fa contains all of the sequences used to generate the phylogenetic tree presented at PalaeoProPhylers manuscript - ALL_PROT_REFERENCE.fa contains all of the sequences generated as part of the Hominid Palaeoproteomic Reference Dataset described above - PER_PROTEIN is a folder containing one fasta file for each protein within the Hominid Palaeoproteomic Reference Dataset, each protein fasta file has the sequences of all individuals for that particular protein - PER_SAMPLE is a folder containing one fasta file for each sample/individual within the Hominid Palaeoproteomic Reference Dataset, each sample fasta file has the sequences of all proteins for that particular sample. Important Note: The dataset is still not fully generated yet. However around 170 modern samples are complete and ready to be used in their appropriate folder (~/PER_SAMPLE /).