Protein sequencing of ancient remains is a rapidly developing field (Welker, 2018). Since proteins preserve better than DNA, protein sequencing offers the possibility to get molecular biological information from ancient remains from deeper time-periods compared to DNA sequencing. Specific proteins preserved in bones such as collagen, can be sequenced with mass spectrometry methods (Welker, 2018). Although these protein sequences represent only protein complements of single genes and offer much less resolution than DNA, these techniques are ideal when no DNA information is obtainable from very old remains. The resolution from collagen protein sequences have been shown previously to distinguish between Neanderthals, Denisovans and Homo sapiens. The mandible from the Xiahe individual from Karst cave in Tibet, from which no workable aDNA could be extracted, has been shown to belong to a Denisovan individual rather than a Neanderthal or Homo sapiens (Chen et al 2019) using protein sequences. Since the Denisovan Neanderthal split time-depth is comparable to the first divergence in the tree of all current Homo sapiens, it is possible that protein information would be able to differtiate (crudely however) between very divergent human lineages. The first split in the modern human tree is between southern African hunter-gatherer Khoe-San groups and the rest of humanity. Using the Neanderthal Denisovan comparison as a proxy - it is very likely that protein sequences thus could differentiate between Khoe-San and non Khoe-San groups. The Human evolution group at Uppsala University together with our South African collaborators, plan to investigate this possibility further. This will be investigated digitally first – using inferred protein protein sequences from full genome DNA sequences from Khoe-San and non-Khoe-San individuals. Thereafter we plan to do direct protein sequencing on aDNA remains from Khoe-San and Bantu-speaker individuals. The mass spectrometry-based proteomics facility at Uppsala University (https://www.kemi.uu.se/research/core-facilities/mass-spectrometry-based-proteomics/) will be used to do the protein sequencing. If this technique works it provides an ideal opportunity to investigate more ancient remains of deeper time-depths from southern Africa. Especially remains where aDNA extraction is unlikely or were unsuccessful before, e.g. Border Cave and Florisbad. The technique could potentially show whether these southern African remains have more affinity to the Khoe-San branch or the non-Khoe-San branch – or alternatively if they are equally distance from both branches. In short, it can show whether these remains were Khoe-San ancestors or not. With previous results showing split times of 300kya between Khoe-San and other populations this is a relevant question and, if there are long population continuity in southern Africa – these individuals might indeed be Khoe-San ancestors. On the other hand – if southern Africa had a large scale population replacement these individuals might be from a now “lost” group and show equal affinities to the Khoe-San and non-Khoe-San branch.