1 Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Københavns Universitet2 SAXO-Institute - Archaeology, Ethnology, Greek & Latin, History, Faculty of Humanities, Københavns Universitet3 Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Københavns Universitet4 Natural History Museum of Denmark, Natural History Museum of Denmark, Faculty of Science, Københavns Universitet5 Department of Environmental Archaeology and Materials Science, The National Museum of Denmark, Copenhagen, Denmark.6 European School of Chemistry, Polymers and Materials Science, University of Strasbourg, Strasbourg, France.7 Natural History Museum of Denmark, Faculty of Science, Københavns Universitet8 SAXO-Institute - Archaeology, Ethnology, Greek & Latin, History, Faculty of Humanities, Københavns Universitet9 Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Københavns Universitet10 Natural History Museum of Denmark, Faculty of Science, Københavns Universitet
comparison between mass spectrometry-based peptide sequencing and microscopy-based methods
Denmark has an extraordinarily large and well-preserved collection of archaeological skin garments found in peat bogs, dated to approximately 920 BC - AD 775. These objects provide not only the possibility to study prehistoric skin costume and technologies, but also to investigate the animal species used for the production of skin garments. Until recently, species identification of archaeological skin was primarily performed by light and scanning electron microscopy or the analysis of ancient DNA. However, the efficacy of these methods can be limited due to the harsh, mostly acidic environment of peat bogs leading to morphological and molecular degradation within the samples. We compared species assignment results of twelve archaeological skin samples from Danish bogs using Mass Spectrometry (MS)-based peptide sequencing, against results obtained using light and scanning electron microscopy. While it was difficult to obtain reliable results using microscopy, MS enabled the identification of several species-diagnostic peptides, mostly from collagen and keratins, allowing confident species discrimination even among taxonomically close organisms, such as sheep and goat. Unlike previous MS-based methods, mostly relying on peptide fingerprinting, the shotgun sequencing approach we describe aims to identify the complete extracted ancient proteome, without preselected specific targets. As an example, we report the identification, in one of the samples, of two peptides uniquely assigned to bovine foetal haemoglobin, indicating the production of skin from a calf slaughtered within the first months of its life. We conclude that MS-based peptide sequencing is a reliable method for species identification of samples from bogs. The mass spectrometry proteomics data were deposited in the ProteomeXchange Consortium with the dataset identifier PXD001029.