Periodic Reporting for period 1 - PROMISE (Proteomic optimization of methods for ancient skeletal elements)
Berichtszeitraum: 2023-12-01 bis 2025-11-30
The PROMISE fellowship aimed to improve methods for the study of skeletal proteomes from the Pleistocene and thereafter apply these methods to archaeological sites in the Levant. Palaeoproteomic analyses can allow for the study of evolution and ecology of past organisms, including extinct hominins. These analyses are, however, complicated by the fact that the studied objects have been buried for a long time, and occasionally stored for a long time after excavation, thereby being covered by contamination from various sources. Additionally, the proteins are slowly degrading and accumulating damage over time. The field of palaeoproteomics is relatively new, and as such, methods to analyse these ancient, degraded, and contaminated proteomes are still in their infancy. PROMISE had three main objectives to address these issues for Pleistocene bones and teeth: 1) Optimising methods for protein extraction, 2) Investigating the effects of microbial attack on the proteome, and 3) Application of gained knowledge and developed methods to Levantine archaeological specimens, an area which is challenging to study due to protein degradation, albeit essential for understanding the evolution of our species. Together, the objectives aimed to significantly advance the field of palaeoproteomics, as the methods, approaches and gained knowledge can be applied to a wider range of palaeoproteomic research contexts.
During PROMISE, method development was performed using archaeological animal bones and teeth of a wide age range, producing data using protein mass spectrometry, particularly LC-MS/MS. Methods for removing protein contamination were evaluated for both dental enamel and bone, using an innovative approach of artificial contamination of archaeological material using saliva and fur from a modern dog (see photo). Optimized methods for demineralization of bone and dental enamel were also developed, showing the effects of different reagents and concentrations on the extracted proteins. Progress was made on evaluating the presence of microbial proteins in archaeological bone, through the complex analysis of metaproteomes. All technical research objectives of PROMISE were therefore achieved. Finally, the work performed in PROMISE established the presence of preserved proteins in a range of Pleistocene archaeological sites in the Levant.
The improved methods for ancient protein extraction developed during PROMISE mean that more high-quality data can be gained from each sample, thereby reducing the need for destructive sampling of limited archaeological materials. Beyond the optimized methods and increased knowledge in palaeoproteomics, PROMISE also established new approaches to method development and experimental design. The research conducted within PROMISE included several international collaborations, both within and outside Europe, with a wide range of scientists from different areas of expertise, strengthening scientific collaborations between countries and fields of research. The training within PROMISE, ranging from laboratory and bioinformatics methods to scientific communication, teaching, and project management, provided a robust base for both carrying out the work within PROMISE, as well as a future research career.