Proteomic optimization of methods for ancient skeletal elements

Project Information

PROMISE

Grant agreement ID: 101106627

DOI

10.3030/101106627

Project closed

EC signature date 11 April 2023

Start date 1 December 2023

End date 30 November 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 214 934,40

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

Periodic Reporting for period 1 - PROMISE (Proteomic optimization of methods for ancient skeletal elements)

Reporting period: 2023-12-01 to 2025-11-30

Summary of the context and overall objectives of the project

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.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

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.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

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.

Contamination of a piece of archaeological dental enamel by the research assistant Tjorven.