HOPE primarily utilized protein mass spectrometry analysis on a range of fossil samples to characterize proteome and protein sequence composition. This included fauna samples, hominin samples, or a combination of both, depending on objectives and material availability. The molecular work was carried out in ancient biomolecular laboratories now housed at the Globe Institute, the University of Copenhagen (Denmark). For comparison, the project also studied a limited number of modern or near-modern dental specimens. During this period, I gained advanced insights into protein mass spectrometry, extraction method (development), and bioinformatic analysis of the resulting datasets. In return, I brought my human evolution knowledge to the hosting institute.
The main outcome of this research was that proteins are recoverable beyond the limits of ancient DNA preservation, and that proteins preserved in enamel specifically survive over extended geological time scales. These proteins remain phylogenetically informative. In other words, their amino acid sequences are variable enough from species to species to determine evolutionary relationships. Simultaneously, be either enlarging the number of proteases used, or entirely eliminating them, the project was involved in enhancing extraction methods for proteins in skeletal material generally. These new approaches either allow access to extremely ancient proteomes, or enhance proteome complexity, and thereby their evolutionary utility.
During HOPE, a 3-month secondment to the group of Dr.. Skoglund at the Crick Institute provided a training opportunity to acquire enhanced insights into population genetic methods and their potential applicability to ancient protein datasets in the future. The training was completed successfully.
