Patrick Leopold Rüther

Discovery of New Age-Related Protein Modifications

Patrick Leopold Rüther£; Meaghan Mackie§£; Enrico Cappellini§; Jesper V. Olsen£

£ Novo Nordisk Center for Protein Reserach, Blegdamsvej 3B, 2200 København, Øster Farimsgade 5A 1353 København; § Natural History Museum of Denmark - University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen, Denmark

Over the past 18 years, Palaeoproteomics has rapidly developed to a stage, at which species identification in reasonably well conserved samples is a relatively simple task. Just like in biomedical proteomics, ancient proteins can provide a lot more information than the origin of a specimen. Therefore, our group and many others have started to focus more and more on post-translational modifications (PTMs). These have the potential of giving us insight into the degradation, conservation, and processing history of proteins in cultural heritage material.

We developed an analysis workflow for LC-MS/MS data, which overcomes the limit of about five measurable PTMs per search and allows us to assess the relative degree of modification in ancient samples. Our strategy is based on a two-step database search starting with the “dependent peptides” feature in MaxQuant, which facilitates unbiased search of modifications by mass-shifts, and finishing with a conventional database search for validation and quantification.

The first successful application of this method was recently published (Mackie et al., Angew. Chem., 2018). With our approach, we were able to detect photo-modifications and glycations, which we would not have discovered with conventional methods. We believe that this contribution to the field of Palaeoproteomics will lead to the discovery of new aging-linked PTMs telling us a more detailed story about the history of ancient proteins.