Palaeoproteomics bootcamp

July 12th, 2018

Centre de Cultura Contemporània de Barcelona (CCCB)

The analysis of ancient proteins from archaeological and paleontological samples requires the implementation of dedicated solutions. Ancient proteins are fragmented and chemically modified due to spontaneous, non-enzymatic reactions occurring over extended time ranges in uncontrolled environmental conditions. They can originate from extinct organisms whose genome is not available, and they are frequently co-extracted together with environmental contaminants and proteins from environmental microorganisms. Specific strategies need to be implanted at peptide-spectra matching stage, to maximise ancient protein sequence reconstruction and to accurately characterise ancient protein damage. During this workshop we will describe, with how some of the functions available in MaxQuant can be used to fulfill specific needs of ancient protein analysis.

The coordinator of the TEMPERA ETN gave a general introduction about the importance of the study of ancient proteins in the archaeology and Cultural Heritage fields using mass spectrometry-based proteomics.

Prof. Cappellini also showed some of the applications from the work of his group in University of Copenhagen, from the use of proteins as source of information for very ancient samples, in which no other biomolecule is preserved, to the application to the study of human evolution, to the investigation and the characterisation of damage of the organic components of artistic materials.

Petra Gutenbrunner, carrying out her PhD project in the Max Plank Institute of Biochemistry in Munich (see her project here), depicted how the MaxQuant software can be optimized for the investigation of ancient proteins, using innovative features such as the Dependent peptides search and the de novo sequencing of previously uncharacterized proteins. In addition, she illustrated the use of novel scoring methods to improve the detection and identification of damaged/modified peptides in archaeological and artistic samples.

For all the news about the MaxQuant software, please refer to this link.

Patrick Rüther, carrying out his PhD project at University of Copenhagen (see the project here), has presented an innovative application of the Dependent Peptides feature in the MaxQuant software. By using this software, several PTMs (post-translational modifications) have been identified in the protective layers of a wall painting, allowing the partial characterisation of the damage of the proteinaceous material.

For all the details about this work, the paper "Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting", by Mackie et al., is available for open-access download following this link.

Photo credits: Patrick Rüther, Fabiana Di Gianvincenzo