Hardware for paleoproteomics

PhD candidate: Diana Samodova

Objectives

The project aims at optimization of mass spectrometry technology for analysis of proteinaceous substances present in ancient artefacts.

Expected results

The elaborated improvements in core technology will be used for analysis of degraded and highly modified proteins of unknown origin, enabling ancient species identification, determination of post-translational modifications and sequence variants. In particular, optimized MS-based proteomics workflows will be applied in the context of TEMPERA network, where research questions include characterization of proteinaceous paint binders in ancient artefacts (e.g. egg caseins or vegetable gums). This should lead to a better understanding and perception of the original appearance of painted objects important for the study and protection of European cultural herritage materials.

My project

In this technology-focused project, improvements in the core bottom-up proteomics technology will be sought for better analysis workflows for degraded proteins of unknown origin present in the cultural heritage materials. The developments will mainly focus on sample preparation (according to the type of sample), workflows optimized to the study of very small sample amounts, optimizations of liquid chromatography and changes to MS methods involving orthogonal fragmentation schemes and evaluation of new MS hardware to increase data quality for normal bottom-up sequencing. Finally, implementation of high end data analytical software tools will enable data interpretation.

The above mentioned MS developments will be performed on the recently introduced Orbitrap Fusion Lumos Tribrid mass spectrometer, that is the industry-leading high-performance mass spectrometer and, at the time of this writing, the instrument with the best sensitivity, best mass resolution, and fastest scan rate. It is equipped with the higher capacity ETD HD fragmentation mode and benefitting from improved transmission of ions into the Orbitrap analyzer. Improved precursor storage capacity in the ETD HD mode leads to a larger fragment ion population thereby increasing the dynamic range of the ETD acquisition scan. These features make it one of the most attractive analytical tools for palaeoproteomic sample analysis. Aiming at minimizing preparation steps to maximize recoveries of analytes from cultural heritage objects, MS procedures will be developed to apply bottom-up tandem MS protein sequencing to digested protein extracts of cultural heritage samples, by taking full advantage of the Orbitrap Fusion Lumos Tribrid advanced features. This instrumentation is available for the Georgia Ntasi (@UoN) and Diana Samodova at both University of Copenhagen and Thermo Fisher Scientific in Bremen.

Networking

Planned secondments:

  1. Secondment period of 6 months at Thermo (Bremen), to collaborate with Thomas Moehring and his colleagues to expand Diana Samodova's experience about hardware development.
  2. Secondment period of 4 months at MPG to assist Petra Gutenbrunner in the development of new control software for the Orbitrap Fusion Lumos Tribrid mass spectrometer.
  3. Secondment period of 3 months at Thermo USA R&D in San Jose (California) to collaborate with colleagues at the USA research facility on development of the most advanced company projects.

At: University of Copenhagen

Supervisor: Christian Kelstrup

Photo credits: Mkotl