Computational Proteomics

ESR7: Computational paleoproteomics (@ MPI).

In the analysis of ancient proteins from cultural heritage material one faces several particular challenges that will all be addressed by development of software modules and algorithms in close collaboration with the experimental partners. These will be implemented as extensions to the established MaxQuant and Andromeda platforms. For several applications in ancient sample analysis, peptide identification from large search spaces are required. For this purpose the Andromeda search engine is further optimized to enable solid identification in this situation. Alternatively, pre-existing de-novo sequencing techniques are further developed to be able to identify peptides and proteins independent of a sequence database. This includes clustering of single spectra de-novo identifications in order to be able to confidently identify regions or domains of proteins that have a sufficient MS/MS sequence coverage, and to map out their modification content.

Algorithm for the search engine driven and for the unrestricted identification of protein modifications will be developed for the specific challenges in ancient samples. An expert system will be developed and trained to be able to automatically apply domain-specific rules for the interpretation of MS/MS spectra. This includes special rules for the proper treatment of deamidation and other modifications in order to aid distinguishing clear cases of ancient sample-specific processes from sample preparation by-products. An expert system-informed localization score will apply this knowledge to calculate reliable localization properties for PTMs. Furthermore a library will be built up with the information obtained on ancient peptides with and without PTMs in order to be able to apply this knowledge to new samples and to improve the dynamic range of detection in these.

The development of Top-down paleoproteomics is supported by the development of a Top-Down version of MaxQuant that will be able to identify and quantify proteins from relatively complex mixtures and the determination of their PTMs from MS/MS spectra acquired with a variety of fragmentation types. This will be done in close collaboration with ESR6 and ESR8. Networking. Within TEMPERA, ESR 7 will interact primarily with:

  1. ESR 6: ESR 7 will spend a secondment period of 6 months at UCPH (JVO co-supervision) to collaborate with ESR 5 to test on ESR 6’s datasets the algorithms ESR 7 will develop.
  2. ESR 8: ESR 7 will spend a secondment period of 4 months at Thermo (Bremen) to develop and test new control software for the Orbitrap Fusion Lumos Tribrid mass spectrometer.