Exploring the synergy of proteogenomics and cold ion spectroscopy of biomolecules

This project aims to develop a long-term training exchange program between PhD students of EPFL and MIPT/INEPCP, involved in the field of cutting-edge bioinformatics of (MIPT/INEPCP) and state of art experimental cold ion spectroscopy (LCPM, EPFL). MIPT is a leading Russian technical university in physics/chemistry/biology. Institute of Energy Problems of Chemical Physics hosts PhD students of MIPT to perform their PhD projects. Our partners at INEPCP (PI Dr. M. Gorshkov, institute director) have worldwide recognition for their developments of bioinformatics software tools for proteogenomics. The group of PI at EPFL is known for development of cold ion spectroscopy of biomolecules and for pioneering analytical applications of this innovative experimental approach. The fields of expertise of the two groups are therefore complementary, enabling a synergy of collaboration for PhD students.

While both groups collaborate in research, there was only a limited exchange of young PhD students between the two labs. We propose to train our EPFL PhD students to the new bioinformatics tools during short visits to INEPCP, while Moscow University of Physics and Technology students, working at INEPCP will be trained at EPFL for experimental cold ion spectroscopy of biomolecules. Each training will be organized as a mini research project, which, if successful, will become a part of the student’s PhD thesis. This exchange will allow the students to complement theory by experiment and vise verse.

EPFL group is particularly interested in proteogenomic analysis, predicting the targets (e.g., isomeric peptides), which identification is critical for discovering of biomarkers (e.g., of cancer), but challenging to perform with conventional techniques. The complex two-dimensional UV-MS experimental method of EPFL has demonstrated its performance for such identifications. The worldwide expertise of the Russian partner in proteogenomics is very valuable for such predictions, but also for training of EPFL's students. In return, training on a state of the art cold ion spectrometer at EPFL will bring an unique experience to MIPT students. They may experimentally verify some of their theoretical predictions, derived by proteogenomic tools, for the presence of certain genetic point mutations in proteins.

We preview 4-5 monthly visits to EPFL for 4 PhD students from Moscow and 3  10-day visits for EPFL students to Moscow.  The duration of the visits is dictated by the complexity of the experiment at EPFL and by the possibility to work remotely from EPFL with bioinformatic tools of the Russian partners.

We also preview a few mutual visits of PI’s, who will give one tutorial lecture each for the students of the respective  courses, regular lectured by the partner.

An indirect objective of the project is to set up a positive example for Russian authorities to increase financing of student’s exchange programs, which so far are largely supported by the Swiss agencies.

 

Participants

Dr. Oleg Boyarkine MER
EPFL
LCPM, ISIC, FSB

Mr. Erik Saparbaev MA
EPFL
LCPM, ISIC, FSB

Dr. Mikhail Gorshkov PhD
Russian Academy of Science
Institute of Energy Problems of Chemical Physics

Mrs Elizaveta Solov'eva MA
MIPT
Department of Molecular and Chemical Physics

Mr. Lev Levitsky MA
MIPT
Deapartment of Molecular and Chemical Physics

Mrs Victoria Aladinskaya MA
EPFL
LCPM (from 01.06.2018)

Mrs Julia Bublis
MIPT
Department of Molecular and Chemical Physics