The article is devoted to the consideration and analysis of factors influencing the formation of a well-rounded specialist who is ready to solve extraordinary tasks, including transdisciplinary orientation. The paper shows that the most effective development of the innovative activity skills of masters is carried out using the methods of project training and in conditions of social partnership on the basis of existing production with its real problems and tasks. Such comprehensive approach based on the university collaboration with different organizations during the realization of joint scientific and technical projects will allow the student to try himself in different professional roles and subsequently make the right choice of the specialization considering the acquired personal qualities in the sphere of modern high-tech productions and also easily adapt to new social and economic challenges and the needs of society. It is shown that the project approach is one of the most prospective pedagogical techniques appropriate for this goal. It is specially noted that the introduction of modern innovative approaches into the masters’ educational process has great prospects for Russia because it gives an opportunity to form the required qualification potential of future graduates of technical universities. The application of project training techniques during the training of engineering specialists is considered on the example of implementation of interdisciplinary projects of the Ural Federal University named after the first President of Russia B. N. Yeltsin. Projects are organized based on the partnership of Institute of Physics and Technology with the Cyclotron Center for Nuclear Medicine and other innovation and implementation centers of UrFU.