Immune reactions after vaccination involve many different specialized cells that interact strongly with each other and the components of the vaccine. These interactions result either in a long-lasting protection, i.e. successful vaccination, or failure thereof. The goal of this research is to develop a robust but simple analytical workflow that would allow a profound and quantitative characterization of the interactions between the involved cells on a functional level, and using found patterns to predict the outcome of the vaccine candidate. By doing so, biological signatures become detectable that could help to better understand the interactions and processes involved. This should ultimately lead to a more rational approach in designing and developing new, better and safer vaccines. Due to pattern recognition, the process of testing candidates is further facilitated and development sped up.