Defining the repertoire of antigenic targets is central to better understanding the immune responses against wether contagious pathogens and those transmitted by arthropod vectors. Traditional molecular approaches of antigen discovery have identified many immunodominant antigens, but they afford limited proteome coverage. Advances in proteomic technologies that are based on peptide library and the increase in genome sequencing that enriched molecular databases, allowed the definition of new analytical strategies with interrogation of the entire proteome for antigens. At the same time, improved technologies for antibodies purification for serum as well as antigens immunocapture lead scientists to revisiting the characterisation of immuno-proteomes, particularly in the frame of contagious or vector-borne animal diseases. Here, we propose an analytical workflow to illustrate how to deepen the definition of the immuno-proteomes, and illustrate the proof of concept targeting Mycoplasma mycoïdes, the causative agent of contagious bovine pleuropneumonia (CBPP).