The meningococcus (Neisseria meningitidis) remains an important threat to human healthworldwide. This Gram-negative bacterium causes elevated disabilities and mortality in infectedindividuals. Despite several available vaccines, currently there is no universal vaccine against allcirculating meningococcal strains ( Vogel et al., 2013 ). Herein, we describe a new protocol that iscapable of identifying only cell surface exposed proteins that play a role in immunity, providing thisresearch field with a more straightforward approach to identify novel vaccine targets. Even though N. meningitidis is used as a model in the protocol herein described, this protocol can be used for anyGram-negative bacteria provided modifications and optimizations are carried out to adapt it to differentbacterial and disease characteristics (e.g., membrane fragility, growth methods, serum antibody levels,etc.).