Although vaccines developed from live organisms have better efficacy than those developed from dead organisms, the mechanisms underlying this differential efficacy remain unexplored. In this study, we combined sub-immunoproteomics with immune challenge to investigate the action of the outer membrane proteome in the immune protection conferred by four Edwardsiella tarda whole-cell vaccines prepared via different treatments and to identify protective immunogens that play a key role in this immune protection. Thirteen spots representing five outer membrane proteins and one cytoplasmic protein were identified, and it was found that their abundance was altered in relation with the immune protective abilities of the four vaccines. Among these proteins, TolC and OmpA were found to be the key immunogens conferring the first and second highest degrees of protection, respectively. TolC was detected in the two effective vaccines (live and inactivated-30-F). The total antiserum and anti-OmpA titers were higher for the two effective vaccines than for the two ineffective vaccines (inactivated-80-F and inactivated-100). Further evidence demonstrated that the live and inactivated-30-F vaccines demonstrated stronger abilities to induce CD8+ and CD4+ T cell differentiation than the other two evaluated vaccines. Our results indicate that the outer membrane proteome changes dramatically following different treatments, which contributes to the effectiveness of whole-cell vaccines.Vaccines are the most effective strategy to control infectious diseases caused by pathogens 1,2 . The type of vaccine can be differentiated based on preparation methods, of which whole-cell vaccines were the earliest developed and are currently in wide use 3 . There are two types of whole bacterial vaccine: the live vaccine and the inactivated vaccine. Inactivated vaccines comprise several subtypes, categorized based on the method of vaccine preparation 4 . In most cases, higher immune protection is detected with live vaccines than with inactivated cells or with vaccines prepared at lower temperatures compared to higher temperatures 5,6 . The strong immune protection induced by live vaccines is attributed to the possibility that live vaccines may mimic natural infection, including secreted proteins, and thus naturally evoke the full immune response of the host 7,8 . This hypothesis partly explains the differential immune protective abilities of different types of vaccines but does not actually provide answers regarding how inactivated vaccines derived from the same cells but treated via different methods lead to the induction of differential immune protection. Given that bacterial proteins may stimulate or inhibit host immune responses 9,10 , we reasoned that whole-cell vaccines stimulate host immunity by placing all surface proteins in contact with the host immune system rather than a single surface protein; thus, the resulting immunity derives from the immune responses stimulated by all of the surface proteins, regardless of whether they stimulate or inhi...