Typhoid fever is an endemic disease that has been acknowledged as a major global health burden. Typhoid fever is a neglected re-emerging infectious disease that is transmitted through fecal oral route. Nevertheless, non-typhoidal Salmonella outbreak has been increasing globally with large number of cases involving immunocompromised individuals. The clinical diagnosis of typhoid is difficult due to the overlapping symptoms of typhoid fever, non-typhoidal Salmonella, and other associated febrile diseases, which causes to delayed treatment. Herein, this study aims to provide a reproducible, discriminative protein fingerprint of two different Salmonella serovars using a differential extraction procedure comprising of whole cell protein (WCP), cell surface protein (CSP) and surface-depleted whole cell protein (sdWCP) derived from whole cell bacterial protein of Salmonella Typhi (S.Typhi) and Salmonella spp (S.spp). In the present research, we perform comparative analysis to characterize protein profiles of two differentially extracted Salmonella serovars by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and dendrogram analysis. The findings showed that the proteins were reproducible in optimized concentration. Separation of protein into three different extractions revealed discriminative protein profiles with major and micro-heterogenicity. We observed the diverseness of differentially extracted proteins between two strains which provided an effective adjunct that can be used in identification of Salmonella strains. The results achieved when differential extraction procedure was applied, provides a promising, future opportunity for further immunoproteomic classifications.