The advent of soft ionization techniques MALDI and ESI have opened the doors of mass spectrometry to biological samples. Particularly protein research exploited this opportunity to the utmost that qualitative, quantitative, structural and distributional analyses of proteins have become achievable. Comparison of all expressed proteins belonging to two or more states is defined as differential proteomics and commonly performed either separating the proteins on a gel or separating the peptides in the mixture within a column. In this study, both of these methods were applied to a parasite that causes to the infectious disease, Leishmaniasis. Consequences of the disease become severe when parasite is multiplied in viscera rather than skin. Occurrence of different clinical manifestations is attributed to the variety in species however some species can cause to both such as L.infantum and L.tropica. The purpose of this study was to investigate this duality in L.infantum. Despite originating from two different species, cutaneous leishmaniasis isolates obtained from ten different patients exhibited considerably similar protein profiling on the gels however isolates belonging to five visceral leishmaniasis patients were discriminated from them with regards to protein abundances. Additionally, several differential proteins between cutaneous leishmaniasis and visceral leishmaniasis samples were determined by gel-free approach. Apart from that, another mass spectrometric strategy for the abovementioned distributional analysis namely mass spectrometry imaging was included in the last section. Herein, a method incorporating the application of enzyme with matrix was developed for easy sample preparation to on-tissue digestion and promising results were obtained for a start.