Mass spectrometry (MS) is a universal technique with a wide range of applications, including proteomic studies of different organisms, particularly the characterization and sequencing of proteins isolated from specific cellular compartments. It is used for the identification of elements exposed on the cell surface of microbial pathogens, which are involved in the initial contact with the human host, and then in the further development of infection. Given the increasing frequency of invasive fungal infections caused by pathogenic yeast from the genus Candida, especially among patients with severe immunological impairments, it appears advisable to study the diversity of cell wall proteins that arise during subsequent stages of infection and that are responsible for several important phenomena correlated with pathogenesis. This study employed a liquid chromatograph-coupled mass spectrometer equipped with an electrospray ionization source (ESI), and an ion trap analyser. For tandem mass spectrometry, two approaches for fragmentation of ions - collision-induced dissociation (CID) and electron transfer dissociation (ETD) - were used to analyse the mixtures of peptides generated after tryptic digestion of fungal cell wall proteins (i.e. the “bottom-up” approach). Several surface proteins from Candida spp. were identified which could be potential drug targets and candidates for vaccine development.