The fungal kingdom is estimated to contain around 11 million different species that vary in structure, functions, and preferred living environments. Many different types of fungi grow on plants and can have either beneficial or harmful effects on the growth and development of certain crops, including potatoes. One of the fungal infections that results in major crop losses in Canada and worldwide is potato wart. The pathogen that causes this infection is not well-understood and the factors that play a role in disease progression remain unknown. Previous research indicated that the fungus responsible for potato wart is capable of producing chemicals that facilitate the infection. Identifying these fungal molecules may aid in understanding the mechanisms the fungus is using to attack potato plants. Mass spectrometry (MS) is an analytical technique that determines the structure and mass of molecules that are present in the sample. The components of the sample mixture are broken down into fragments that are then detected by the instrument. These generated fragments are characteristic of their overall chemical structure, where fragmentation patterns can be compared and matched to libraries of previously identified chemicals to confirm their identity. In this study, mass spectrometry was used to compare the differences in protein levels between uninfected and infected tubers. Overall, around 600 proteins were identified in each variety. Following data analysis, it was determined that different potato varieties respond to infection differently.