Through continued development, the two-dimensional PAGE gel technique developed by O'Farrell in 1975 has emerged as the hallmark technology utilized in virtually all protein expression analyses. The principle objective of this study was the development and validation of a proteome analysis methodology using this technique suitable for use in determining the quantifiable proteome differences between prion containing [PSI+] and wild type [psi-] strains of Saccharomyces cerevisiae. In addition to the development of an assay, which yields highly reproducible whole proteome isolates from both strains, was the elicitation of statistically significant proteome changes between the two strains. Thus, this study concludes that there is a quantifiable and reproducible effect on protein expression conveyed by the prion state in yeast, which warrants future studies to realize this implication within the context of epigenetics. Future studies will further benefit via the implementation of the methodology proven viable in this work in determining the specific nature of the observed proteome differential expression.