Document Type



Master of Science


Chemistry, Biochemistry

Date of Defense


Graduate Advisor

Chung Wong


Cynthia Dupureur

Michael Nichols


2-Dimensional Electrophoresis is one of the tools in the identification of proteins by molecular weight and pH. The display of molecular weight allows the researcher to quickly identify whether a specific protein or peptide string is in the sample. The pH measurement allows even better resolution between different species in the sample. The MultiEnzyme ElectroPhoresis (MEEP) program tries to model that by providing a graph that displays separated protein strings by both molecular weight and pH. The ability to cleave the protein with 43 different enzyme variations allows the researcher to analyze appropriate enzymes to isolate a protein subsequence before the actual experiment or to compare the experimental data with the simulated electrophoresis. This thesis reviews protein cutting simulations that have been done in the past or are currently available. It then describes the MEEP program: how it appears to the user, how the user makes it operate, and how it is structured. The thesis provides validation information for the calculation of molecular weight and isoelectric point. The program will hopefully provide a useful addition for the researcher’s work.