The work in this thesis centres on understanding how electrostatic interactions modulate the function of proteins. A computational method is presented to predict the reduction potential shift of copper protein mutants. Two test mutants have been synthesised and their experimentally determined reduction potentials are compared to predictions. The focus of the thesis then shifts from considering how electrostatic interactions modulate the function of a single protein, to that of entire proteomes. Electrostatic-based methods for pKa and reactivity prediction are applied to the high-throughput proteomics data that are accruing for cysteine and lysine modifications. Conclusions are made on the biophysical factors which contribute to modification mechanisms, and cysteine/lysine susceptibility to specific modifications.