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Cysteine residues perform many essential cellular functions, including nucleophilic and redox catalysis, metal coordination, structural stabilization and cellular protection. Cysteine-related mutations are oftentimes related to diseases due to the amino acid’s functional importance. This has led cysteine to become a focus of small molecule drug discovery. A comparison of the cysteine proteome of diseased cells versus healthy cells can elucidate novel cysteine residues that play an important role in progressing the disease state. Two disease models were chosen to be the focus of this proteomic study; breast cancer through the human epithelial MCF10 progression series and immunoactivation through the Raw 246.7 mouse macrophage cell line. Comparative proteomics with mass spectrometry revealed several changes within the cysteine proteome when the cells were diseased. Some cysteines had changes in …