Significance Protein S -nitrosation ( SNO -protein) is a posttranslational modification in which a cysteine (Cys) residue is modified by nitric oxide ( SNO -Cys). SNO -proteins impact many biological systems, but their identification has been technically challenging. We developed a chemical proteomic strategy— SNO TRAP ( SNO trapping by triaryl phosphine)—that allows improved identification of SNO -proteins by mass spectrometry. We found that S-nitrosation is elevated during early stages of neurodegeneration, preceding cognitive decline. We identified changes in the SNO -proteome during early neurodegeneration that are potentially relevant for synapse function, metabolism, and Alzheimer’s disease pathology. SNO -proteome analysis further reveals a potential linear motif for SNO -Cys sites that are altered during neurodegeneration. Our strategy can be applied to multiple cellular and disease contexts and can reveal signaling networks that aid drug development.