Polyunsaturated fatty acids are primary targets during oxidative stress. Diffusible electrophilic α,β-unsaturated aldehydes, such as 4-hydroxynonenal (HNE), have been shown to modify proteins that mediate cell signaling and modify gene expression pathways. We describe a global strategy for identifying the protein targets of HNE modification. A similar approach can be used for any electrophiles derived from an oxidized lipid.