Carbonyl group formation on protein side chains is a common biochemical marker of oxidative stress and is frequently observed in a variety of acute and chronic neurological diseases including stroke, Alzheimer’s disease, and Parkinson’s disease. Given that proteins are often the immediate targets of cellular oxidative stress, it is of utmost importance to determine how adductions by reactive electrophiles and other oxidative reactions can irreversibly alter protein structure and function. Previously, protein adduction was thought to be a random process, but recently it has become increasingly clear that these protein modifications are specific and selective. In this work, two methodological approaches are presented which allow for the detection of protein carbonyl groups. While the OxyBlot methodology allows for the evaluation of general oxidative stress, the use of the novel and powerful biotin–avidin-capture methodology allows for the identification of specific proteins that have been targeted by oxidative stress.