There is a body of evidence lending credence to the idea that oxidative stress may be responsible for age-related deleterious changes in brain function, and that protein carbonylation is a potential marker for such changes. An investigation of oxidative damage to mitochondrial proteins from aged rat brains was done using gel electrophoresis coupled with carbonylation-specific immunostaining. Six proteins that appeared to be susceptible to oxidative modification were identified by in-gel trypsin digestion followed by matrix-assisted laser desorption/ionization mass spectrometry and tandem mass spectrometry. Two subunits of the H(+)-transporting ATP synthase, adenine nucleotide translocator, voltage-dependent anion channel, glutamate oxaloacetate transaminase, and aconitase were identified as likely targets of age-associated carbonylation.