Oxidative stress leads to damage of protein molecules, particularly accumulation of protein carbonyls. Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS-susceptibility essential. The radiation-resistant bacterium Deinococcus radiodurans accumulates less carbonylation than sensitive organisms, making it a key model for deciphering properties governing oxidative stress resistance. We measured protein damage by 6.7 kGy of γ-irradiation in Escherichia coli and D. radiodurans by LC-MS/MS, and analyzed this result both to identify protein carbonyls at residue-resolution and quantifying relative abundance changes following irradiation.