Oxidized phospholipids play an important role in execution of the mitochondrial stage of apoptosis and clearance of apoptotic cells by macrophages. Therefore, the identification and quantification of oxidized phospholipids generated during apoptosis are very important. These can be achieved successfully by a newly developed approach--oxidative lipidomics, including a combination of electrospray ionization/mass spectrometry (ESI-MS) and fluorescence high-performance liquid chromatography techniques. Using oxidative lipidomics allows the quantification of specific phospholipids and their hydroperoxides. We characterized selective oxidation of two anionic phospholipids: cardiolipin (CL) in mitochondria and phosphatidylserine (PS) outside of mitochondria. ESI-MS analysis of cytochrome c/H(2)O(2)-driven tetralinoleoyl-CL (TLCL) oxidized molecular species demonstrated accumulation of products monohydroxy-TLCL; monohydroxy-monohydroperoxy-TLCL, monohydroxy-dihydroperoxy-TLCL, monohydroxy-trihydroperoxy-TLCL; and monohydroxy-tetrahydroperoxy-TLCL. We explored the application of oxidative lipidomics in a number of conditions in both in vitro and in vivo models where there is a known contribution of apoptosis and/or inflammation. Accumulation of CL hydroperoxides, originated from molecular species of CL containing C(22:6) after experimental traumatic brain injury, was shown. ESI-MS analysis of intestine CL in mouse after gamma-irradiation detected several CL oxidized molecular species: (C(18:2))(3)/(C(18:2+OOH)); (C(18:2))(2)/(C(18:2+OOH))(2); (C(18:2))(1)/(C(18:2+OOH))(3); and (C(18:2+OOH))(4). ESI-MS analysis and tandem MS/MS experiments revealed that PS with oxidized C(22:6) [m/z866 (C(18:0)/C(22:6+OOH)) originated from the ion at m/z 834 (C(18:0)/C(22:6))] was the major oxidized molecular species in the tested models in vitro and in vivo, including (1) cytochrome c/H(2)O(2) catalyzed oxidation of rat brain PS; (2) after experimental traumatic rat brain injury in rats, (3) in postmortem brain samples from patients with Alzheimer's disease, and (4) in the small intestine in gamma-irradiated mouse. We conclude that oxidative lipidomics is a powerful technique to study lipid oxidation and its role in cell death across a spectrum of tissues and insults.