Coordination ion-spray mass spectrometry (CIS-MS) is a useful tool in the detection and identification of complex mixtures of cholesterol ester and phospholipid hydroperoxides. The methyl ester, cholesterol ester, and phospholipid hydroperoxides of docosahexaenoic acid were analyzed by LC-CIS-MS and their elution orders were identified. Their corresponding alcohols were also identified. The methyl hydroperoxydocosahexaenoate (HPDHE) elution order is 14, 17, 16, 13, 20, 11, 10, 4, 7, 8 while the methyl hydroxydocosahexaenoate (HDHE) elution order is 14 > or = 17, 16, 13, 11, 10, 20, 7, 8, 4. The cholesteryl HPDHE elution order is 14, 17, 16, 13, 20, 11 > or = 10, 4, 7, 8 and the cholesteryl HDHE elution order is 17, 14, 16, 13, 11, 20, 10, 7, 8, 4. The elution order of the 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylcholine (PDPC) hydroperoxides and alcohols is 20, 16, 17, 13, 14, 10, 11, 7, 8, 4.