The purpose of this study is to develop a higher sensitivity method to detect phospholipid peroxides in tissues to more effectively investigate the role of lipid peroxidation in pathology. We recently presented a gas chromatography-mass spectrometry (GC-MS) method for identification and measurement of phospholipid peroxides at the 10 ng level (van Kuijk, et al. J. Free Rad. Biol. Med., 1:215-225, 1985) based on transesterification to form fatty acid methyl ester derivatives. While this method is quite useful under some circumstances, more sensitivity was desirable to analyse trace amounts of lipid peroxidation products in small samples of various tissues. We present a method to prepare pentafluorobenzyl esters of fatty acids and hydroxy fatty acids directly from phospholipids by transesterification at room temperature or from triglycerides at 60 degrees C. Oxidized lipids are extracted into dichloromethane and peroxide functions are reduced with sodium borohydride. Transesterification of phospholipids is carried out in dichloromethane with 20% (v/v) pentafluorobenzyl alcohol, 1% (w/v) potassium tert-butoxide and 0.2 N (m-trifluoromethyl phenyl) trimethyl ammonium hydroxide at room temperature for 30 min. Pentafluorobenzyl esters are purified on open silica columns, O-trimethyl silyl derivatives of the alcohol functions are formed, and GC-MS is carried out with negative ion chemical ionization detection. The single or double oxidation products of oleate, linoleate, arachidonate, and docosahexaenoate were detected with 10 pg sensitivity in oxidized rat retina phospholipids or synthetic phospholipids, by negative ion chemical ionization with specific ion monitoring of carboxylate anions.