The use of electron capture negative ion desorption chemical ionization mass spectrometry was demonstrated in the analysis of phospholipid molecular species at the 1,3-dinitrobenzoate (DNB) diglyceride derivative. Modification of phosphatidylcholine (PC) or phosphatidylethanolamine (PE) by phospholipase C treatment and acylation of the resultant diglyceride with 3,5-dinitrobenzoylchloride afforded separation of the alkylacyl, alkenylacyl, and diacyl dinitrobenzoate subclasses by thin-layer chromatography (TLC). Separation of alkylacyl DNB into individual molecular species by reverse-phase high-performance liquid chromatography (RPHPLC) was demonstraed. Electron capture desorption chemical ionization of individual molecular species (10-25 ng) from a direct probe yielded a mass spectrum characterized by an intense molecular anion. This molecular anion was the base peak of the spectrum accounting for greater than 80% of the total ionization. From this molecular anion the total carbon number and degree of unsaturation of the fatty chains could be determined. Analysis of fatty acid content of the molecular species allowed unequivocal assignment of structure for the alkyl ether phospholipids. Using selected ion monitoring as little as 0.5 pmol of these species could be detected with a signal-to-noise ratio 23. This technique was useful in the analysis of low picomolar amounts of molecular species of ether phospholipids in the rat lung. Given an appropriate internal standard, analysis of dynamic changes in turnover, metabolism and precursor product relationships could be undertaken.