We analyzed the molecular species composition of the glycosylphosphatidylinositol (GPI) anchor of Torpedo marmorata acetylcholinesterase (AChE) and compared it to that of the membrane phosphatidylinositol (PI) as well as the other major phospholipid classes of T. marmorata electrocytes. Purified amphiphilic AChE was treated with PI-specific phospholipase C in order to release the diradylglycerol moiety from the membrane anchoring domain. Subsequently, the diradylglycerols were derivatized into their diradylglycer-obenzoates and separated into subclasses (diacyl, alkylacyl, and alk-1-enylacyl types). The molecular species within each subclass were separated and quantitated by high performance liquid chromatography and UV detection and directly introduced through the thermospray interface into a mass spectrometer for identification. The PI moiety of the GPI anchor of AChE consisted exclusively of diacyl molecular species. Over 85% of the molecular species were composed of palmitoyl (16:0), stearoyl (18:0), and oleoyl (18:1) fatty acyl chains in the sn-1 and sn-2 positions. Less than 5% of the molecular species of the GPI anchor contained polyunsaturated fatty acyl chains, as compared to more than 70% of the diacyl molecular species of the PI from electrocyte membranes. Since the GPI anchors of AChE from both human and bovine erythrocytes contain alkylacyl molecular species of PI (Roberts, W. L., Myher, J. J., Kuksis, A., Low, M. G., and Rosenberry, T. L. (1988) J. Biol. Chem. 263, 18766-18775), our results on AChE from Torpedo demonstrate that the composition of the PI moiety of the GPI anchor of a protein is not characteristic for that protein but may vary between species.