Phosphatidylethanolamines (PE) and phosphatidylcholines (PC) are important phospholipids frequently present in many types of cells. In some cases, PE has been equated with PC because they are chemically very similar and are often isomeric species. In this study, we demonstrate that noncovalent complexation between PE and 18-crown-6 ether (18C6) can be used to quantitatively mass shift and separate PE from PC phospholipids. Detection of PE is also more sensitive by approximately an order of magnitude with addition of 18C6. This noncovalent complexation approach is used to separate and quantitatively characterize PE in a soy bean asolectin extract. 18C6 (modified with an iodobenzoyl moiety) can also be used to efficiently generate radical PE lipids following photoactivation in the gas phase. Subsequent collisional activation of these lipid radical ions leads to radical directed dissociation (RDD), which generates unique fragment ions relative to dissociation of comparable even electron ions. Interestingly, RDD produces fragment ions that reveal carbon bonding features within the lipid acyl chain substituents, such as double bond location or the presence of branching. Furthermore, several novel and abundant fragments were observed in unsaturated lipids. Mechanisms that can account for the high abundance of some of these product ions are proposed.