Ozone-induced dissociation (OzID) exploits the gas-phase reaction between mass-selected lipid ions and ozone vapor to determine the position(s) of unsaturation. In this contribution, we describe the modification of a tandem linear ion-trap mass spectrometer specifically for OzID analyses wherein ozone vapor is supplied to the collision cell. This instrumental configuration provides spatial separation between mass-selection, the ozonolysis reaction, and mass-analysis steps in the OzID process and thus delivers significant enhancements in speed and sensitivity (ca. 30-fold). These improvements allow spectra revealing the double-bond position(s) within unsaturated lipids to be acquired within 1 s: significantly enhancing the utility of OzID in high-throughput lipidomic protocols. The stable ozone concentration afforded by this modified instrument also allows direct comparison of relative reactivity of isomeric lipids and reveals reactivity trends related to (1) double-bond position, (2) substitution position on the glycerol backbone, and (3) stereochemistry. For cis-and trans-isomers, differences were also observed in the branching ratio of product ions arising from the gas-phase ozonolysis reaction, suggesting that relative ion abundances could be exploited as markers for double-bond geometry. Additional activation energy applied to mass-selected lipid ions during injection into the collision cell (with ozone present) was found to yield spectra containing both OzID and classical-CID fragment ions. This combination CID-OzID acquisition on an ostensibly simple monounsaturated phosphatidylcholine within a cow brain lipid extract provided evidence for up to four structurally distinct phospholipids differing in both double-bond position and sn-substitution. (J Am Soc Mass Spectrom 2010, 21, 1989 . There are a wide range of lipid subclasses with different biochemical roles, including glycerophospholipids (GPLs) that act as primary building blocks of membranes and precursors for intracellular signaling molecules; fatty acids (FAs) and triacylglycerols (TAGs) that are the major source of energy in plants and animals; and sterols that modulate membrane stability and act as biochemical messengers [2]. The specific functions of lipid classes, and indeed individual lipids, are related to their chemical and physical properties that in turn depend on specific molecular features [3]. As such, even small changes in molecular structure can affect the role of a lipid within a living organism. Recent research has indicated that within living organisms, different lipid isomers play different, and in some cases contrasting, metabolic roles. For example, one study focusing on the effect of conjugated linoleic acid isomers on development of atherosclerosis in ApoE knockout mice revealed that while one isomer (10E,12Z-18:2) had a profound atherogenic effect, an alternate isomer (9Z, 11E-18:2) was anti-atherogenic [4]. While differences in molecular structure arising from double-bond position and/or stereoisomerism (vide infra) can be cha...