Highly unsaturated fatty acids (HUFAs) are vulnerable to oxygen attack, thus making HUFA-rich, high metabolic rate/reactive oxygen species (ROS)-generating neurological tissue particularly susceptible to increased oxidative stress. Lipid oxidation is a putative early stage marker of neurodegenerative diseases, suggesting that reliable monitoring of oxidized neural lipids in vivo reveals early pathogenesis. Here, we present a novel methodology to detect and quantify intactin vivo ROS-driven peroxidized phospholipids (LPOx-PLs) in bovine retina extract. A protocol for preparing autoxidized pure phospholipids (PLs) and complex retinal extracts served as reference standards and was adapted to enable analytical parameter development. Fatty acid profiles of bovine retinas were first established with routine gas chromatography (GC) methods and used to customize mass spectrometry scanning for major HUFA-carrying PLs in the retinal extract. Targeted multiple reaction monitoring (MRM) scanning via triple quadrupole tandem mass spectrometry detected native (unoxidized) and oxidation-damaged PL regardless of the position of the O or O2 addition along the acyl chains and enabled quantification of relative signals from intact native and oxidized PL (5%-10% CV). MRM-triggered information-dependent acquisition (IDA) spectra confirmed the structure of peroxidized PLs, revealing that peroxidized species (+O-OH) dominated over single O-added species in vitro and in vivo. Positive identification and relative quantification are reported for 12 selected in vivo native and peroxidized phosphatidylcholines and phosphatidylethanolamines. These results enable future studies of the initial peroxidation due to toxins, genetics, or other initiating events influencing in vivo oxidation levels and potentially the effectiveness of strategies to mitigate this mechanism of action.