Due to recent advances in electrospray-ionization mass spectrometry (ESI-MS) and liquid chromatography (LC) protocols, LC-MS is gaining wider acceptance as an alternative approach to the identification and quantification of FAs in biological extracts. In these protocols, free FA (or those liberated by hydrolysis) can be subjected to LC-MS directly or analysis of complex lipids can be analyzed by LC-MS with subsequent interrogation of the FA building blocks enabled by fragmentation of the precursor lipid in tandem mass spectrometry (MS/MS) modalities. When subjected to conventional low energy collision-induced dissociation (CID), singly deprotonated FA anions (denoted [FA -H]‾ and formed directly or as fragmentation products ions from complex lipids) typically results in very little fragmentation from dissociation of the carbon-carbon bonds in the acyl chain, as the dominant product ions observed correspond to decarboxylation (-CO2) and dehydration (-H2O) of the FA precursor anion. To increase the generation of structurally informative product ions, charge-inversion of FAs has been explored, often in concert with novel laser-based dissociation strategies like photodissociation (PD) and ultraviolet photodissociation (UVPD). Extending the radical-directed dissociation approaches for complex lipids developed by the Julian and Blanksby groups, the Xia group has identified the location(s) of methyl branching in bacterial glycerophospholipids, including sphingomyelins, phosphatidylcholines, and phosphatidylethanolamines. Recently, we have described the efficacy of gas-phase ion/ion charge inversion reactions for the identification of FA both in non-esterified forms and also when esterified within complex lipids. This strategy has significant advantages as it can exploit the preferred ionization and fragmentation of many lipids in negative ion mode while taking advantage of structurally-selective chargeremote fragmentation in charge-inverted positive ions. Herein, we demonstrate the ability of chargeinversion ion/ion reactions combined with CID to differentiate isomeric BCFAs. Additionally, we present the development of a LC-MS/MS method that deploys post-column charge-switch derivatization to provide online and unambiguous discrimination of (1) non-branched and branched acyl chains from isomeric methyl branched lipid structures and (2) the identification of methyl chain branching site in saturated BCFAs.