Lipopolysaccharide (LPS) is a major component of the outer membrane of Gram-negative bacteria. The lipid A region of LPS stimulates the immune system in a structure-dependent manner. We have previously identified the two major lipid A species from Francisella tularensis as asymmetric tetraacylated structures containing four long acyl chains (16 and 18 carbons) and a single phosphate group that is partially modified by galactosamine (Phillips, N. J.; Schilling B.; McLendon, M. K.; Apicella, M. A.; Gibson, B. W. Infect. Immun. 2004, 72, 5340-5348). In the current study, we used matrix-assisted laser desorption/ionization on an intermediate vacuum source (vMALDI) coupled to a linear ion trap (LIT) mass spectrometer in multiple-stage mass fragmentation mode (MSn) to determine the structures of several minor and low abundant lipid A species present in F. tularensis, Francisella novicida, and Francisella philomiragia LPS that have not been previously characterized. Comprehensive vMALDI-MSn fragmentation studies allowed us to deduce the composition and the position of the fatty acid substituents within the lipid A moieties. Unexpectedly, most of these minor lipid A species consisted of multiple isobaric species with acyl chains of various lengths. Moreover, we found that a small portion of these lipid A species may be modified by the addition of a hexose or hexosamine sugar, in addition to the galactosamine that was previously identified. Overall, we found that MSn analysis on the vMALDI-LIT-MS platform was highly efficient and sensitive, allowing for thorough analysis of very minor lipid A species.