The analytical utility of plasma desorption mass spectrometry (PDMS) and electrospray mass spectrometry (ESMS) is compared for the determination of molecular weights and structures of lipid A components produced by Enterobacter agglomerans, a bacterium which often colonizes field cotton. For the analysis of such lipid A preparations, electrospray ionization is found to be approximately one order of magnitude more sensitive than plasma desorption for positive ion work, and ESMS exhibits an even greater margin of improved sensitivity for negative ion work. The degree of fragmentation can be controlled rather directly after ion formation during the electrospray process. The translational energy, hence, the energy of collisions between ions and neutral gas molecules can be varied systematically via variations in voltages applied to the ion source. Control of fragmentation behavior in PDMS is much less direct. The formation of oxonium ions and distal adduct ions in plasma desorption and electrospray, respectively, has provided valuable information pertaining to the elucidation of lipid A structures.