Lipid A isolated from several bacteria (Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, and various strains of Yersinia) showed abundant formation of pyrophosphate anions upon ion dissociation. Pyrophosphate [H3P2O7] ؊ and/or [HP2O6] ؊ anions were observed as dominant fragments from diphosphorylated lipid A anions regardless of the ionization mode (matrix-assisted laser desorption ionization or electrospray ionization), excitation mode (collisional activation or infrared photoexcitation), or mass analyzer (time-of-flight/time-of-flight, tandem quadrupole, Fourier transform-ion cyclotron resonance mass spectrometry). Dissociations of anions from model lipid phosphate, pyrophosphate, and hexose diphosphates confirmed that pyrophosphate fragments were formed abundantly only in the presence of an intact pyrophosphate group in the analyte molecule and were not due to intramolecular rearrangement upon ionization, ion-molecule reactions, or rearrangement following activation. This indicated that pyrophosphate groups are present in diphosphorylated lipid A from a variety of Gram-negative bacteria.pyrophosphorylation ͉ tandem mass spectrometry ͉ Yersinia pestis L ipopolysaccharide (LPS) is the primary constituent of the outer leaflet of the outer membrane of Gram-negative bacteria (1). In addition to being the major surface molecule in Gram-negative bacteria, LPS is also considered a major pathogenic factor. Lipid A, also referred to as endotoxin, is the hydrophobic membrane anchor of LPS and is known to be a potent inducer of the host innate immune system (1, 2). Structurally, lipid A is characterized as a phosphoglycolipid defined by a conserved diglucosamine disaccharide with structural variations occurring by fatty acid position and identity, phosphorylation, and additional monosaccharide modification. Alteration of lipid A structure (i.e., changes in acylation, phosphorylation, and glycosylation) greatly affects the bacterium's virulence and can occur via a variety of environmental stimuli including divalent ion concentration, temperature, and other growth conditions (1, 3-6).The phosphorylation pattern of lipid A has been shown to be important for its biological activity. For example, removal of a phosphate group has been shown to substantially reduce lipid A toxicity (7, 8) and interleukin-1 induction capacity (9). By contrast, masking of lipid A phosphate groups (e.g., addition of aminoarabinose) has been shown to affect bacterial resistance to host cationic antimicrobial peptides (10). The biochemical effects of phosphate groups in lipid A have been attributed to their negative charge that affects recognition by the Toll-like receptor 4 and further LPS-induced signaling in the host immune response to bacterial infection (11). Furthermore, monosaccharide modification to lipid A is thought to occur via an ester linkage with the phosphate substituents.The biosynthesis of lipid A, as characterized in Escherichia coli, involves LPS intermediates that have a 1-position pyrophosphate and a 4Ј-position mo...