Abstract The structural analysis of post-translational modifications (PTM) of lipoproteins is difficult due to the hydrophobic properties of their fatty acid moieties. At the present time, the relative positions of fatty acid components on the N-acyl-S-diacylglycerylcysteine core structure has not been specifically identified in any natural or bacterial expressed recombinant lipoproteins. In this study, we describe a rapid solid-phase extraction using acetonitrile and isopropanol method that can be performed manually to isolate large amounts of relatively pure lipopeptides generated by the limited tryptic-digestion of recombinant lipoproteins. Using these lipopeptides and LC/MS mass spectra analysis, two groups of N-terminal lipidated (diacyl or triacyl) molecules that differ by one fatty acid unit were successfully identified. This LC/MS method also provided the separation of lipopeptides differing by 14 Da for the on-line mass spectrometric identification. Multiple stage fragmentation analyses of the di- and triacyl lipopeptides using both the positive and negative ion modes, enabled to identify the putative structure of the N-acyl-S- diacylglycerylcysteine containing an amide bond to palmitic acid at the N-terminal cysteine, a palmitic acid at sn1 position, and an unsaturated fatty acid of either hexadecenoic acid, cyclopropaneoctanoic acid, oleic acid and nonadecenoic acid at sn2 position of diacylglycerol residue through ester bonding. For diacyl lipoprotein, the saturated palmitoyl fatty acid group is absent at sn1 position of glycerol-derived lipid residue of lipopeptide.
