Negative and positive ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and positive ion nano-electrospray ionization quadrupole ion trap mass spectrometry of peptidoglycan fragments isolated from various Bacillus species

A general approach for the detailed characterization of sodium borohydride- reduced peptidoglycan fragments (syn. muropeptides), produced by muramidase digestion of the purified sacculus isolated from Bacillus subtilis (vegeta tive cell form of the wild type and a dacA mutant) and Bacillus megaterium (endospore form), is outlined based on UV matrix-assisted laser desorption/ ionization time-of-flight (MALDI-TOF) and nano-electrospray ionization (nES I) quadrupole ion trap (QIT) mass spectrometry (MS). After enzymatic digest ion and reduction of the resulting muropeptides, the complex glycopeptide m ixture was separated and fractionated by reversed-phase high-performance li quid chromatography. Prior to mass spectrometric analysis, the muropeptide samples were subjected to a desalting step and an aliquot was taken for ami no acid analysis. Initial molecular mass determination of these peptidoglyc an fragments (ranging from monomeric to tetrameric muropeptides) was perfor med by positive and negative ion MALDI-MS using the thin-layer technique wi th the matrix alpha -cyano-4-hydroxycinnamic acid. The results demonstrated that for the fast molecular mass determination of large sample numbers in the 0.8-10 pmol range and with a mass accuracy of +/-0.07%, negative ion MA LDI-MS in the linear TOF mode is the method of choice. After this kind of m uropeptide screening often a detailed primary structural analysis is requir ed owing to ambiguous data. Structural data could be obtained from peptidog lycan monomers by post-source decay (PSD) fragment ion analysis, but not fr om dimers or higher oligomers and not with the necessary sensitivity. Multi stage collision-induced dissociation (CID) experiments performed on an nESI -QIT instrument were found to be the superior method for structural charact erization of not only monomeric but also of dimeric and trimeric muropeptid es. Up to MS4 experiments were sometimes necessary to obtain unambiguous st ructural information. Three examples are presented: (a) CID MSn (n = 2-4) o f a peptidoglycan monomer (disaccharide-tripeptide) isolated from B. subtil is (wild type, vegetative cell form), (b) CID MSn (n = 2-4) of a peptidogly can dimer (bis-disaccharide-tetrapentapeptide) obtained from a B, subtilis mutant (vegetative cell form) and (c) CID MS2 of a peptidoglycan trimer (a linear hexasaccharide with two peptide side chains) isolated from the spore cortex of B. megaterium. All MSn experiments were performed on singly char ged precursor ions and the MS2 spectra were dominated by fragments derived from interglycosidic bond cleavages. MS3 and MS4 spectra exhibited mainly p eptide moiety fragment ions. In case of the bis-disaccharide-tetrapentapept ide, the peptide branching point could be determined based on MS3 and MS4 s pectra. The results demonstrate the utility of nESI-QIT-MS towards the faci le determination of the glycan sequence, the peptide linkage and the peptid e sequence and branching of purified muropeptides (monomeric up to trimeric forms). The wealth of structural information generated by nESI-QIT-MSn is unsurpassed by any other individual technique. Copyright (C) 2001 John Wile y & Sons, Ltd.