Protein glycosylation is an emerging field in bacteriology and, particularly, the envisaged medical and biotechnological applications make prokaryotic glycoproteins an interesting system for further analysis and exploitation (for details, see references 19, 23, 30, 33, 36, 40, 41, and 43). This endeavor requires a thorough understanding of the protein glycosylation processes that occur in the prokaryotic cell.The glycosylated surface layer (S-layer) protein SgsE from Geobacillus stearothermophilus NRS 2004/3a is a promising model for studies on prokaryotic glycosylation because of the homopolymeric nature of the glycan, which is composed only of rhamnose residues (35). In sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE) analysis, the mature S-layer glycoprotein is separated into four bands. Three of them represent broad bands in the molecular mass range of approximately 119 to 170 kDa which also give a positive periodic acid-Schiff (PAS) staining reaction, indicating the presence of covalently linked glycan chains (7,14,35). The 93-kDa band is nonglycosylated, and the estimated molecular mass concurs with the calculated mass derived from the amino acid sequence of the mature structural protein, SgsE, after cleavage of the 30-amino-acid signal peptide from the precursor protein (GenBank accession number AF328862) (35). Dependent on the cultivation conditions of the organism (batch versus continuous culture), variations exist in the degree of glycosylation of the individual protein bands, all of which possess identical N termini indicative of identical protein portions (20,35). Previous nuclear magnetic resonance (NMR) experiments have demonstrated that only one type of glycan chain is present on the individual glycoprotein species, however, with considerable length variations. The S-layer glycans consist of trisaccharide repeats with the structure [32)-␣-L-Rhap-(133)--L-Rhap-(132)-␣-L-Rhap-(13] n and of a short core saccharide consisting of ␣-1,3-linked L-Rhap residues, attached to carbon 3 of a -D-galactose residue that serves as the linkage sugar to the S-layer polypeptide backbone (35). So far, two glycosylation sites for O-linked glycans have been determined after a papain degradation experiment of SgsE glycoprotein, namely, amino acids threonine-620 and serine-794 (with the numbers referring to the positions on the precursor protein) (35). These data, however, cannot satisfactorily explain the existence of three broad S-layer glycoprotein bands on SDS-PAGE gels.To better understand the glycosylation pattern of the S-layer glycoprotein of G. stearothermophilus NRS 2004/3a, we have investigated the intact, glycosylated S-layer protein SgsE and selected glycopeptides derived thereof using different mass spectrometric approaches. These data will allow interpretation of S-layer protein glycosylation in a more general way, because similar SDS-PAGE patterns of S-layer glycoproteins have also been observed with other organisms (24).