With the advances of molecular biology and with improved analytical techniq
ues a significant change of perception has taken place regarding prokaryoti
c glycoproteins. Glycosylation of proteins from prokaryotes is no longer co
nsidered a specific feature of certain organisms but has been demonstrated
for many archaea and bacteria. Besides the occurrence of glycosylated enzym
es, antigens and other cell envelope components, surface layer (S-layer) gl
ycoproteins represent the best-studied examples of glycosylated prokaryotic
proteins. They are widely distributed among archaeal wildtype strains, but
among bacteria they have been mainly observed with Gram-positive organisms
. There is, in general, an enormous increase of reports on the presence of
glycosylated proteins among prokaryotes. For their isolation and characteri
zation a great number of methods are available, aiming at the identificatio
n of the covalent linkage between the carbohydrate and the polypeptide port
ion. So far, several differences in structure and biosynthesis have been ob
served in comparison to eukaryotic glycoproteins. In this review we introdu
ce a protocol which has been successfully applied to the investigation of t
he complex structures, linkage units, and polypeptide consensus sequences o
f glycosylated bacterial S-layer proteins.