Using a defined acceptor substrate peptide as an affinity chromatography ligand we have developed a purification scheme for a unique human polypeptide, UDPGalNAc:polypeptide N-acetylgalactosaminyltransferase (GalNAc-transferase) (White, T., Bennett, E. P., Takio, K., Sørensen, T., Bonding, N., and Clausen, H. (1995) J. Biol. Chem. 270, 24156 -24165). Here we report detailed studies of the acceptor substrate specificity of GalNActransferase purified by this scheme as well as the GalNAc-transferase activity, which, upon repeated affinity chromatography, evaded purification by this affinity ligand. Using a panel of acceptor peptides, a qualitative difference in specificity between these separated transferase preparations was identified. Analysis of GalNActransferase activities in four rat organs and two human organs also revealed qualitative differences in specificity. The results support the existence of multiple GalNAc-transferase activities and suggest that these are differentially expressed in different organs. As the number of GalNAc-transferases existing is unknown, as is the specificity of the until now cloned and expressed GalNAc-transferases (T1 and T2), it is as yet impossible to relate the results obtained to specific enzyme proteins. The identification of acceptor peptides that can be used to discriminate GalNAc-transferase activities is an important step toward understanding the molecular basis of GalNAc O-linked glycosylation in cells and organs and in pathological conditions. Glycosylation of proteins in eukaryotes is fundamental for the integrity of the individual cell and the organism as a whole (Varki, 1993). A number of different types of protein glycosylations have been identified (for a recent review see Lis and Sharon, 1993). Biosynthesis of the initial glycosylation of the protein backbone has been established in most cases and the involved glycosyltransferases partly characterized. In several cases characterization of glycosylation sites has identified peptide motifs that suggest the nature of the acceptor substrate specificities of transferases initiating protein glycosylation.Thus N-linked asparagine glycosylation is restricted to the sequence -Asn-Xaa-Ser/Thr-(where Xaa may be any amino acid except proline). Proteoglycan-type glycosylation of serine is restricted to -Ser-Gly-Xaa-Gly- (Bourdon et al., 1987). The GlcNAc-type glycosylation of serine or threonine appears to be adjacent to an acidic amino acid and within two residues of a proline (Haltiwanger et al., 1992). The fucose-type glycosylation of serine/threonine seems to be restricted to the peptide sequence -Gly-Gly-Thr/Ser-Cys-, although the enzyme has yet to be characterized (Harris and Spellman, 1993).In contrast, a defined peptide motif for GalNAc O-glycosylation (mucin type) and the equivalent yeast Man-type glycosylation of serine/threonine has not emerged. A number of studies have attempted to identify a consensus sequence for mammalian GalNAc O-glycosylation by studying sequences around identified glycosylation sites (Goole...