The recombinant proteins of the two novel UDP-N-acetylgalactosamine (GalNAc) glycopeptide:N-acetylgalactosaminyltransferases (designated gpGaNTase-T7 and gpGaNTase-T9) were assayed with O-glycosylated products obtained from the prior action of the ubiquitous transferases (GaNTase-T1 and GaNTase-T2) towards MUC5AC mucin motif peptides (GTTPSPVPTTSTTSAP and peptides with single amino acid substitutions, GTTPSAVPTTSTTSVP and GTTPSPVPTTSITSVP, that are a reflection of mucin molecule polymorphism). gpGaNTase-T9 is known to be expressed differentially and more abundantly than gpGaNTase-T7 in some tissues; the results of in vitro glycosylation also indicates a difference in acceptor substrate specificities between the gpGaNTase isoforms. With the use of capillary electrophoresis, MS and Edman degradation, our study suggests that, in the O-glycosylation of mucin-type proteins, approach and recognition signalling by gpGaNTase-T7 and gpGaNTase-T9 depend largely on the peptide's primary structure (for example the presence of multiple clusters of hydroxy amino acids and the number of GalNAc residues attached to the peptide backbone). O-glycosylation in terms of sites of attachment seems to be less random than previously described and, if sequential reactions are ordered throughout the Golgi stack, the complete O-glycosylation of the mucin molecules seems to be finely tuned to respond to specific damage to, or attack on, epithelia.