The site-specific O-glycosylation of MUC1 tandem repeat peptides from secretory mucin of T47D breast cancer cells was analyzed. After affinity isolation on immobilized BC3 antibody, MUC1 was partially deglycosylated by enzymatic treatment with alpha-sialidase/beta-galactosidase and fragmented by proteolytic cleavage with the Arg-C-specific endopeptidase clostripain. The PAP20 glycopeptides were isolated by reversed phase high pressure liquid chromatography and subjected to the structural analyses by quadrupole time-of-flight electrospray ionization mass spectrometry and to the sequencing by Edman degradation. All five positions of the repeat peptide were revealed as O-glycosylation targets in the tumor cell, including the Thr within the DTR motif. The degree of substitution was estimated to average 4.8 glycans per repeat, which compares to 2.6 glycosylated sites per repeat for the mucin from milk (Müller, S., Goletz, S., Packer, N., Gooley, A. A., Lawson, A. M., and Hanisch, F.-G. (1997) J. Biol. Chem. 272, 24780-24793). In addition to a modification by glycosylation, the immunodominant DTR motif on T47D-MUC1 is altered by amino acid replacements (PAPGSTAPAAHGVTSAPESR), which were revealed in about 50% of PAP20 peptides. The high incidence of these replacements and their detection also in other cancer cell lines imply that the conserved tandem repeat domain of MUC1 is polymorphic with respect to the peptide sequence.