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Cancer is often difficult to achieve early diagnosis, which is however a crucial factor for good outcome in cancer treatments. Cancer biomarkers have been sought for several purposes preferably in blood and pinpointing cancer cells-derived aberrant glycoproteins would be a well-grounded approach to cancer biomarker discovery. One of the glycosyltransferases responsible for aberrant glycosylation in cancer is N- acetylglucosaminyltransferase V (GnT-V), which catalyzes an addition of β1,6-N- acetylglucosamine (GlcNAc) to the core N-glycan, and many lines of evidence have demonstrated the role of N-acetylglucosaminyltransferase V (GnT-V) in cancer development. To identify target proteins for GnT-V as cancer biomarker candidates in sera, we developed a protocol in which L-PHA, a lectin recognizing β1,6-GlcNAc, is conjugated to avidin-agarose complex to capture β1,6-N-acetylglucosaminylated glycoproteins from immuno-depleted sera, and the captured glycoproteins were tryptic-digested for sequence determination in an LTQ-FTICR mass spectrometer. Candidate proteins showing high sensitivity and specificity during the discovery phase were selected and the panel of biomarker candidates will be subjected to in-depth analyses for validation.