As one of the most important post-translational modifications (PTMs), glycosylation has a significant effect on the structure and functions of proteins. One of the important tools for glycoprotein research is lectins, which are known to have the ability to bind specific oligosaccharide moieties. Many different pure lectins are commercially available in an immobilized form suitable for glycoprotein purification, in which, wheat germ agglutinin (WGA) is the most popular one for its broad binding ability for different glycans. Lectins are usually used for the enrichment of glycoproteins or glycopeptides. In our research, the amide bind of peptides, including glycopeptides, can be cleavaged when the peptide mixture passes through the lectin column, which will lead a failure in sequent identification. Four standard proteins were used to verify this phenomenon and the peptide degradation was confirmed. The cleavage can occur at many positions, but more inclined to the C-terminal of the peptides with the amino acid residual of phenylalanine (Phe), leucine (Leu) and tyrosine (Tyr). From this result, we first revealed the problem existed in the affinity separation strategy of glycopeptides using WGA in proteomics research very popularly and suggested that using partial or no enzyme digestion database searching parameter would be more suitable for glycopeptides identification after WGA enrichment.