Identification of post-translational modifications is one of the most challenging tasks in proteomics, and the analysis of glycosylation is a very important yet difficult one among all post-translational modifications, which has attracted more and more attention in recent years. Mass spectrometry provides an effective way for the high-throughput analysis of glycosylation. Comparing with most of the other post-translational modifications, glycans are large and hetorogeneous, and glycans themselves could be fragmented in tandem mass spectrometry, in particular, the fragmentation patterns of glycans are quite different from those of peptides, resulting in difficulties in simultaneously identifying glycans and peptides of intact glycopeptides using proteomic analytical methods and software tools. The identification of intact N-glycopeptides is a hot spot in glycosylation research, for which various mass spectrometry-based analytical methods have been developed in recent years, including deglycosylation for the identification of N-glycosylated sites, electron transfer dissociation for the identification of peptide backbones, the combination of higher energy collisional dissociation and electron transfer dissociation or the combination of collision-induced dissociation and MS3 for complete identification of intact N-glycopeptides. In this article, we reviewed these analytical methods, and briefly pointed out the deficiencies of existing software tools, and suggested some future work.