The mass spectrometric analysis of glycan composition and structure is a difficult but essential part in future study following the present glycoprotein identification. Intact glycopeptides analysis is an attracting field, in considering its capability to provide glycosite and corresponding glycan structure information at the same time. Mass spectrometry has been proven to be an important and a key tool for glycan analysis over the past few years. Making use of two soft ionization techniques-matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI), through tandem mass spectrometry (MS/MS) analysis, the information for glycans of the glycopeptides can be obtained in the investigation. Meanwhile, by comparing the MALDI-MS/MS and ESI-MS/MS approaches using model glycoprotein (horseradish peroxidase, HRP), the complementary results have been verified experimentally. We believe that the combination of the two techniques is necessary and will provide useful information for the understanding of protein glycosylation.