The glycosylation of the Fc fragment of human immunoglobulin G is very diverse and variable depending on different external and internal influences on the organism. For this reason, changes in glycosylation and glycan profiles are intensively investigated and linked to various conditions and diseases to serve as potential biomarkers in diagnosis or targets in therapy. Reliable and accurate data obtained from glycobiological analyzes are required to ensure correct conclusions. Since such analyzes most often involve complex biological samples in which the analytes of interest are in very small quantities, the purification step plays a very important role in the analysis process. In this paper, three purification methods are compared in order to obtain the most consistent and accurate results of the analysis of glycopeptides of the Fc fragment of human immunoglobulin G obtained by trypsinization. The sample was purified on three stationary phases: microcrystalline cellulose and C18 and HILIC adsorbent. After purification, the eluates were analyzed by the LCMS method to give extracted ion chromatograms with three groups of peaks corresponding to the IgG1, IgG2 and IgG4 subclasses. Summarized glycan mass spectra were also obtained from each group. Twenty glycans bound to three different peptides were detected, ie a total of sixty different glycopeptides. Further analysis of the data by LaCyTools (v.1.0.1) yielded data on the relative presence of each glycopeptide, the signal-to-noise ratio, and the quality of the isotope distribution. The C18 adsorbent method shows the best results in all observed categories, and microcrystalline cellulose proved to be the most variable. Purification on C18 adsorbent was also found to be the most cost-effective, while HILIC was the most expensive option, but somewhat shorter in duration.