Characterization of highly glycosylated biopharma-ceuticals by mass spectrometry is challenging because of the huge chemical space of coexistent glycoforms present. Here, we report the use of an array of HPLC-mass spectrometry–based approaches at different structural levels of released glycan, glycopeptide, and hitherto unexplored intact glycoforms to scrutinize the biopharmaceutical Myozyme, containing the highly complex lysosomal enzyme recombinant acid α-glucosidase. The intrinsic heterogeneity of recombinant acid α-glucosidase glycoforms was unraveled using a novel strong anion exchange HPLC-mass spectrometry approach involving a pH-gradient of volatile buffers to facilitate chromatographic separation of glycoforms based on their degree of sialylation, followed by the acquisition of native mass spectra in an Orbitrap mass spectrometer. Upon considering the structures of 60 different glycans attached to seven glycosylation sites in the intact protein, the large set of interdependent data acquired at different structural levels was integrated using a set of bioinformatic tools and allowed the annotation of intact glycoforms unraveling more than 1,000,000 putative intact glycoforms. Detectable isoforms also included several mannose-6-phosphate variants, which are essential for directing the drug toward its target, the lysosomes. Finally, for the first time, we sought to validate the intact glycoform annotations by integrating experimental data on the enzymatically dissected proteoforms, which reduced the number of glycoforms supported by experimental evidence to 42,104. The latter verification clearly revealed the strengths but also intrinsic limitations of this approach for fully characterizing such highly complex glycoproteins by mass spectrometry. Display omitted •Hybrid mass spectrometry approach to characterize Myozyme at the different structural levels.•Intact Myozyme analysis by a novel strong anion exchange-HPLC-mass spectrometry approach enabling the separation of proteoforms based on their sialylation degree and acquisition of native mass spectra in a semi-automated fashion.•Enzymatic dissection with peptide:N-glycosidase F and sialidase to reduce spectral complexity at intact protein level.•Multilevel data integration using the software MoFi to annotate intact protein mass spectra.•Application of the approach to calculate the percentage of the biologically relevant phosphorylated glycoforms. Compared to the total number of mammalian genes, the structural diversity of glycoproteins as a consequence of posttranslational glycosylation is enormous. We propose an integrated HPLC-mass spectrometry approach to explore the highly glycosylated protein recombinant acid alpha-glucosidase (Myozyme). The glycosylation complexity of this protein is reflected in a huge chemical space of more than 40,000 glycoforms, which were experimentally revealed through HPLC-mass spectrometry analyses and bioinformatic data integration at different structural levels of released glycans, glycopeptides, and intact glycoforms.