N-glycosylation plays an essential role in regulating protein folding and function in eukaryotic cells. N-glycan structures and occupancy can be impacted by the physiological state of cells and in disease. Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) is a powerful data independent acquisition (DIA) MS method for qualitative and quantitative analysis of glycoproteins and their glycan modifications. By separating the entire m/z range into consecutive isolation windows, DIA-MS allows comprehensive MS data acquisition and high-sensitivity detection of molecules of interest. The use of variable width DIA windows allows optimal analyte measurement, as peptide ions are not evenly distributed across the full m/z range. However, the m/z distribution of glycopeptides is different to that of unmodified peptides because of their modification with large complex glycan structures. Here, we improved the performance of DIA glycoproteomics by using variable width windows optimized for glycopeptides. This method allocates narrow windows at m/z ranges rich in glycopeptides, improving analytical specificity and performance for DIA glycoproteomics. We demonstrate the utility of the new variable window DIA method by comparing the glycoproteomes of wild type and N-glycan biosynthesis pathway deficient yeast. Our results highlight the importance of appropriately optimized DIA methods for measurement of post-translationally modified peptides.