Sparkling wine is enjoyed around the world in celebrations and festivities. The sensory properties of sparkling wine depends on both consumer expectations and on a complex interplay between the chemical and biochemical components in the final product. Glycoproteins have been linked to positive and negative qualities in sparkling wine, but glycosylation profiles of sparkling wine have not been previously investigated in detail. Here, we used SWATH-MS to study the glycoproteme based on glycopeptides identified by Byonic. We applied the optimised workflow to three pairs of experimental sparkling wines highlighting several differences between conditions and the grape used. These included differences in protein abundance, glycans at specific sites and the overall abundance of yeast or grape glycoproteins. The workflow developed for SWATH/DIA glycoproteomics is applicable to the study of other glycoproteomes and could also be applied to still or base wine and complements other tools that measure the sensory properties of sparkling wine.