Protein glycosylation is conserved in eukaryotes from yeast to humans, and is critical in protein folding and in regulating protein functions. N-linked glycosylation of nascent polypeptides takes place in the Endoplasmic Reticulum, and genetic or chemical inhibition of this process lowers the efficiency of protein folding. We developed Data Independent Acquisition SWATH Mass Spectrometry glycoproteomic methods to map site-specific glycosylation in folding and mature proteins. This showed that unglycosylated proteins are retained in the ER, and that this effect is synergistic, with lack of glycosylation at multiple sites leading to enhanced retention. When yeast glycoproteins fold correctly, they traffic through the Golgi and are secreted. To measure the effect of inefficient glycosylation on glycoprotein function, we used this secretome from yeast with defects in N-glycosylation together with a modified thermal proteome profiling approach to efficiently assay the global consequences of site-specific glycosylation defects on glycoprotein thermal stability. Finally, as the yeast secretome contained abundant and diverse glycoproteins, we used glycoproteomic mass spectrometry to investigate their presence in industrially relevant spent media - sparkling wine. This identified highly abundant and structurally heterogeneous O-glycosylated yeast proteins which are important for sensory properties and foam formation.