Saccharomyces cerevisiae is an advantageous host organism for expression of a number of proteins, particularly those requiring post-translational processing such as disulfide bond formation. Proteins bound for secretion from yeast are subject to quality control mechanisms in the endoplasmic reticulum believed to ensure only fully folded, native proteins are exported from the ER and secreted from the cell. This quality control mechanism has been exploited to engineer proteins for increased thermal stability and secretion level using yeast surface display. We have recently probed the limits of yeast's ability to discriminate two-domain fusion proteins based on differences in thermostability. Secretion products of model proteins demonstrating moderate to high stability were characterized by flow cytometry and Western blotting of surface-expressed fusions. Results indicate that proteins with domains of moderate stability can be secreted in a heterogeneously truncated form, with truncations proceeding from the C-terminus. Inhibitor studies suggest that truncation results from partial proteasomal degradation, suggesting that targeting of incompletely folded secretory proteins to the endoplasmic reticulum-associated degradation pathway in yeast is not irreversible.