The bioprocessing of a fusion protein is characterised by low yields and at a series of recovery and purification stages that leads to an overall 90% loss. Much of this apparent loss is due to the denaturation of a protein, missing a vital affinity ligand. However, there is evidence of the protection of degradation products which occurs in the presence of shear plus air/liquid interfaces. This study seeks out to characterise the loss and use ultra-scale-down studies to predict its occurrence and hence shows these may be diminished by the use of protective reagents such as Pluronic F68.