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The present study aimed at modelling the effect of meal mix properties, measured by the water soluble protein (WSP) and the water holding capacity (WHC), on the extrusion system response and the pellet quality of aquafeeds. For this purpose, six diets were formulated using three quality fish meal and three inclusion levels of hydrolysed feather meal (8, 16 and 24%). The meal mixes were extruded at different levels of temperature (around 100, 110 or 130ºC) and moisture (around 22, 25 or 28%), using a twin screw extruder. The response of the extruder was characterized by the specific mechanical energy (SME), specific thermal energy (STE) and screw back pressure (SBP). The pellet quality was defined as the radial expansion index, bulk density, retention, oil absorption capacity, oil leakage and starch gelatinization. The data were analysed using the flexible framework of generalized additive models (GAMs). The results showed that the SME increased with increasing WSP (P<0.001) while STE decreased (P<0.001). The SBP was only affected by the process parameters; increased T led to increased SBP while moisture had the opposite effect (P<0.01). The pellet quality variables were affected by both the meal mix properties and the process parameters, often in interaction. In general the models explained between 64.1 and 95.4% of the variance, and showed that WSP and WHC described well the meal mix effect on the variables investigated. Replacing WSP and WHC by the diet as a factor in the GAMs led to significant decrease in the variance explained for bulk density (88.4 and 31.3%) and oil absorption capacity (65.1 and 44.4%) because of the inability to model the interactions. The results suggest that, WSP and WHC could explain to some extent the effect of meal mixes on extrusion system response and pellet quality indicators.