To investigate the formation of whey protein-citrus pectin conjugates during extrusion processing, extrusion trials were performed by a co-rotating twin screw extruder. The processing conditions such as mechanical stress, reaction time and temperature, are varied by varying screw configuration (with/without reverse elements), and barrel temperature (80 degrees C-180 degrees C). Biopolymer reactions, such as protein and pectin degradation, protein aggregation as well as conjugation were examined by SDS-PAGE and fluorescence spectroscopy. The highest formation of conjugates was observed in the samples treated with reverse elements and the barrel temperature of 140 degrees C. As a measure for the processing conditions, material temperature at the die T-m, specific mechanical energy SME, and residence time distribution RTD were measured. The analysis of these parameters showed that T-m and SME are of significant influence on conjugate formation and degradation. Nevertheless, further analyses at defined conditions (time, temperature, shear stress) are necessary to get a better insight on the reactions taking place in extrusion. (C) 2016 Elsevier Ltd. All rights reserved.