In the search for a replacement for fossil fuels, due to their depletion as well as an increased concern about our environment, 2nd generation bioethanol comes out as one of the most promising alternatives. There are challenges in several steps of lignocellulose processing – especially due to the formation of for yeast inhibitory compounds during pretreatment and hydrolysis. It has previously been shown that encapsulation of the yeast in membranes made of an alginate gel enables the yeast to survive otherwise toxic hydrolysates. The physiological changes arising from encapsulation are however largely unknown, although it has been shown that the macromolecular composition of the yeast changes during prolonged cultivation. In this study we have therefore performed a comparative proteomic study of yeast grown in capsules and in suspension in anaerobic batch cultivations.