Updated project metadata. We investigated the granulocyte proteome from healthy horses, horses with a spontaneous autoimmune disease (equine recurrent uveitis) and the reaction of granulocytes to different stimuli (IL8, PMA, LPS) on protein level. A total of 2032 proteins describing the whole granulocyte proteome were identified, including 245 proteins (12% of proteome) newly associated to in vivo expression in primary granulocytes (hypothetical proteins). Our studies provide novel information on the granulocyte proteome and contribute to a better understanding of molecular mechanisms involved in activation and recruitment of neutrophils and the role of these cells in modulating and regulating autoimmune diseases. The data presented here is highly relevant for veterinary medicine and has translational quality for spontaneous autoimmune uveitis in man.