Plants have a wide variety of ways to defend against pathogens. To assist efforts to counter severe losses of Solanum tuberosum (potato) yields caused by various pathogens, we have studied immune responses of potato plants using quantitative proteomic techniques. We have combined protein isolation and subcellular fractionation to identify proteins that change in abundance during the immune response. This dataset contains the analysis of subcellular fraction 2 of our experiment. In a previous analysis, another fraction was analyzed using a different methodology. For this reason, the two datasets are submitted separately.