Proteome-We utilized both quantitative MS-based proteomics techniques and more traditional 2D gel analysis to provide the first detailed analysis of changes in the human nucleolar proteome after infection with a human pathogen. These data reveal novel nucleolar antigens that were affected by adenovirus infection and therefore identify new candidate proteins that may play either a direct or indirect role in viral infection. In addition, our data illustrate the benefits offered by confocal microscopy when assessing proteomics analysis of a subcellular fraction. We feel this combination of techniques is crucial for several reasons. First, viral infection may have unsuspected effects on the integrity of cellular compartments that could affect the fractionation process. Second, this combination enables targets identified by proteomics analysis to be prioritized for further in-depth analysis. Finally, a proportion of the proteins in our SILAC analysis were only identified by one peptide, and for these proteins further verification is important.