The mouse mpkCCD cell line is a continuous cultured epithelial cell line with characteristics of renal collecting duct principal cells. This line is widely used to study epithelial transport and its regulation. To provide a data resource useful for experimental design and interpretation in studies using mpkCCD cells, we have carried out 'deep' proteomic profiling of these cells using three levels of fractionation (differential centrifugation, SDS-PAGE, HPLC) followed by tandem mass spectrometry to identify and quantify proteins. The analysis of all resulting samples generated 34.6 GB of spectral data. As a result, we identified 6766 proteins in mpkCCD cells at a high level of stringency. These proteins are expressed over 8 orders of magnitude of protein abundance. The data are provided to users as a public database (https://helixweb.nih.gov/ESBL/Database/mpkFractions/. The MS data were mapped back to their gel slices to generate 'virtual western blots' for each protein. For most of the 6766 proteins, the apparent molecular weight from SDS-PAGE agreed closely with the calculated molecular weight. However, a substantial fraction (>15%) of proteins was found to run aberrantly, either with much higher or much lower mobilities than predicted. These proteins were analyzed to identify mechanisms responsible for altered mobility on SDS-PAGE, including high or low isoelectric point, high or low hydrophobicity, physiological cleavage, residence in the lysosome, post-translational modifications, and expression of alternative isoforms due to alternative exon usage. Additionally, this analysis identified a previously unrecognized isoform of aquaporin-2 with apparent molecular weight <20 kD.