Mass spectrometric protein quantitation has emerged as a high-throughput tool to yield large amounts of data on peptide and protein abundances. Currently, differential abundance data can be calculated from peptide intensity ratios by several automated quantitation software packages available. There is, however, still a great need for additional processing to validate and refine the quantitation results. Here, we present a software tool, termed StatQuant, that offers a set of statistical tools to process, filter, compare and represent data from several quantitative proteomics software packages such as MSQuant. StatQuant offers the researcher post-processing methods to achieve improved confidence on the obtained protein ratios.