iProXpress (integrated Protein eXpression) is an integrated protein expression analysis system, which is designed to help analyze proteomic and genomic data such as protein/peptide and gene profiles from IP, 2D and MS proteomic and microarray gene expression experiments. The system includes the following functionalities: 1) Gene/Peptide to Protein Mapping; 2) Protein Information Matrix; 3) Protein Data Analysis for Pathway and Network Discovery. We have built the pipeline and the analysis interface for this system. iProXpress has been applied to the following data sets: Chi et al., 2006, Hu et al., 2007 and Hu et al., 2008. For more details on the iProXpress system, see (McGarvey, et al., 2011, Hu, et al., 2011 and Huang, et al., 2007).