We use Proteomics to study how the concentrations of proteins change under inflammation and as effected by different foods. Using the mouse model, we extract proteins from the same gut sample that we extract the mRNA, label the proteins using Cy dyes, separate the proteins by 2D electrophoresis, and then quantitate changes in protein concentrations using decodon software. Proteins that show significant changes in amount between treatments are identified using LCMS. We have developed a database of mouse 2D gel data that allow us to rapidly identify spots we have worked with before, and to compare different experiments. The proteomics data is also compared with transcriptomics data in order to understand the physiological changes occurring under inflammation and those due to diet and to explore commonalities.