Abstract: Objective:To explore the feasibility of research the pathophysiology of functional gastrointestinal disorders with proteomical methods.Methods: Different IBS（irritable bowel syndrome,IBS） subtype patients were chosen to study.Proteomical methods were used to explore.Performing two dimensional gel electrophoresis followed with different staining methods,analyzing the gel maps with software Image Master 2D Elite.Results: Average protein spots were 426 in the diarrhoea-predominant IBS group by using Coomassie brilliant blue staining,while the constipation-dominant IBS group by using silver staining got average 581 protein sptos.Conclusion: By using the two dimensional gel electrophoresis technique,proteome maps of human colonic mucosa were obtained.The resolution of silver staining is higher than that of the Coomassie brilliant blue staining.