Many diseases are caused by proteins or peptides folding incorrectly and aggregating into fibrils or plaques, including Alzheimer's disease, Parkinson's disease and type II diabetes. Amyloid formation in the human pancreas occurs via the aggregation of a 37 amino acid peptide called amylin or IAPP which is shown to be toxic to pancreatic β cells. Amylin (IAPP) aggregation initiates a large number of events, leading ultimately to cell death. However the exact cytotoxic action of human IAPP and also the underlying molecular events leading from amylin (IAPP) aggregation to β cell death is still unknown. The toxic effect of human amylin (IAPP) is thought to involve changes in the expression of several genes and proteins. Further transcriptional and proteomics studies in this field can therefore facilitate the identifications of new targets whose expression are affected by amylin (IAPP). These information could be further used to construct an integrated model of the signalling and regulatory pathways through which amylin (IAPP) interacts with cellular metabolism.To investigate the effects of amylin (IAPP) aggregation on the islets proteome in this study, rat Rin-5F cell line, reported as a model of pancreatic β cell, was used. MTT assay was initially performed to determine the effect of IAPP on the cell viability at different time points. The isolated proteins form the untreated and IAPP treated Rin-5F cells were then fractionated by off gel electrophoresis and analysed by quantitative label free LC- MS/MS approach.Label free quantification of IAPP treated Rin-5F cells has identified the altered expression of many proteins, some of which were previously suggested in the literature to be involved in the pathogenesis of type 2 diabetes. These proteins were map to several pathways (including glycolysis and proteasome) whose expressions were significantly affected upon amylin (IAPP) exposure. The IAPP responsive proteins were also structured into a well connected network. Some of the hub proteins identified in this network were greatly affected as the result of IAPP treatments of RIN-5F cells. Our data therefore revealed the effect of IAPP on several proteins and pathways that might be important in the pathogenesis of type 2 diabetes.