Shotgun proteomics refers to the untargeted and unbiased analysis of the global proteome as this occurs in a biological system. The overarching aim of my research is to develop a proteomics methodology for the in-depth profiling of tissue and cell-lines and apply this novel methodology in mouse model and human samples in order to identify molecular mechanisms and novel therapeutic targets of obesity and obesity-related chronic diseases, including Alzheimer's disease and oesophageal adenocarcinoma. The innovative quantitative proteomics methodology we developed for the global, untargeted proteomic profiling of cell lines and tissue has wide applications in different subject areas of biomedical research. Depending on the samples analysed and experimental design, this methodological approach can provide novel insight into physiological processes, the pathophysiology of disease, as well as identify novel therapeutic targets and disease markers.