The progressive decline of pancreatic beta cell function is key to the pathogenesis of type-2 diabetes. Protein phosphorylation represents an important mechanism controlling glucose-stimulated insulin secretion from the beta cell. Mass spectrometry (MS)-based phosphoproteomics now enables the global measurement of protein phosphorylation in an unbiased manner, making this an attractive means of studying pathogenic changes underlying disease. However, owing to technological limitations, studies involving minuscule amounts of protein have largely remained out of reach for deep phosphoproteome analysis. We recently made major improvements to our “EasyPhos” phosphoproteomics workflow, which collectively have improved the sensitivity of the method several-fold, and have also improved throughput, reduced sample handling and processing time, and minimized technical variability. Coupled with recent benchtop Orbitrap mass spectrometers employing enhanced ion optics, these methods now enable deep and reproducible phosphoproteomics studies from limited starting materials. Here, we applied these technologies to perform in-depth characterization of changes in signalling networks of pancreatic cells from various models, including islets isolated from diabetic mice, as well as from healthy humans. To obtain a comprehensive view of signalling network rewiring we combined our phosphoproteomic analysis with a characterization of proteome changes. Our analysis revealed drastic remodelling of the proteome and phosphoproteome, including numerous proteins involved in the control of insulin secretion, glucose uptake, and metabolism. This study highlighted a novel signalling axis contributing to beta cell failure, that we demonstrated is amenable to therapeutic intervention.