Altered glucose metabolism in response to peripheral insulin resistance is a hallmark of type 2 diabetes (T2D), clinically observed as the inability to maintain postprandial blood glucose levels (BGL). Associated with energetic excess arising from caloric overload, T2D is linked to excess non-esterified fatty acid production and rising nutrient levels, which influence metabolic processes. The liver plays a pivotal role in the pathogenesis of T2D, as both an insulin sensitive organ and by gluconeogenesis, whereby glycogen stores are liberated, further elevating BGL. It is important to understand the molecular adaptations of the liver to the metabolic flux and insulin resistance arising from T2D. We developed a T2D rat model which complements energetic excess from elevated dietary fat intake and insulin insufficiency from pancreatic beta cell damage. To investigate cellular changes to T2D, we performed a proteomic analysis which included targeting post-translational modifications by phosphoproteomics, cysteine redox proteomics and glycomics. To quantify alterations in protein and PTM abundance, samples were isobarically tagged prior to mass spectrometry (MS). Discovery glycomics was achieved by untargeted MS methods. We used untargeted lipidomic and targeted metabolomic analysis for functional validation. We quantified close to 20,000 phosphopeptides, 7,500 cysteine redox peptides, 7,000 proteins, and 18 N-glycan structures. PTM analysis showed that amino acid metabolic pathways were greatly altered by both phosphorylation and redox modifications. Using metabolomics, we observed a concurrent change in branched chain amino acids (BCAA) and metabolites facilitating amino acid metabolism. Given that our model alters only dietary fat intake, and hepatic availability to glucose via altered insulin levels, altered level of BCAA are of particular interest.