The power of proteomics lies in the simultaneous and unbiased analysis of multiple protein species. The heart, which is comprised largely of cardiomyocytes, has a broad dynamic range, with a relatively small number of highly abundant sarcolemma / contractile and mitochondrial proteins accounting for ~50% of total protein. This can be further complicated by the role of the heart in distribution of blood, which is found in the chambers and coronary circulation, and contributes a similarly and well known dynamic range effect. Thus many studies assume the heart to be relatively low complexity in terms of unique protein species, because standard proteomics identifies only the most abundant proteins. We have utilized two approaches to limit these dynamic range effects and thus identify the low abundance myocardial proteome. We employ ex vivo perfusion to facilitate blood wash out and to provide a controlled environment to study, in contracting animal model hearts, several diseases (e.g. ischemia / reperfusion [I/R] injury). Secondly, we utilize several enrichment techniques for specific post-translational modifications (PTMs). We describe how this approach has been used to investigate how type II diabetes mellitus (T2DM) alters the cardiac proteome. Clinically, diabetic patients are a 2-4x greater risk of I/R leading to acute myocardial infarction (AMI), and furthermore surviving T2DM patients also recover from AMI more poorly than their otherwise healthy counterparts. This suggests that T2DM hearts undergo molecular and cellular adaptations even prior to I/R that makes them more susceptible to damage. Langendorff perfused hearts from T2DM and control animals are subjected to an integrated ‘omics approach including proteomics, metabolomics, lipidomics and PTM analysis. Using strategies for the enrichment of modified peptides including phosphorylation and redox PTMs we have mapped >7500 cardiac proteins, in comparison to ~3500 proteins using traditional proteomics alone. Changes at the proteomics and ‘modificomics’ levels were validated via metabolomics, lipidomics and ex vivo functional assays. In the setting of T2DM, we have observed changes in basal signaling and redox protection that likely impact the ability of these hearts to recover post-I/R compared to otherwise healthy models. The ability to see beyond changes in proteins regulating metabolic processes may provide a key to understanding the poor recovery of T2DM patients following AMI.