Ischemic heart disease involves the occlusion of blood vessels resulting in a cessation of oxygenated blood flow to the heart. This hypoxia, and the necessary reperfusion to salvage surviving myocytes, induces cellular damage. Notably mitochondrial dysfunction occurs, increasing the production of reactive oxygen and nitrogen species (ROS/RNS). This increase in ROS/RNS overwhelms cellular antioxidant defence mechanisms and can alter protein structure / function via various protein post-translational modifications (PTMs). The most redox active amino acid is Cysteine (Cys) and Cys redox PTMs can be classed as either those that are biologically reversible (e.g. S-glutathionylation) or ‘irreversible’ (sulfinic and sulfonic acid; Cys-SO2H/SO3H). Irreversible Cys redox PTM occur with sufficient exposure to high levels of ROS/RNS and are associated with protein dysfunction and/or degradation. A mass spectrometry technique based on parallel reaction monitoring was employed to detect changes in irreversible Cys modification in a Langendorff model of myocardial ischemia/reperfusion injury (I/R). Due to the low abundance of Cys, and low abundance of Cys PTMs, an enrichment strategy was used to better profile the changes in irreversible Cys PTM. I/R significantly increased the abundance of Cys-SO2H/SO3H-modified peptides from proteins involved in the tricarboxylic acid (TCA) cycle. Concurrent perturbations in the concentration of metabolites involved in the TCA cycle also occurred during I/R. The addition of an aminothiol antioxidant MPG (N-2-mercaptopropionylglycine) in reperfusion improved functional recovery of hearts, ameliorated irreversible modification of Cys, and improved the recovery from TCA cycle metabolic dysfunction induced by ischemia.