Label-free protein profiling of formalin-fixed paraffin-embedded (FFPE) heart tissue reveals immediate mitochondrial impairment after ionising radiation

► Label-free method is suitable for quantitative proteome analysis of FFPE tissue. ► Ionising radiation (IR) induces changes in three main biological pathways. ► IR causes down-regulation of mitochondrial complex proteins. ► Fatty acid metabolism and citric acid cycle were impaired by IR. ► Radiation-induced alteration in the glucose oxidative pathway was observed.