Duchenne muscular dystrophy is a highly complex multi-system disorder caused by primary abnormalities in the Dmd gene encoding the membrane cytoskeletal protein dystrophin. The resulting loss of the dystrophin protein triggers a concomitant disintegration of the dystrophin-associated glycoprotein complex at the sarcolemma. This complex links intracellular actin to components of the extracellular matrix and serves as a stabilising support network during normal muscle excitation-contraction-relaxation cycles. In Duchenne muscular dystrophy, the loss of dystrophin and its associated protein complex leads to membrane instability and micro-rupturing, the influx of excessive levels of calcium ions, the activation of proteases, sterile inflammation and eventually muscle degeneration and infiltration of adipose and connective tissue. Affected children suffer from severe and progressive skeletal muscle wasting with a loss of independent ambulation occurring during the early teenage years. In addition to muscle wasting, other manifestations of the disease include cardiomyopathy, respiratory insufficiency and scoliosis, along with non-progressive cognitive impairments in a subset of patients. Proteomics represents an ideal bioanalytical tool for the elucidation of the molecular mechanisms that underlie muscular dystrophy and for the identification of novel biomarker candidates. The research presented here has employed label-free liquid chromatography mass spectrometry along with chemical cross-linking mass spectrometry to characterise alterations in protein abundance and protein interaction patterns, respectively, in the mdx-4cv animal model of Duchenne muscular dystrophy. Proteins of particular interest have been further verified by biochemical assays including comparative immunoblotting and enzyme-linked immunosorbent assays. In-depth analyses have been performed on skeletal muscle, the aged heart, and brain tissue to investigate proteome-wide changes in the skeletal musculature, the cardiorespiratory system and the central nervous system. In addition, proteomic profiling of serum and saliva samples from dystrophic mdx-4cv mice has been conducted to identify potential minimally invasive biomarker candidates for the improved diagnosis, prognosis and therapy-monitoring of X-linked muscular dystrophy.