Duchenne muscular dystrophy is a progressive neuromuscular disorder of early childhood. Genetic abnormalities in the DMD gene result in a lack of the crucial cytolinker protein named dystrophin. In skeletal muscles, the full-length dystrophin isoform Dp427-M is expressed in the membrane cytoskeleton. Without this membrane stabilising protein, cellular damage occurs, resulting in muscle weakness, severe myonecrosis, chronic inflammation and reactive myofibrosis. Mass spectrometry allows for accurate identification of proteins present in a tissue or biofluid sample. The proteome of a dystrophin-deficient muscle can be compared to that of a healthy control. If a protein shows significant changes in its abundance in dystrophinopathy, then it may be considered a novel biomarker candidate for this disease. This thesis has focused on the description of mass spectrometry-based proteomics with special reference to dystrophic skeletal muscle and biofluids from an established murine animal model. The proteomic profiling was mostly concerned with the chemically induced mdx-4cv mutant mouse model of Duchenne muscular dystrophy. Studies have included (i) the detailed description of sample preparation for proteomics and mass spectrometry for bottom-up proteomics, (ii) sample preparation and protein determination for top-down proteomics, (iii) the proteomic identification of markers of membrane repair, regeneration and fibrosis in the aged and dystrophic mdx-4cv mouse diaphragm, (iv) the mass spectrometric profiling of extraocular muscle and proteomic adaptations in the mdx-4cv mouse, and (v) the identification of biofluid marker proteins of muscular dystrophy in the urine proteome from the mdx-4cv mouse. The newly identified proteomic biomarker candidates can now be evaluated for their suitability as indicators of disease initiation and progression. Future studies could potentially establish new protein markers for improved diagnostic and prognostic methods, as well as therapeutic monitoring.