Proteomics of skeletal muscular dystrophies is limited by the amount of protein which can be provided from patient biopsies. Cells and tissues derived from patient induced pluripotent stem cells (iPSCs) can be an expandable alternative source. We have patterned iPSCs from three Du-chenne Muscular Dystrophy (DMD) patient lines into skeletal muscle cells using a 2-dimensional as well as our 3-dimensional organoid differentiation system. Probes with sufficient protein amounts could be extracted and prepared for mass spectrometry. In total, 3007 proteins in 2D and 2709 proteins in 3D were detected in DMD patient probes. 83 proteins in 2D and 338 proteins in 3D can be described as differentially expressed between DMD and control patient probes in a post-hoc-Test. We have identified and propose Myosin-9, Collagen 18A, Tropomyosin 1, BASP1, RUVBL1 and NCAM1 as proteins specifically altered in their expression in DMD for further in-vestigations. Proteomics of skeletal muscle organoids resulted in greater consistency of results between cell lines in comparison to the 2-dimensional myogenic differentiation protocol.