{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T22:43:36Z","timestamp":1777934616218,"version":"3.51.4"},"reference-count":51,"publisher":"MDPI AG","issue":"21","license":[{"start":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T00:00:00Z","timestamp":1761609600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Deutsche Duchenne Stiftung, Duchenne Deutschland e.V.","award":["DFP2018"],"award-info":[{"award-number":["DFP2018"]}]},{"name":"Protein Research Unit Ruhr within Europe (PURE), funded by the Ministry of Innovation, Science and Research (MIWF) of North-Rhine Westphalia, Germany","award":["233\u20131.08.03.03\u2013031-68079"],"award-info":[{"award-number":["233\u20131.08.03.03\u2013031-68079"]}]},{"name":"Center for Protein Diagnostics (PRODI), funded by the Ministry of Culture and Science (MKW) of the State of North Rhine-Westphalia, Germany","award":["111.08.03.05\u2013133974"],"award-info":[{"award-number":["111.08.03.05\u2013133974"]}]},{"name":"Federal Ministry of Education and Research in the frame of de.NBI\/ELIXiR-DE","award":["W-de.NBI-005"],"award-info":[{"award-number":["W-de.NBI-005"]}]},{"name":"Georg E. und Marianne Kosing-Stiftung, Deutsches Stiftungszentrum, Essen"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>Proteomics of dystrophic muscle samples is limited by the amount of protein that can be extracted from patient biopsies. Cells and tissues derived from patient-derived induced pluripotent stem cells (iPSCs) can be an expandable alternative source. We have patterned iPSCs from three Duchenne muscular dystrophy (DMD) patient lines into skeletal muscle cells using a two-dimensional as well as our three-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. A total of 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 we propose Myosin-9, Collagen 18A, Tropomyosin 1, BASP1, RUVBL1, and NCAM1 as proteins specifically altered in their expression in DMD for further investigation. Proteomics of skeletal muscle organoids resulted in greater consistency of results between cell lines in comparison to the two-dimensional myogenic differentiation protocol.<\/jats:p>","DOI":"10.3390\/cells14211688","type":"journal-article","created":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T11:47:19Z","timestamp":1761652039000},"page":"1688","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Proteomics of Duchenne Muscular Dystrophy Patient iPSC-Derived Skeletal Muscle Cells Reveal Differential Expression of Cytoskeletal and Extracellular Matrix Proteins"],"prefix":"10.3390","volume":"14","author":[{"given":"Sarah-Marie","family":"Gallert","sequence":"first","affiliation":[{"name":"Department of Anatomy and Molecular Embryology, Institute of Anatomy, Faculty of Medicine, Ruhr University Bochum, 44801 Bochum, NRW, Germany"},{"name":"Medical Proteome Center, Faculty of Medicine, Ruhr University Bochum, 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