Congenital myopathies (CMs) are progressive diseases that constitute a diverse group of hereditary neuromuscular disorders that have been studied due to their diagnostic and therapeutic complexity. Due to the great clinical and molecular heterogeneity of CMs, this set of diseases constantly challenges healthcare teams and researchers pushing the multidisciplinary teams to better characterize biomarkers for more efficient diagnostic, enrichment of clinical trials design and therapeutic strategies. In this work we propose to characterize the molecular signature of nemaline, central core, multiminicore and fiber type disproportion myopathies as well as Duchenne and Becker dystrophy using a label free Mass Spectrometry NANOLC-MS/MS proteomic approach.