In this study, we used cell cultures of skin fibroblasts from two patients carrying missense mutations in the core subunit MT-ND5 and NDUFS1 of complex I (CI), respectively. We applied quantitative proteome- and metabolome profiling together with cell respiration assays and conventional biochemical methods to dissect the underlying mechanisms of CI dysfunction. Label-free quantification (LFQ) proteome profiling showed that the N-module of CI was severely downregulated in the NDUFS1 patient, indicating a disassembly of CI, which was further confirmed by Blue Native PAGE (BN PAGE) and Western Blot.