Hereditary myopathy with early respiratory failure (HMERF) caused by A-band TTN mutations shows a clinical and histopathological overlap with myofibrillar myopathies (MFM) characterized by disintegration of myofibrils and protein aggregation in muscle fibers. We applied a proteomic approach to decipher the aggregate composition in HMERF and compared the proteomic profile with findings in MFM subtypes. Nine skeletal muscle samples from HMERF patients with three different mutations in A-band titin and histopathological findings consistent with MFM were analyzed. Protein aggregates and intraindividual control samples (from aggregate-free muscle fibers) were collected by laser microdissection and analysed by a label-free mass spectrometric approach for identification and relative quantification of proteins. Fifty-eight proteins showed a statistically significant accumulation in aggregates with a ratio > 1.8 compared to control samples. The over-represented proteins desmin, filamin C, Xirp2, N-RAP, alphaB-crystallin, nestin, myotilin, Xin and Hsp27 were highly abundant in aggregates. The same was found in different MFM subtypes. The detection of further Z-disc proteins, chaperones, proteins involved in protein degradation and sarcolemmal proteins was also typical of MFM. In addition, we identified an over-representation of proteins that are involved in signaling pathways (e.g. inhibitors of the Rho/ROCK signaling pathway and ankyrin repeat domain-containing proteins). Titin was slightly but significant under-represented in aggregates (ratio 0.83). In conclusion, the proteomic profile of aggregates in HMERF associated with mutations in A-band titin is typical of MFM and confirms that this type of titinopathy is a new MFM subtype. The finding that titin is under-represented in aggregates indicates that aggregate formation is mediated by secondary effects. The detected over-representation of proteins involved in signaling pathways may play a role in pathogenesis.