Inclusion body myopathy-3 (IBM-3) is a dominant human disease causing progressive degradation of the muscle, particularly in the shoulder and pelvic girdles. IBM-3 is caused by a missense mutation of myosin heavy chain type IIa that changes the amino acid at position 706 from a negative glutamic acid to a positively charged lysine residue in a highly conserved SH1 helix. Our lab created a Drosophila model, known as E701K, that has the IBM-3 mutation in its muscle myosin heavy chain protein. The mutant phenotype mimics the human disease. The proteomics of the insoluble fraction of indirect flight muscle (IFM) in homozygous mutant flies were compared to wild type flies at young and old ages to determine differences in protein levels. Six proteins were over-accumulated and twelve proteins were under-accumulated in the protein aggregates in the mutant flies at both ages. While some of these proteins have unknown functions, others serve structural, metabolic, protein folding, protein turnover, signaling, synthesis, or transcription roles. I tested the hypotheses a) that these proteins play a critical role in wild-type muscle and b) that manipulating the level of these proteins will lead to improvement or detrimental effects on the phenotype of the E701K/+ mutant flies. I used IFM driver lines (Actin88F-GAL4 and fln-GAL4) to knock down (with RNAi) or over-express each gene in IFM. Manipulating expression levels of Abba/thin (abba), myofilin (mf), CG9775, CG7409, hsp20, or hsp23 negatively affects the development and/or maintenance of wild-type IFM as determined by decreased flight ability. The proteins that were assessed in the IBM-3/+ background thus far did not rescue the phenotype. However, the manipulation of abba, oxen, mf, CG7409, CHCHD2, CG9775, hsp20, or HSP60B levels exacerbated the IBM-3/+ phenotype. Structural defects in the IFM were seen in the knock-down of abba, or over-expression of abba or mf in the wild-type and IBM-3/+ backgrounds using the Actin88F-GAL4 driver. Overall, these studies will lead to an understanding of the roles that aggregation-prone proteins play in normal muscle and aggregate-based myopathies in regard to their muscle structure and function.