A. Flight muscles were dissected from Drosophila adults and fractionated into cytoplasmic and myofibrillar components. Shown are representative samples of whole muscles (lane 2), cytoplasmic fraction (lane 3), and myofibrillar fraction (lane 4). A gel strip corresponding to the myofibrillar fraction, with the myosin heavy-chain (MHC) band removed, was submitted for LC-MS/MS analysis. A separate dissection and fractionation was used for a duplicate analysis. B. List of identified proteins and their corresponding Drosophila gene. Number of different peptide-to-spectrum matches (PSMs) for each protein identified in first or second LC-MS/MS screens are indicated in columns 2 and 3, respectively.