Proteomic analysis of skeletal muscle tissue using SELDI-TOF MS: application to disuse atrophy

Skeletal muscle atrophy in response to disuse/unloading is a complex adaptation that involves many components of the muscle tissue. The underlying mechanisms that initiate and control the loss of muscle tissue during this response, especially contractile proteins located within the myofibers, are as yet unclear. One approach capable of distinguishing protein changes specifically associated with disuse/unloading-induced skeletal muscle atrophy is to compare the proteomic profiles of similar muscles between control, unloaded/atrophied, and unloaded/"atrophy-protected" experimental conditions. By utilizing a subtractive proteomic analysis approach, those proteins specifically modulated during the atrophic response can be identified and discriminated from those associated with disuse in general. We here describe the use of SELDI-TOF MS coupled with micro-scale preparative ion-exchange chromatography to detect proteins potentially specifically associated with the atrophic response in rat skeletal muscle.