The body protein pool constantly turns over while achieving a dynamic steady state in healthy living organisms to accomplish homeostasis, indicating a close match between the rate of protein synthesis and breakdown (i.e., protein turnover). However, dysregulation of protein turnover in muscle over time leads to muscle wasting conditions such as sarcopenia, cachexia, and heart failure. Furthermore, altered muscle metabolism in obesity, insulin resistance, and diabetes. Therefore, skeletal muscle in wasting conditions is an important target for drug development. Since muscle mass is controlled by the balance between the rate of muscle protein synthesis (MPS) and muscle protein breakdown (MPB), a change in muscle mass can occur due to various permutations of the two rates (i.e., MPS and MPB). Elucidation of molecular mechanisms involved in the control of protein turnover provides invaluable data but misses the dynamic (i.e., kinetic) nature of the proteome, information of which stable isotope tracer methodology can provide. Combining stable isotope tracer methodology and molecular biology tools enables an in-depth understanding of protein metabolism in physiological and pathophysiological conditions, consequently facilitating the development of effective therapeutic approaches (optimal nutrition, exercise, and drugs) to treat muscle wasting diseases. In this review, we will discuss the significance of obtaining kinetic information for a better understanding of protein metabolism, and stable isotope tracer methodologies that enable exploration of muscle protein kinetics and direct muscle mass in vivo. These methodologies can be applied to metabolic research regarding pathophysiological conditions in both humans and animals.