Skeletal muscle tissue contains slow as well as fast twitch muscle fibers that possess different metabolic and contractile properties. Although the distribution of individual proteins in fast and slow fibers has been investigated extensively, a comprehensive proteomic analysis, which is key for any systems biology approach to muscle tissues, is missing. Here, we compared the global protein levels and gene expression profiles of the predominantly slow soleus and fast extensor digitorum longus muscles using the principle of in vivo stable isotope labeling with amino acids based on a fully lysine-6 labeled SILAC-mouse. We identified 551 proteins with significant quantitative differences between slow soleus and fast extensor digitorum longus fibers out of >2000 quantified proteins, which greatly extends the repertoire of proteins differentially regulated between both muscle types. Most of the differentially regulated proteins mediate cellular contraction, ion homeostasis, glycolysis, and oxidation, which reflect the major functional differences between both muscle types. Comparison of proteomics and transcriptomics data uncovered the existence of fiber-type specific posttranscriptional regulatory mechanisms resulting in differential accumulation of Myosin-8 and ␣-protein kinase 3 proteins and mRNAs among others. Phosphoproteome analysis of soleus and extensor digitorum longus muscles identified 2573 phosphosites on 973 proteins including 1040 novel phosphosites. The in vivo stable isotope labeling with amino acids-mouse approach used in our study provides a comprehensive view into the protein networks that direct fiber-type specific functions and allows a detailed dissection of the molecular composition of slow and fast muscle tissues with unprecedented Skeletal muscles contain different types of fibers, which are responsible for specific biological properties and functions of individual muscles. Muscle fibers have been classified into slow type I and fast type II fibers mainly based on myofibrillar ATP staining and immunohistochemistry using specific antibodies (1).Slow type I fibers show a red tint, contain high numbers of mitochondria, and their energy supply is mainly based on oxidative metabolism. These features enable slow fibers to execute long lasting contractions, which are essential for the maintenance of body posture. The primary function of type II fibers is the rapid contraction of muscles. Fast fibers are divided into three additional subclasses: Type IIb and IIx (also known as IId) are glycolytic fibers, whereas type IIa fibers are more comparable to oxidative type I fibers (2). Type II fibers, which mainly derive their energy from glycolysis, are thus more susceptible to fatigue compared with Type I fibers.Muscle fibers have also been classified based on the expression of different isoforms of myosin heavy chain (MyHC) proteins. Myosins are the major contractile proteins and their activation by ATP and Ca 2ϩ ions results in shortening of muscle fibers. For example, slow type I fibers express MyHCI a...