The dipeptide alanyl-glutamine (Ala-Gln) is a well-known parenteral nutritional supplement. The Ala-Gln supplementation is a potential treatment for muscle-related diseases and injuries. However, molecular mechanisms underlying the polyphenic effects of Ala-Gln supplementation remain elusive. Here, we performed NMR-based metabolomic profiling to analyze the effects of Ala-Gln, and the free alanine (Ala) and glutamine (Gln) supplementations on the mouse myoblast cell line C2C12 injured by glucose and glutamine deprivation. All the three supplementations can promote the differentiation ability of the injured C2C12 cells, while only Ala-Gln supplementation can facilitate the proliferation of the injured cells. Ala-Gln supplementation can partially restore the metabolic profile of C2C12 myoblasts disturbed by glucose and glutamine deprivation, and exhibits more significant effects than Ala and Gln supplementations. Our results suggest that Ala-Gln supplementation can promote MyoD1 protein synthesis, upregulate the muscle ATP-storage phosphocreatine (PCr), maintain TCA cycle anaplerosis, enhance the antioxidant capacity through promoting GSH biosynthesis, and stabilize lipid membranes by suppressing glycerophospholipids metabolism. This work provides new insight into mechanistic understanding of the polyphenic effects of Ala-Gln supplementation on muscle cells injured by energy deprivation. Fig. 4 PLS-DA analysis for identifying significant metabolites primarily responsible for discriminations of metabolic profiles between the NGG group and other four groups. (A, C, E and G) PLS-DA scores plots for NGG vs. Nor (A), Ala vs. NGG (C), Gln vs. NGG (E), Ala-Gln vs. NGG (G). Differential metabolites were identified by student's t-test analysis based on the significant metabolites. Thereafter, characteristic metabolites were identified by a combination of the significant metabolites and differential metabolites. (B, D, F and H) Fold changes of characteristic metabolite levels for comparisons between NGG vs. Nor (B), Ala vs. NGG (D), Gln vs. NGG (F), Ala-Gln vs. NGG (H). 16120 | RSC Adv., 2018, 8, 16114-16125 This journal is