In this study we aimed to provide an in-depth proteomic analysis of differentially expressed proteins in the hearts of transgenic mouse models of pathological and physiological cardiac hypertrophy using tandem mass tag labeling and liquid chromatography tandem mass spectrometry. The Δ43 mouse model, expressing the 43-amino-acid N-terminally truncated myosin essential light chain (ELC) served as a tool to study the mechanisms of physiological cardiac remodeling, while the pathological hypertrophy was investigated in A57G (Alanine 57 → Glycine) ELC mice. The results showed that 30 proteins were differentially expressed in Δ43 versus A57G hearts as determined by multiple pair comparisons of the mutant versus wild-type (WT) samples with P < 0.05. The A57G hearts showed differential expression of nine mitochondrial proteins involved in metabolic processes compared to four proteins for Δ43 hearts when both mutants were compared to WT hearts. Comparisons between Δ43 and A57G hearts showed an upregulation of three metabolically important mitochondrial proteins but downregulation of nine proteins in Δ43 hearts. The physiological model of cardiac hypertrophy (Δ43) showed no changes in the levels of Ca2+-binding proteins relative to WT, while the pathologic model (A57G) showed the upregulation of three Ca2+-binding proteins, including sarcalumenin. Unique differences in chaperone and fatty acid metabolism proteins were also observed in Δ43 versus A57G hearts. The proteomics data support the results from functional studies performed previously on both animal models of cardiac hypertrophy and suggest that the A57G- and not Δ43- mediated alterations in fatty acid metabolism and Ca2+ homeostasis may contribute to pathological cardiac remodeling in A57G hearts.