Quality protein maize (QPM) (Zea mays L.) varieties contain enhanced levels of tryptophan and lysine, exhibiting improved nutritive value for humans and livestock.  However, breeding QPM varieties remains challenging due to the complex process of rebalancing storage protein.  This study conducted transcriptome and proteome analyses to investigate the process of storage proteins rebalancing in opaque2 (o2) and QPM.  We found a weak correlation between the transcriptome and proteome, suggesting a significant modulating effect of post-transcriptional events on non-zein protein abundances in Mo17o2 and QPM.  These results highlight the advantages of proteomics.  Compared with Mo17, 672 differentially expressed proteins (DEPs) were identified both in Mo17o2 and QPM, and several of them were associated with storage protein, starch, and amino acid synthesis.  We identified 178 non-zeins as DEPs in Mo17o2 and QPM kernels.  The up-regulated non-zein DEPs were enriched in lysine, tryptophan, and methionine, which affected the protein quality.  Co-expression network analysis identified regulators of storage protein synthesis in QPM, including O2, PBF1, and several transcription factors.  Our results revealed how storage protein rebalancing occurs and identified non-zein DEPs that may facilitate superior-quality QPM breeding.