Mass spectrometry-based proteomic technology has greatly improved and has been widely applied in various biological science fields. However, proteome-wide accurate quantification of proteins in signaling pathways remains challenging. Here, we report a genome-wide amino acid coding-decoding quantitative proteomic (GwAAP) system to facilitate precise proteome quantification. For each protein, a unique code peptide was assigned and incorporated into the N-terminus of the targeted protein and used for identification and quantification. As a proof of principle, we systematically tagged 40 yeast proteins with codes and employed mass spectrometry to decode. We successfully recovered all 40 code peptides with a large and consistent quantitative dynamic range (CV slope <10%, R² > 0.8). We further verified the alteration of the glucose and galactose metabolism pathways in yeast under different carbon source conditions. The GwAAP system could potentially provide a strategy to achieve absolute quantification of the entire yeast proteome without bias.