This submission contains the mass spectrometry proteomics dataset collected from the oleaginous yeast Yarrowia lipolytica. The data was collected from three strains grown in glycerol mineral medium: a parental control strain (PAR), a genetically modified carotenoid-producing strain (CAR), and a genetically modified lipid-producing strain (OBE). Samples were taken during two distinct physiological states: the initial exponential growth phase and the subsequent nitrogen-limited (Nlim) phase. The proteomics data was primarily used to constrain a newly reconstructed enzyme-constrained genome-scale model (ecGEM) of Y. lipolytica. The analysis provides insights into the physiological states of the engineered strains across the different phases and helped to assess the impact of genetic modifications on the production of target molecules. An average of 4,329 unique proteins were detected. The mass spectrometry acquisition utilized a Data Independent Analysis (DIA) method , and the raw data was processed using Dia-NN software.