The objective of this study was to investigate differentially abundant proteins (DAPs) of wheat seeds produced under two nitrogen levels (0 and 240 kg/ha) before and after germination. We selected samples at 8 and after imbibition (HAI) to identify DAPs by iTRAQ. The results showed 190 and 124 DAPs at 8 and 72 respectively. Alpha-gliadin and chlorophyll a-b binding protein showed the biggest difference in abundance before and after germination. In GO enrichment analysis, the most significantly enriched GO term was nutrient reservoir activity at 8 HAI and endopeptidase inhibitor activity at 72 HAI. Moreover, many DAPs involved mobilization of stored nutrients and photosynthesis were mapped to KEGG pathways. Dough development dough stability time and seedling chlorophyll content under N240 were significantly higher than those under which validated the results of proteomic analysis. These results are crucial for food nutrition and food processing.