mdn1-1 is a weak mutant of the Arabidopsis MDN1 gene. mdn1-1 exhibits an increased seed-size phenotype. To further figure out the proteome changes in the mdn1-1 seeds, we applied the iTRAQ-based LC-MS/MS analysis. A total of 3217 proteins were identified in dry seeds of both wild type and mdn1-1. The significantly differentially expressed proteins (DEPs) were filtered out based on the fold change (FC > 1.5 or < 0.667) of expression level and P value (< 0.05). We defined 282 up- and 40 downregulated proteins in mdn1-1.