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This data article contains data related to the research article titled proteomic and comparative genomic analysis reveal adaptability of Brassica napus to phosphorus-deficient stress [1]. Proteome alterations of roots and leaves in two B. napus contrasting genotypes, P-efficient ‘Eyou Changjia’ and P-inefficient ‘B104-2’, under long-term low phosphorus (P) and short-term P-free starvation was investigated, and then comparative gnomic analysis was conducted to interpret the interrelation of the differential abundance protein species responding to P deficiency with quantitative trait loci (QTLs) for P deficiency tolerance. The report concluded with the results that nearly 50% of the identified protein species was mapped in the confidence intervals of QTLs for P efficiency related traits. The tables presented here represented the detail information of protein spots detected, as well as protein species identified.