Experimental design and statistical rationale

Three biological replicates were performed at each time point of 0 h, 12 h, 24 h, 48 h and 72 h in SCR-resistant and -susceptible maize. The samples used for protein quantification and acetylated protein quantification are from the same biological replicate. All samples used for protein quantification and acetylated protein quantification were performed following the experimental procedures described above. After LC-MS/MS analysis and database search, the results of protein quantification experiments were summarized into one matrix with FDR was set to 0.01 for protein and peptide levels, and the results of acetylated protein quantification experiments were summarized into another matrix with FDR was set to 0.05 for protein and peptide levels. Global normalization of each matrix was performed using Equalize Medians parameters, hypothesis testing was conducted using moderated t-test, and multiple comparisons were performed using the Benjamini-Hochberg adjustment method. Differentially expressed levels of acetylated proteins were determined after protein level normalization by fold changes > 1.5 with t-test p-value < 0.05, reflecting a shifting of average intensity at each time point in three replicates for SRC-resistant and -susceptible maize.