Figure shows the performance of each evaluated R-package with dataset PXD000279 analyzed with MaxQuant. For each protein, if the true and estimated protein abundance ratios are both greater than 1 in the same direction and the adjusted p-value is less than 0.05, we define it as "true positive". If the true protein abundance ratio is greater than 1, but the estimated ratio is not greater than 1 or the adjusted pvalue is greater than 0.05, this protein is a "false negative".