PSM abundances were aggregated to protein abundances by selecting the maximum values and the individual TMT run data merged. The run data were separately either quantile normalized or normalized by centering each TMT channel around its mean or around the median of all channels and selected the appropriate method by visual inspection of boxplots of the merged normalized data. We removed batch effects by regressing on the TMT runs ( ) and retained the residual matrix which was subjected to a variance stabilizing transformation for subsequent manipulations. .