Data analysis was done in the R programming language environment, based on Bioconductor original methods that allows analysis of mass spec data starting from PSM hits. Such lists were exported from Proteome discoverer for further analysis. Each plate runs (12 LC MS/MS runs per 96 well plater) were analyzed separately for statistical evaluation and normalization purposes, and the data subsequently were combined for the normalization step to remove batch effect amongst the different 96 well plates. After the normalization procedure all data were consolidated for the DE (differentially expressed) analysis workflow.