Figure 2

Evaluation of protein identification and reproducibility within the datasets. Label free quantification of the raw spectral information was performed in MaxQuant to produce protein datasets at the ED and EN. (A) The overlap between all identified proteins at the ED and EN was represented as a Venn diagram. (B) As a measure of reproducibility the overlap of the 4 biological replicates at the (B) ED and (C) EN was calculated and visualised as a Venn diagram. (D) A Pearson’s correlation matrix was performed as an additional measure of reproducibility at the protein level. Correlation factors were calculated for proteins in a pairwise manner across the entire matrix for each fraction of each biological replicate versus another.