Fig. 8

Qualitative and Quantitative reproducibility for differently stained FFPE tissues. a Numbers of identified Proteins (ID) for each replicate of the different histological stained tonsil tissues with H&E (purple), Hematoxylin (blue), Hemalaun (pink) and unstained (white) are shown. For each staining, the mean and standard deviation (SD) of the ID as well as the proteome overlap were calculated. X_Y refers to the number of biological (X) and technical replicate (Y). b Log2 transformed label-free quantitation values (LFQ) of the four replicates per staining were plotted against each other and the Pearson correlation coefficient (r) was calculated. The plots and Pearson correlation coefficient of the first two replicates for technical and biological replicates are shown while for the other correlations the range of the obtained r-values is given for each staining method