Data Analysis

MaxQuant (version 1.5.3.30) was used for analysis of raw files. Searches were performed towards a reviewed UniProt human database with standard contaminants (downloaded 2015-11-17) in Andromeda. Enzyme specificity were set for trypsin with max two missed cleavages and a mass accuracy of 4.5 ppm for precursors and 20 ppm for fragment ions. Carbamidometylation was set as fixed modification and methionine oxidation as variable. For both proteins and peptides, a false discovery rate of 1% was used. The proteomics data was deposited to the ProteomeXchange Consortium via the PRIDE partner repository [51] with the dataset identifier (PXD012322). Adjusted intensity values were calculated by multiplying raw intensity with tissue density (μg/mm3) specific for each patient to obtain intensity per mm3. For repopulated sca ffolds, the dry weight of cells is assumed to be negligible and adjusted with the same density as for the original sca ffold.
