Figure 3

Estimated abundance for the experimentally identified proteins. Experimentally identified proteins were compared with a reference dataset of an osteosarcoma cell line (U2OS cell line) [26]. X-axis: copies per cell, for the proteins identified in the reference proteome; Y-axis: number of proteins correspond to a specific abundance window. We align the experimentally identified proteins with the reference set, and plot the number of proteins from this study that correspond to the reference abundance levels. Light grey histogram: protein abundance distribution of the reference set; mild grey: protein abundance of 4,169 from the 7,367 of experimentally identified proteins using loose criteria (protein FDR = 1% and minimum number of peptides = 1); dark grey: experimentally identified proteins (1% FDR, min 1 peptides) filtered based on the frequency of identification of each protein in the biological samples, using criteria described in Methods (1,194 of 1,475 proteins are plotted); back columns: filtered experimentally identified proteins as described in Figure 1 - venn diagram (947 of the 1,079 proteins are plotted).