Fig. 3
Protein detection rates scale with abundance. The a number and b fraction of proteins detected in yeast at different orders of magnitude of abundance. Ghaemmaghami et al comprehensively estimated protein copies per cell in yeast (light blue area, 3868 total proteins) using high-affinity epitope tagging. While top-20 DDA (red line, 1798 total proteins) can measure some low abundant proteins at 1% protein-level FDR, the strategy only detected 48% of mid-range proteins with estimated copies per cell between 103 and 104. In contrast, at 1% protein-level FDR, wide-window DIA using a Walnut-based chromatogram library (blue line, 2519 total proteins) detected 71% of these proteins and overall recapitulated 91% of proteins found in the entire Walnut-based chromatogram library (black line, 2754 total proteins)
