Supplementary Figure 3: LC-MS Data acquisition scheme and qualitative peptide identification analysis
From: Building ProteomeTools based on a complete synthetic human proteome
(a) Data acquisition scheme used for all peptide pools. After an initial 1h survey run using HCD fragmentation with Orbitrap readout and CID fragmentation with ion trap readout, an inclusion list was generated. The three subsequent LC-MS runs from every pool utilized the inclusion list to target fully synthesized peptides by the indicated fragmentation techniques and collision energies. (b) Violin plots of the average Andromeda score (top panel), average number of matched fragment ions (middle panel) and the average intensity that could be explained by Andromeda in the tandem MS spectra (lower panel). Only identifications with an Andromeda score >100 were considered here. The numbers on top of each violin indicates the number of peptides.
