(C) Table of best substrate candidates of two GeLC experiments. In order to assess possible cleavage sites in combination with topology information, the QARIP software Ivankov et al., 2013() was used to summarize results from experiments 1 and 2. Abundance ratios (YqgP/YqgP.S288A) for the intracellular parts of proteins were calculated for each gel slice separately by QARIP from peptide ratios computed by MaxQuant Cox & Mann, 2008(). Substrate candidates highlighted in red were identified in both experiments. 