Fig. 1
Experimental workflow of the proteogenomic analysis of Xe. The Xe strains 85–10, 85* and 85-10ΔsX13 were grown in NYG, Minimal medium A pH 7 and XVM2, respectively, at 30 °C until OD600 of either 0.5 (exponential), 0.8 (early stationary) or 1.2 (stationary). Proteins extracted from Xe 85–10, 85-10ΔsX13 and 85* cell lysates were separated by 12% SDS PAGE and Tricine PAGE. Gel fractions and cell lysate were digested by trypsin. Samples were analyzed by LC–MS/MS. A database search against a six-frame translation database of Xe 85–10 was performed. Peptides were mapped to the genome of Xe using a TBlastN-based approach. The dataset from Abendroth et al. is originally a comparative study between Xe strains 85–10 and 85-10ΔsX13 and is based on the original genome annotation. The MS spectra of this dataset were also searched against the six-frame database