Fig. 4

Shigella ratios deduced from the contributions of S. flexneri 2a str. 301 and Salmonella bongori NCTC 12419 strain signatures. The Shigella ratios (black circles) are in very good agreement with sample experimental ratios (linear regression R², 0.993; slope, 0.97; R² to expected, 0.992). Ratios calculated from specific peptides (medium blue circles) that (i) can only be calculated at species level and (ii) are biased by the high sequencing density and the phylogenetic proximity of the Shigella/Escherichia genera, reducing the number of specific peptides for Shigella flexneri and underestimating Shigella flexneri percentages (R² to expected, 0.647). Ratios estimated from the number of peptide-to-spectrum matches for the two strains (light blue circles) are highly biased by the high amount of shared peptides between both organisms (R² to expected, 0.666). Ratios estimated using the sum of spectral counts of proteins with more than two unique peptides (orange circles), as proposed by Kleiner et al. [11], are still biased by the shared peptides fraction (R² to expected, 0.911). Error bars are ± 1SD based on biological replicates