Fig. 1
Comparison of peptide identification results between a pair of simulated and real proteogenomic databases of similar sizes for yeast (1T2Dy and 6FTTy) (a) and human (1T2Dh and SGTh) (b). Database searches were performed using X!Tandem. The number of peptides at 1% FDR is shown. TD: target-decoy search strategy. BP: TD with a refined scoring-metric calculated by the self-boosted Percolator. MB: mixture model-based method. SepTD, SepBP, and SepMB denote separate filtering of known and novel (or simulated novel) peptides with TD, BP, and MB, respectively. The blue bars and numbers in white denote the number of known peptides. The red bars and numbers in red denote the number of novel (or simulated novel) peptides