Fig. 2.

Performance evaluation on the Synthetic-BS3 dataset. a Venn diagram for the results of Kojak, pLink 1, pLink 2, and the benchmark. A total of 904 PSMs were correctly identified consistently by the three engines; these were used to be a new and fair standard dataset. b The numbers of correctly identified PSMs by each search engine. c The percentage of correct α-peptides ranking in the top-k in the open search stage of pLink 2. d Similar to c, but for β-peptides. The “Original” database contains only the sequences of 38 synthetic peptides, “ + E. coli” database contains sequences from the “Original” database and the E. coli whole proteome database, and “ + Worm” and “ + Human” are similar to “ + E. coli”