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Table 4 Number of peptides with charge 3+ at 1% FDR identified from search against real proteogenomic databases using X!Tandem

From: Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification

Database (target + decoy) TD BP MB SepTD SepBP SepMB
6FTTy + 6FTDy Total 1,705 3,452 2,403 2,054 4,072 2,490
Known 1,697 3,407 2,385 2,053 4,071 2,489
Novel 8 45 18 1 1 1
6FTTh + 6FTDh Total 1,436 3,001 1,022 2,363 3,055 2,356
Known 1,413 2,959 1,005 2,348 3,044 2,352
Novel 23 42 17 15 11 4
SGTh + SGDh Total 3,467 6,552 2,705 3,840 6,568 3,518
Known 3,433 6,526 2,680 3,836 6,562 3,511
Novel 34 26 25 4 6 7
  1. 6FTTy (or 6FTTh): proteogenomic database constructed by 6-frame translation of yeast (or human) genome. 6FTDy (or 6FTDh): decoy database for 6FTTy (or 6FTTh). SGTh: proteogenomic database constructed by splicing information obtained from human RNA sequencing data. SGDh: decoy database for SGTh. TD: target-decoy strategy. BP: target-decoy strategy using a refined score calculated by the self-boosted Percolator. MB: mixture model-based method. SepTD, SepBP, and SepMB denote separate filtering of known and novel peptides using TD, BP, and MB, respectively