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Table 3 Number of peptides with charge 2+ 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 3,626 4,281 3,807 3,942 4,515 3,870
Known 3,603 4,106 3,781 3,942 4,443 3,870
Novel 23 175 26 0 72 0
6FTTh + 6FTDh Total 4,177 5,620 4,813 6,347 6,018 6,188
Known 4,115 5,316 4,765 6,336 5,950 6,180
Novel 62 304 48 11 68 8
SGTh + SGDh Total 8,034 11,059 9,152 8,957 11,150 9,552
Known 7,966 11,016 9,087 8,940 11,136 9,531
Novel 68 43 65 17 14 21
  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