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

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

Database (target + decoy)		TD	BP	MB	SepTD	SepBP	SepMB
6FTT_y + 6FTD_y	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
6FTT_h + 6FTD_h	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
SGT_h + SGD_h	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

6FTT_y (or 6FTT_h): proteogenomic database constructed by 6-frame translation of yeast (or human) genome. 6FTD_y (or 6FTD_h): decoy database for 6FTT_y (or 6FTT_h). SGT_h: proteogenomic database constructed by splicing information obtained from human RNA sequencing data. SGD_h: decoy database for SGT_h. 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

ISSN: 1471-2164