. 2019 Oct 24;10:2395. doi: 10.3389/fmicb.2019.02395

TABLE 1.

Two-round search performances obtained for each methodology.

	Database	Number of proteins	Number of peptide	Coverage of peptide	Number of distinct	Number of proteins
		in database	spectra identified^a	spectra identified (%)	peptides Identified^a	after validation^a,b
First-round searches
Gel-free	AM-DB	64,613	24,684	7.8	3,237	347
	NAM-DB	462,821	35,430	11.1	4,295	834
	TAX-DB	13,426,277	10,626	3.3	1,624	607
Gel-based	AM-DB	64,613	2,066	24.7	1,408	201
	NAM-DB	462,821	2,584	30.9	1,849	652
	TAX-DB	13,426,277	2,304	27.5	1,526	496
Second-round searches
Gel-free	AM-DB	782	42,831	13.4	8,487	549
	NAM-DB	4,277	57,840	18.2	9,113	1,131
	TAX-DB	18,480	31,700	10.0	4,497	464
	Comb-DB	23,405	56,530	17.7	8,273	1,048
Gel-based	AM-DB	377	2,619	31.3	1,815	277
	NAM-DB	3,080	2,897	34.6	2,034	714
	TAX-DB	19,036	2,951	35.3	1,777	434
	Comb-DB	22,493	3,684	44.0	2,244	700

^aValues comprised in 95% confidence interval. ^bValues at 1% global FDR and after manual validation for proteins identified with one peptide. Searching parameters are provided in the section “Materials and Methods.”