Scientific workflow optimization for improved peptide and protein identification

BMC Bioinformatics

Table 1 Results from the X!Tandem and PeptideProphet optimization of the six test datasets with information on number of unique peptides and the optimal MME

Species	Mass analyzer	PSMs	PSMs [M + 2H]²⁺	Unique	opt. MME-	opt. MME+	opt. PSMs	opt. PSMs [M + 2H]²⁺	opt. unique
E. coli	ion trap	12889	8393	1197	0.31	7.32	14057 (+9.1 %)	9260 (+10.3 %)	1296 (+8.3 %)
E. coli	TOF	11285	9608	3840	5.57	17.62	13221 (+17.2 %)	11264 (+17.2 %)	4356 (+13.4 %)
E. coli	orbitrap	18343	11129	7419	0.80	15.00	18548 (+1.1 %)	11366 (+2.1 %)	7526 (+1.4 %)
H. sapiens	ion trap	8152	5316	528	9.02	5.32	8490 (+4.1 %)	5571 (+4.8 %)	577 (+9.3 %)
H. sapiens	TOF	8650	5802	3835	0.31	6.33	8619 (-0.4 %)	5833 (+0.5 %)	4300 (+12.1 %)
H. sapiens	orbitrap	17413	12239	4287	0.01	0.01	19551 (+12.3 %)	13772 (+12.5 %)	5164 (+20.5 %)

ISSN: 1471-2105