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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

From: Scientific workflow optimization for improved peptide and protein identification

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 %)