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Table 3 Results from the second optimization, in which different numbers of missed cleavages and different enzyme fidelities were also investigated for the E. coli hybrid ion trap/TOF data

From: Scientific workflow optimization for improved peptide and protein identification

  PSMs PSMs [M + 2H]2+ Unique MME- MME+ Missed Fidelity
Default 14057 (+1.2 %) 9260 1292 (-1.9 %) 0.31 7.32 2 full
Optimized 13888 (-1.2 %) 9282 (+0.2 %) 1271 (-1.9 %) 0.28 7.17 1 full