Figure 7.

Cumulative identification ratio versus E-value cutoff for compound spectra. Panel A/B and C/D displays the cumulative identification ratio as a function of E-value cutoff for the five database search tools when analyzing compound spectra constructed by the SUM2/SUM3 method while combining the LTQ/LTQ single-peptide spectra (A/B) and unique-peptide spectra (C/D) in the co-identifiable set. The symbols CTP1, CTP2 and CTP3 correspond respectively to the cumulative number of true positives (TP) identified with E-value equal to or smaller than the specified cutoff when analyzing single-peptide spectra, compound spectra of two peptides, and compound spectra of three peptides.