Figure 2

Average cumulative number of false positives versus E -values. Average cumulative number of false positives versus E-values. Theoretically speaking, average number of false positives with E-values less than or equal to a cutoff E _c should be E _c provided that the number of trials is large enough. The accuracy of E-values assigned by RAId_DbS is tested along with three other methods, X! Tandem(v1.0), Mascot(v2.1) and OMSSA(v2.0). For X! Tandem, Mascot and OMSSA searches, default parameters of each program are used except the maximum number of miscleavages, which is set to 3 uniformly for this test. The diagonal solid lines in each panel are the theoretical lines. There are two curves associated with each method. The dashed line corresponds to the results using regular nr. The solid line corresponds to the results using nr with cluster removal, which we anticipate to be a better representative of a random database. See text for additional details.