Table 1. K-S test evaluations of the calibration of different score functions.

Here, we report the D values from K-S tests performed on nearly 30,000 entrapment PSMs from the concatenated runs of ISB18 mix Orbitrap spectra searched through two different bipartite databases. In the first experiment, we used a shuffled entrapment database; in the second, we used an entrapment database of H. influenzae sequences.

Method	Shuffled entrapment K-S D value	H. influenzae entrapment K-S D value
Separate target-decoy analysis, XCorr	0.028	0.028
Target-decoy competition, XCorr	0.011	0.013
Percolator 1.14, without intraset features	0.026	0.035
Percolator 1.03, with intraset features	0.087	0.116
X!Tandem	0.747	0.738
MS-GFDB	0.210	0.225