Figure 5.

Distribution of minimal score values of MS/MS spectra. The score of a spectrum is the best match to the peptide library. The solidcurve results from correlating a set of MS/MS spectra with a peptide library containing the query peptide, while the dashed curve results from matcheswith a library not containing the query at all (i.e. all matches are random). Threshold is set to be the location of the cross-point of the two distributions, which minimizes the sum of false-positives and false-negatives. Therefore, if a match had a score less than 3.8, it was considered highly probable that the spectrum was produced as result of the matched peptide.