Figure 1: ModLS score versus false localization rate and number of correctly localized PSMs. A) Number of correctly localized PSMs for varying false localization rates and B) the false localization rates for varying ModLS score thresholds on the phosphorylation datasets. As phosphorylated PSMs are filtered with an increasing ModLS score threshold, the false localisation rate declines rapidly, while the number of correctly localized PSMs decline slowly. A ModLS score threshold can be selected to achieve a desired false localization rate, or trade-off between FLR and phospho-peptide assignments.