ModLS MD Score [5] Improvement vs MD Score Fragmentation ModLS Threshold Peptides PSMs Peptides PSMs Peptides PSMs CID 12 79 1071 60 503 +32% +121% MSA 10 87 1006 77 535 +13% +88% HCD 27 118 693 85 393 +39% +76% HCD (Reduced) 25 124 740 131 789 -5% -6%

Table 1: Performance of ModLS for phosphorylation site localization compared to the MD Score method. Peptides and PSMs columns list counts of correctly localized phosphorylated peptides and PSMs for each fragmentation methods. Filtering has been performed to a 1% False Localization Rate (FLR). MD Score values listed are the highest reported by Savitski et al. [3] for filtered or unfiltered data. Results demonstrate that ModLS outperforms MD Score for CID and MSA datasets, and is comparable for HCD data.