Here are the scripts associated with the manuscript "Comparison of phosphoproteomics data analysis pipelines: search engines and localization scoring algorithms" where we compared pipelines implemented in the main software used for bottom-up phosphoproteomics analysis (MaxQuant, Proteome Discoverer, PeptideShaker). We tested six search engines (Andromeda, Comet, Mascot, MS Amanda, SequestHT, X!Tandem) in combination with several localization scoring algorithms (delta scores, D-scores, PTM-score, phosphoRS, Ascore) on two published data sets. We compared their performances, and estimated which false localization rate these thresholds translate to across the different analysis pipelines.