The following figure shows the decisions that determine how the application displays a modification on the Peptide Groups page.

Decision tree determining the display of modifications on the Peptide Groups page
2x Phospho[S9(98.0); S14(80.0)]Example 22x Phospho[S9(80.0); S/T)]Example 31x Oxidation[M]Example 41x Oxidation[M13]Example 51x Oxidation[M13; M17]Example 1YesYesYesYesNoNoNoNoThe report displays themodification with allpossible targets, positions,and site probability scores,when available.Start the display for each modification.PSMs of Peptide GroupReport only the most likely positions for the modification?Select PSM with highestbinomial site localizationscore.Is a site localizationscore available?Is the number of modifications with the highest PSM probability equal to the number of modifications in thePSM?Is the number ofscores above thethreshold higher orequal to the number ofmodifications?The report displays the modifications with the best score until the number of modifications in the peptide is matched.The report displays only targets without positions.The report displays the modifications with the most likely targets and positions.For modifications with scores above the threshold, the report displays target, position, and scores. For all remaining modifications, it displays only the possible targets.Collect all modifications on the identified targets. Store the best PSM confidence levels and the best site probabilities with highest confidence and best binomial site score for each modification target site.