DERIVATION OF PHOSPHORYLATION SITE LOCALIZATION PROBABILITIES FROM THE PTM SCORE
The matrix represents amino acid positions for a doubly phosphorylated peptide, with red positions indicating candidate phosphorylation sites. The second position is phosphorylated in each of the top four PTM scores but the second phosphorylation site could be located at position 4,5,6 or 7. The table shows a specific example of this situation (phosphopeptide of Eps8). The five top scoring possibilities for phosphorylation have PTM scores from 30.4 to 29.64. Corresponding inverted probabilities add up to 4954.31, which is set equal to one. P-site is the proportional probability for each possibility and is assigned to the two phosphorylation sites in each case. Next, probabilities are summed up for each candidate site.