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.