Switching between the two is done in this dialog. Here you can also decide if only validated hits are to be included in the methods.
Often it can be interesting to see the amino acids immediately in front of or
after the currently studied peptide. This information (plus the charge and
the m/z of the precursor) is displayed above the spectrum in the Overview tab.
To change the number of amino acids displayed simply change the value in the
field and click the OK button.
The location of PTMs is benchmarked using two scores: (1) the delta score is based on the score achieved by the second best peptide with another modification site; (2) the A-score deduces and scores the best modification location. The PTM scoring thresholds are used to distinguish ambiguous PTM site assignments from confident assignments. The confidence of the site assignment can be reviewed in the Modifications tab. Note that PTM specific study with PeptideShaker is at its genesis. Feel free to contact the developers if you have special needs.