Preferences

MS//MS Quantification

PeptideShaker supports to types of MS//MS quantification methods:

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.


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Surrounding Amino Acids

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.


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PTM Scoring

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.


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