Processing Preferences Dialog
Introduction
The Processing Preferences are provided to PeptideShaker for the creation of your project. They are set
before processing and cannot be changed subsequently. It is thus important to carefully inspect these before creating
the project.
Go to top of page
Processing Parameters
The processing parameters comprise PSM, peptide and protein level convenience FDR threshold which are used for
an initial validation of the matches. The validation of the matches can be changed once the project is created in the
Validation tab without having to recreate a project.
For more help on validation of matches see Chapter 1.5 in our tutorial.
Go to top of page
PTM Scoring
The distinction of PTM sites is crucial for the distinction of peptides and scoring of proteins. PeptideShaker
combines two scores to infer the confidence of a PTM localization: the D-score
and a probabilistic score. For more information on PTM site scoring, we recommend this review form Chalkley and Clauser.
In this dialog, you can tune the settings regarding PTM scoring. Note that since these will have strong impact on peptide inference and protein scoring,
these settings cannot be changed after the project has been created.
You can choose to (i) turn off the probabilistic score, the import will be faster but the data of lower quality; (ii) select the score of your choice; (iii)
select whether the score shall account for peaks with neutral losses; (iv) use an automatic threshold; and (v) use a manual threshold.
Probabilistic algorithms rely on the model that an ion is present or not in the spectrum. They are generally confused when a peak can match two different
ions. This is notably the case when working with neutral losses. Thus, it is recommended to disable the use of neutral losses in order to reduce the
search space.
When using an automatic threshold, PeptideShaker will use both scores to validate only the most confident ones, typically reaching < 1% FLR. You
can also set a manual threshold.
Go to top of page
Fractions (beta)
Set the protein confidence level required before a protein is included in the Fractions molecular weight plot.
Go to top of page