Before using the Mascot node, set the default confidence threshold parameters.

Procedure

  1. From the application menu bar, select Administration > Configuration.
  2. Under Processing Settings, expand the Mascot folder.
  3. Select Mascot Node.
  4. The Default Confidence Thresholds (configuration parameters) for the Mascot node appear.
  5. Set the Default Confidence Thresholds parameters by doing one of the following:
  6. Select Significance High to calculate the thresholds for high-confidence peptides. The application automatically sets this value to the calculated relaxed significance when it performs a decoy search.
  7. Select Significance Middle to calculate the thresholds for medium-confidence peptides. The application automatically sets this value to the calculated relaxed significance when it performs a decoy search.
  8. Select Apply.
  9. Select OK in the Administration message box.

  10. NOTE

    Select to return to the default values.