Setting up the quantification method is a similar task for both precursor ion quantification and reporter ion quantification.

To see if the Proteome Discoverer application already contains the qualification method you need, select Administration > Maintain Quantification Methods.

If you do not see an appropriate quantification method listed, you can create one by using one of the following methods:

  • Create a new method from factory default settings that come with a new application installation.
  • Create a new method from an existing similar quantification method.

  • NOTE

    The list of methods is the same as that given in the Method Name column of the Quantification Methods view.

  • Create a new method from scratch by using a template.

NOTE

There is a template for Precursor Ion Quan Method and a template for Reporter Ion Quan Method (this method requires an additional license).

The examples in this procedure are for TMT (reporter ion quantification), but the steps apply to both reporter ion quantification and precursor ion quantification.

NOTE

After you have added a quantification method to a study, the quantification method is separate from the server version. When you change the quantification method on the Administration page, the quantification method in the study remains unchanged. Also, any changes you make to the quantification method in the study do not impact the version on the Administration page.

If you create a new quantification method from the factory default template or an existing method, some entries are write-protected. You cannot change the reporter ion masses, change the mass tags, or edit the relations among the impurities.

Procedure

  1. Do one of the following:
  2. Select Administration > Maintain Quantification Methods.
  3. Select Maintain Quantification Methods .
  4. The Quantification Methods view opens. The view lists the available methods for precursor ion quantification and reporter ion quantification.
  6. Double-click the row of the appropriate method in the Method Name column or Description column, or select the column to the left of the Status column for the method, and select Add.
  7. The Create New Quantification Method dialog box opens.
  9. Do one of the following:
  10. Select From Factory Defaults (Default) to create a new method that uses the same settings as one of the default settings that come with a new application installation.
  11. Select From Existing Method to use the settings of the existing quantification method that you select. The list of methods is the same as that given in the Method Name column of the Quantification Methods view.
  12. Select From Scratch to use one of the following templates for your quantification method:
    - Reporter Ion Quan Method (This method requires an additional license.)
    - Precursor Ion Quan Method
  13. Select Create, and then follow one of these procedures to use the Method Editor to finish creating your new quantification method.
  14. Use the Method Editor for reporter ion quantification
  15. Use the Method Editor for precursor ion quantification