This topic provides instructions for using the method editor for reporter ion quantification. If you are using precursor ion quantification, see Use the Method Editor for precursor ion quantification.

See the Reporter ion quantification topic for a list of the masses of the reporter ions of the tags available in the different TMT kits. The masses for the original TMT reagents, which are no longer available, are also included for reference.

In this procedure, the From Existing Method option and the TMT 10plex method are selected in the Create New Quantification Method.

NOTE

You can set up a quantification method for isotopic impurities. When you buy a TMT kit from Pierce, you receive a Certificate of Analysis (COA). The COA includes a table with the exact masses of the different labels and their isotopic impurities. You can add quantification channel data like monoisotopic masses, isotopic impurities, and associated isotopic variant relations to the corresponding quantification method.

Prerequisites

  1. You have the Quantification Method Editor dialog box open. See Create a quantification method.

Procedure

  1. (Optional) In the Active column of the Quantification Method Editor, clear the checkboxes for channels that are not used for the given experiment.
  3. (Optional) To correct for impurities stated in the COA, enter the isotopic impurities from the certificate of analysis for TMT reagent labels used for the experiment.

  4. NOTE

    You can move to the next cell in a row by pressing the TAB key.

  6. Select OK.
  7. The Save Quantification Method dialog box opens.
  8. Enter the name of the quantification method, for example, TMT 10plex corrected.
  9. Select Save.
  10. The application adds the new method to the Quantification Methods view.

To create a new quantification method to correct for isotopic impurities in TMT 10plex kits, see Excluding PSMs with high levels of coisolation.