1. For a top down analysis experiment, you entered an experiment name, loaded the raw data files and entered the conditions (if applicable), and selected a protein sequence on the Top Down Analysis page.


  1. In the Processing Method area of the Top Down Analysis page, select a processing method in the table and select Start Processing.
  2. The processing method editing wizard opens the Component Detection page under the Parameters tab, showing the component detection parameters in the open method.
  3. To create a custom method, modify the parameters in a default method and save your specifications using a different name.
  4. Use the processing method editing wizard on the Component Detection and Identification pages to specify the appropriate parameters for the processing method.
  5. See the following topics:
  6. Edit the Component Detection page
  7. Edit the Identification page
  8. Edit the Save Experiment page
  9. For a batch experiment, the application derives the default scan filters, fragmentation type, m/z range, and resolution at 400 m/z parameter values based on information retrieved from each individual raw data file.
  10. For a multiconsensus experiment with multiple raw data files, by default, the application uses the above information from the first loaded raw data file.
  11. The application automatically determines the other component detection and identification parameters for the experiment and displays these parameters on the pages under the Parameters tab. You can edit these parameters as needed.
  12. When you are finished editing the parameters on each page, select Next in the command bar to advance to the next page.
  13. On the last page, the Save Experiment page, save the modified processing method.
  14. See Save a processing method.
  15. NOTE

    If you edit a default processing method, you must save your customized method under a new name.

    You cannot overwrite a default processing method.

  16. The application saves the processing method and the method appears in the list in the Processing Method area on the Top Down Analysis page. You can then select the method to process your current and future experiments.