The BioPharma Finder application provides the Top Down Default Method processing method optimized for Top Down Analysis experiments.

You can edit the processing parameters in the default method and save the customized method to apply it to your experiment.

NOTE

In the Top Down Analysis workflow, you cannot edit a processing method without actively running an experiment.

Figure Select the Start Processing button to open the processing method editing wizard
12
No.DescriptionNo.Description

1

Select a processing method

2

Open the processing method editing wizard to edit parameters and submit experiment

On the Top Down Analysis page, in the Processing Method area, select a method and then select the Start Processing button in the Processing Method area to open the processing method editing wizard.

Prerequisites

  1. You are viewing the Top Down Analysis page.
  2. On the Top Down Analysis page, you have entered an experiment name, loaded the raw data files and entered the conditions (if applicable), and selected a protein sequence.

Procedure

  1. On the Top Down Analysis page, in the Processing Method area, select the checkbox for the processing method you want to edit for your experiment.
  2. Select the Start Processing button.
  3. The processing method editing wizard opens. By default, the Component Detection subpage is displayed.
  4. Figure Processing method editing wizard subpage navigation
    123
    No.DescriptionNo.Description

    1

    Edit Component Detection parameters

    3

    Save and submit experiment

    2

    Edit Identification parameters

  5. Navigate through the subpages of the wizard and edit the parameters as appropriate:
  6. On each subpage, select the Next button to progress to the next subpage of the wizard.
  7. Or, on the wizard navigation bar, select a subpage tab to open that subpage.
  8. The table below describes the parameters in each subpage of the processing method editing wizard.
  9. For more information on a subpage, select the subpage link in the table.
Table Processing method editing wizard subpages

Wizard subpage

Summary of parameters

Component Detection

  • Select the chromatographic peaks to use in the analysis and specify the deconvolution parameters () for each peak
  • View the chromatogram and Intact Fragmentation and Intact Deconvolution source spectra for each peak added to the experiment

Identification

  • Add, delete, or edit sequences added to the experiment
  • For Intact Deconvolution experiments, specify the sequence matching mass tolerance and multiconsensus merge parameters

Save Experiment

  • Save changes to the open processing method and submit the experiment for processing

IMPORTANT

If you modify any of the parameters in a processing method, you must save the edited method using a new name to preserve your modifications.

  1. On the last page, the Save Method page, save the processing method.
  2. The application saves the processing method and the method appears in the list in the Processing Method area on the Intact Mass Analysis page. You can then select the method to process your current and future experiments.