Default and custom processing methods

The BioPharma Finder application provides a variety of default Intact Mass Analysis processing methods optimized for specific experiment types.

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

Figure Select the Edit Method button to open the processing method editing wizard
12345
No.DescriptionNo.Description

1

Select a processing method

4

Submit experiment to the run queue for automatic processing

2

Select checkboxes tp enable features (as appropriate)

5

Open the Process and Review page to manually process experiment

3

Open the processing method editing wizard to edit parameters

On the Intact Mass Analysis page, in the Processing Method area, select a method and then select the Edit Method button in the Processing Method area to open the processing method editing wizard.

Prerequisites

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

Procedure

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

    1

    Edit Component Detection parameters

    4

    Define sequence-specific and component-based export filters for an intact report workbook

    2

    Edit Identification parameters

    5

    Save changes to the processing method

    3

    Specify sections to add to deconvolution report

  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 deconvolution algorithm and source spectra method to use in the analysis
  • Opt to generate an extracted ion chromatogram (XIC) for each component result
  • Specify a variety of advanced chromatogram, deconvolution, and peak modeling parameters

Identification

  • Enable target sequence matching for the experiment
  • Enable drug-antibody ratio (DAR) calculation for the experiment
  • Specify multiconsensus merge parameters

Report

  • Select parameters to include in the intact deconvolution report

Export Filter

  • Define sequence-specific and component-based export filters for an intact report workbook.

Save Method

  • Save changes to the open processing method

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.