Default and custom processing methods

The BioPharma Finder application provides several default Peptide Mapping Analysis processing methods optimized for specific experiment types:

  • Basic Default Method
  • Disulfide Bond Default Method
  • HDX Default Method
  • Targeted Default Method
  • Default Host Cell Protein Method

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

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

Figure Select the Edit Method button to open the processing method editing wizard
123
No.DescriptionNo.Description

1

Select a processing method

3

Open the processing method editing wizard to edit parameters

2

Start processing (without editing parameters)

Edit a processing method

Prerequisites

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

Procedure

  1. On the Peptide Mapping 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
    123456
    No.DescriptionNo.Description

    1

    Edit Component Detection parameters

    4

    Enable/edit HDX parameters

    2

    Edit Identification parameters

    5

    Enable/edit theoretical digestion and alias naming parameters

    3

    Enable/edit HCP parameters

    6

    Save changes as a new method

  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.
Processing method editing wizard subpages

Wizard subpage

Summary of parameters

Component Detection

  • Edit the signal threshold required for component detection
  • Select the experiment task to be performed
  • Specify peak detection, ion alignment, and mass measurement parameters

Identification

  • Specify peptide identification parameters
  • Indicate advanced search and disulfide bond search preferences
  • Designate custom proteases

Host Cell Protein

  • Add and customize an HCP database search
  • Specify basic properties, digestion parameters, and static/variable modification constraints for the search

Hydrogen Deuterium Exchange

  • Input HDX experiment conditions
  • Edit protection factor and back-exchange modeling parameters

Customize Results

  • Perform a theoretical digestion of the selected protein sequence
  • Apply a custom naming scheme to theoretical components

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 Peptide Mapping Analysis page. You can then select the method to process your current and future experiments.