Default and custom processing methods

The BioPharma Finder application provides the Basic Default Method processing method optimized for Oligonucleotide Analysis experiments.

You can edit the processing parameters in the 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
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)

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

Edit a processing method

Prerequisites

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

Procedure

  1. On the Oligonucleotide 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
    1234
    No.DescriptionNo.Description

    1

    Edit Component Detection parameters

    3

    Enable/edit theoretical digestion and alias naming parameters

    2

    Edit Identification parameters

    4

    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.

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.

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 oligonucleotide identification parameters
  • Indicate advanced search preferences
  • Designate the ribonuclease

Customize Results

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

Save Method

  • Save changes to the open processing method
  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 Oligonucleotide Analysis page. You can then select the method to process your current and future experiments.