After you add a sequence and specify processing parameters, generate theoretical components by selecting the Process button in the Theoretical Protein/Peptide Manager. The Results table displays the theoretical component results and you can save all or selected results as a target peptide workbook or other file type as needed.

Generate theoretical component results

Prerequisites

  1. You are viewing the Theoretical Protein/Peptide Manager.
  2. You added a protein sequence to the Theoretical Protein/Peptide Manager.
  3. You specified digestion and target m/z processing parameters and added modifications to the sequence, as necessary.

Procedure

  1. In the Theoretical Protein/Peptide Manager, select the Process button to generate theoretical components.
  2. On the right side of the page, the Results table displays the theoretical component results.
  3. You can reprocess all or selected results as needed, depending on the processing mode selected on the Add/Edit Target m/z tab.

Save theoretical components to a target peptide workbook

TIP

For more information on creating and managing BioPharma Finder workbooks, see Introduction to BioPharma Finder workbooks.

Prerequisites

  1. You have generated theoretical components using the Theoretical Protein/Peptide tool.

Procedure

  1. (Optional) In the Theoretical Protein/Peptide Manager Results table, select the checkbox in the row of each component that you want to save.

  2. IMPORTANT

    You can save a maximum of 250 components to a target peptide or oligo workbook.

  3. To save results to a target peptide workbook, select Save As Peptide Workbook on the command bar.
  4. Select one of the following submenu commands:
  5. All to export all components in the table to a workbook.
  6. Checked to export only the selected components to a workbook.
  7. The Save Peptide Workbook As dialog box opens.
  8. In the Save Peptide Workbook As dialog box, select one of the following options:
  9. Create a New Peptide Workbook to add the components to a new workbook.
  10. Select an Existing Workbook to add the components to an existing workbook.
  11. (For the Create a New Peptide Workbook option) In the Workbook Name box, type a name for the workbook.

  12. TIP

    Workbook names can contain alphanumeric, space, underscore (“_”), and period (“.”) characters.

  13. IMPORTANT

    You can overwrite an existing workbook by entering the same workbook name.

  14. (For the Select an Existing Workbook option) In the table, select the checkbox for an existing workbook you want to update.
  15. (Optional) In the Description box, type a description for the workbook.
  16. In the Number of Isotopes per Peptide box, specify the number of isotopes you want to include for the selected components.
  17. Select Save.
  18. The application saves the selected components to a new or existing target peptide workbook, as indicated.

Save theoretical components as a different file type

TIP

Save your theoretical component results as an .msqc file to open the results in the BioPharma Finder application later.

Prerequisites

  1. You have generated theoretical components using the Theoretical Protein/Peptide tool.

Procedure

  1. (Optional) In the Results table, select the checkbox in the row of each component that you want to save.
  2. To save results to an Excel (.xlsx) or BioPharma Finder (.bpf) file, select Export Results on the command bar.
  3. Select one of the following submenu commands:
  4. All to export all components in the table.
  5. Checked to export only the selected components.
  6. Then, select one of the following additional submenu commands:
  7. As Displayed to export the components as an Excel file (.xlsx).
  8. Chromeleon to export the components as a BioPharma Finder file (.bpf).
  9. To save all components as a data file (.msqc), select Save Results As on the command bar.
  10. The Save As dialog box opens.
  11. In the Save As dialog box, browse to the folder location where you want to save the file, type a name for the file, and select Save.
  12. The file containing the theoretical component results is saved in the specified file location.