Edit an oligo workbook - BioPharma Finder Software - Edit an oligo workbook - BioPharma Finder Software - BioPharma Finder Software

Procedure

1. On the BioPharma Finder home page, select the Oligonucleotide Analysis workflow link in the Experiment Types pane or below the splash graphic.
2. The Oligonucleotide Analysis page opens.
2. Select the Calculator and Workbook tab on the navigation bar.
3. If necessary, select the Workbook Manager subtab.
4. The Workbook Manager page opens, showing the saved workbooks in a table.
5. See Workbook Manager page parameters.
4. To edit a workbook, select its row (not checkbox) in the table and then select Edit in the command bar or double-click the workbook row.
5. The Oligonucleotide Calculator and Workbook Editor opens, displaying the Oligonucleotide Workbook Parameters pane at the top of the page and the Results table and Simulated and Predicted MS2 Spectrum panes at the bottom of the page. The Results table contains information at three levels: sequence (top), charge state (second), and isotope (bottom).
5. In addition to experimental results, you can add theoretical sequences to your oligo workbook as needed. See Use the Oligonucleotide Calculator and Workbook to generate theoretical results.
6. On the right side of the Manual Sequence subpage of the Oligonucleotide Calculator and Workbook Editor page, change the Manual Sequence parameters as needed and select Apply.

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8. You can change several parameters including the charge state, m/z, and mass ranges, as well as the number of isotopes for all or selected oligonucleotide sequences in the Results table.
9. You can also choose to include adducts (Na⁺, K⁺) and base losses in the Results table by selecting the "Adducts" and/or "M−B" checkboxes in the Optional Columns section. These optional columns appear at the charge state level.
10. See Oligonucleotide Calculator and Workbook commands and parameters for more information on the Manual Sequence parameters.
11. The Results table updates to include changes made to the Manual Sequence parameters. See Oligo Calculator and Workbook Editor Results table parameters.

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13. NOTE

    For oligo workbooks containing only experimental results (no theoretical sequences), the other subpages (Modification, Add/Edit Building Blocks) of the Oligonucleotide Calculator and Workbook Editor are inactive. These subpages contain parameters that apply only to theoretical results and are thus inactive for workbooks containing only experimental results.

    For oligo workbooks containing both theoretical and experimental results, updating the parameters on these subpages will affect only the theoretical results added to the workbook.

7. Select a component row in the Results table at the sequence (top), charge state (second), or isotope (bottom) level.
8. The Simulated Spectrum and Predicted MS2 Spectrum plots at the bottom right of the page update with the results for the sequence currently selected in the table.
9. The Simulated Spectrum plot displays the peaks for each individual charge state for the sequence in a different color and labels the peaks with their respective m/z ratios. At the sequence level, the Simulated Spectrum plot displays all isotopes for all of the charge states of the sequence. At the charge state level, the Simulated Spectrum plot displays only the isotopes for the selected charge state.
10. The Predicted MS2 Spectrum plot displays the fragment ion peaks for a selected charge state and labels the peaks with their respective m/z ratios. At the sequence level, the Predicted MS2 Spectrum plot is blank. You must select a charge state to view the predicted MS2 spectrum for a sequence.
11. See Simulated Spectrum and Predicted MS2 Spectrum pane commands.

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8. (Optional) Do any of the following:
1. To delete one or more entries in the workbook, select their rows in the table and then select Delete Checked at the top of the table, or press the DELETE key. To delete all entries in the workbook, select Delete All at the top of the table.
2. To save your changes to the workbook, select Save and then enter the workbook name and description.
3. You can enter a new name or retain the current name to overwrite.
4. The maximum number of components that you can save to a workbook is 250. You cannot add additional components to an existing workbook if it already contains this maximum number of components.
5. The saved workbook remains open until you edit another workbook or exit the application.
1. To export entries in the workbook, select Export in the command bar and then select one of the following:
2. •As Displayed (.xlsx) to export the results as a Microsoft™ Excel™ workbook in the format currently displayed in the Oligo Workbook table.
3. •Workbook (.wpbf) to export the results as a Chromeleon™-compatible oligo workbook.
9. For the As Displayed export option, select one the following submenu commands:
10. •Sequence Only to export the results at the sequence level (top level) only.
11. •Sequence and Charge State to export the results at both the sequence and charge state levels (top two levels) only.
12. •All Levels to export the results at all levels (sequence, charge state, and isotope levels).
10. For the Workbook export option, select one of the following submenu commands:
11. •Export All to export all of the components in the workbook.
12. •Export Checked to export only the selected components in the workbook.
13. To select or deselect a component to export, select or clear the checkbox in that row. To select or deselect all of the entries at one time, select or clear the checkbox in the column header.
14. A dialog box opens showing the default export location: C:\Xcalibur\data.
15. You can browse and export the workbook to another folder as necessary.
16. The application exports the workbooks as Chromeleon™-compatible BioPharma Finder workbook (.wbpf) files using the same file name as the workbook.
17. If the folder selected for export already contains files with these names, the application prompts you to confirm overwriting them. If you do not want to overwrite this file, you can enter a different file name
11. To close the workbook, select Close.
12. If you made changes to the workbook, the application asks you whether you want to save them.
13. The application returns to the Workbook Manager page.