In the Oligonucleotide Calculator and Workbook Editor, you can generate and customize theoretical oligonucleotide components that can be shared with the Chromeleon™ chromatography data system as an oligo workbook.

You also can save experimental results to an oligo workbook, similar to a target peptide or intact workbook. See Save an oligo workbook and Use a Chromeleon-compatible workbook: Oligo for more information on working with an oligo workbook containing experimental results.

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.
  3. Select the Calculator and Workbook tab on the navigation bar.
  4. On the command bar of the Calculator and Workbook page, select New.
  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.
  6. New workbook in the Oligonucleotide Calculator and Workbook Editor
    New workbook in the Oligonucleotide Calculator and Workbook Editor
  7. Add theoretical sequences the oligo workbook as needed.
  8. See Add theoretical sequences to the oligo workbook.
  9. The Results table displays the added sequences and contains information at three levels: sequence (top), charge state, and isotope (bottom). See Oligo Calculator and Workbook Editor Results table parameters.
  10. Results table in the Oligonucleotide Calculator and Workbook Editor updated with imported oligonucleotide sequences
    Results table in the Oligonucleotide Calculator and Workbook Editor updated with imported oligonucleotide sequences
  11. Edit the parameters on the Manual Sequence, Modification, and Add/Edit Building Blocks subpages of the Oligonucleotide Calculator and Workbook Editor as needed.
  12. See Edit oligo workbook parameters.

  13. NOTE

    For oligo workbooks containing theoretical results, all subpages (Manual Sequence, Modification, Add/Edit Building Blocks) of the Oligonucleotide Calculator and Workbook Editor are active. However, the Modification and Add/Edit Building Blocks subpages contain parameters that apply only to theoretical results, not 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.

  14. Select a component row in the Results table at the sequence (top), charge state (second), or isotope (bottom) level.
  15. 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.
  16. 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.
  17. 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.
  18. See Simulated Spectrum and Predicted MS2 Spectrum pane commands.
  19. Spectrum panes in the Oligonucleotide Calculator and Workbook Editor
    Spectrum panes in the Oligonucleotide Calculator and Workbook Editor
  20. You can edit, save, and export the oligo workbook as needed.
  21. See Edit an oligo workbook.