The BioPharma Finder application uses the kinetic model to predict oligonucleotide MS2 (MS/MS) spectra. In the MS2 Spectra pane on the Process and Review page, you can change the parameters to regenerate the predicted spectrum using the model.

Prerequisites

  1. For an oligonucleotide analysis experiment, you have processed your experiment and are viewing the results on the Process and Review page.

Procedure

  1. On the Process and Review page, select the MS2 Spectra subtab.
  2. Select a row in the Results table that displays "MS2" in the ID Type column.
  3. Right-click the MS2 Spectra pane and select Predict Oligo MS/MS (Kinetic Model).
  4. The application opens the Predict Oligo MS/MS (Kinetic Model) dialog box.
  5. Predict Oligo MS/MS (Kinetic Model) dialog box
    Predict Oligo MS/MS (Kinetic Model) dialog box
  6. In the Sequence box, type the three-letter codes for a nucleotide sequence.
  7. Enter values for the following parameters:
  8. To set the charge state, the isolation width used for fragmentation, the resolution at m/z = 400, and the activation time (ms), enter a value in their boxes.
  9. To define a fragmentation method, select from the available options in the list.
  10. To choose an instrument, select an instrument name from the list.
  11. To define the collision energy or reagent target, enter a value in the box.
  12. Specify normalized collision energy as a percentage value (%) or specify the reagent ion target value for the ETD fragmentation method.
  13. Select OK to view the predicted MS2 spectrum.
  14. The application displays the changes in the predicted spectrum in the MS2 Spectra pane.
  15. See View the predicted and experimental MS/MS spectra.
Predicted MS2 spectrum after applying the kinetic model
Predicted MS2 spectrum after applying the kinetic model