In the MS2 Spectra pane, the predicted MS/MS spectrum is displayed on the top of the experimental spectrum by default. You can change this view to compare the experimental spectra of two different components.

Prerequisites

  1. You have loaded the experiment results and are viewing the MS2 Spectra pane on the Process and Review page.

Procedure

  1. In the Results table, select the row of a component that has an MS/MS spectrum.

  2. TIP

    In the Results table, filter the ID Type column to "MS2" to display the components with an associated MS/MS spectrum.

  3. The MS2 Spectra pane view displays the predicted spectrum on the top and the experimental spectrum on the bottom for the selected component.
  4. In the MS2 Spectra pane, right-click anywhere on the spectra.
  5. In the shortcut menu, the "Predicted view" checkbox is selected by default.
  6. Select the "Set bottom spectrum as a reference (move to top)" option in the shortcut menu.
  7. The "Predicted view" checkbox is cleared.
  8. The experimental MS/MS spectrum on the bottom moves to the top view and replaces the predicted spectrum. This experimental spectrum is now set as the reference spectrum.
  9. In the Results table, select the row of a different component that has an MS/MS spectrum you want to compare.
  10. The MS2 Spectra pane displays the stacked spectra for comparison with the reference spectrum displayed on the top.
  11. image/svg+xml
    Comparing the MS/MS spectra of two components, shown for a peptide mapping analysis experiment

  12. NOTE

    The experimental reference spectrum that you set in the MS2 Spectra pane is not linked between pages in the application.

    That is, when you set a component spectrum as the reference on the Process and Review page, this information is not passed to the Mapping page.

  13. When comparing two experimental spectra, the Predict Peptide MS/MS (Kinetic Model) functionality is deactivated on the shortcut menu.
  14. The experimental reference spectrum remains in its location on top until you right-click and select the "Predicted view" checkbox to restore the default view.
  15. When you select "Predicted view", the experimental reference spectrum is replaced with the predicted spectrum of the component whose experimental spectrum is on the bottom.