The Peptide Match ID pane on the Process and Review page provides detailed fragment information for a selected component when MS/MS data is available.

Procedure

  1. Open the results of your experiment from the Queue page or from the Load Results page.
  2. See Open results.
  3. The Process and Review page opens by default and displays the results of your Peptide Mapping Analysis experiment, including the peptide match ID results.
  4. On the top left side of the Process and Review page, select the Peptide Match ID Details tab (tabbed together with the Chromatogram pane).
  5. Peptide Match ID pane
    Figure Peptide Match ID pane
  6. The Peptide Match ID Details pane opens and contains two expandable sections: Select Fragments and Component Summary.
  7. The Select Fragments section contains the following parameters: Ion Series, Neutral Losses, and Internal Fragments.
  8. Select a component row in the Results table to edit the Select Fragments and Component Summary sections of the Peptide Match ID Details tab.
  9. In the Select Fragments section, select the checkbox for the fragments you want to display in the Component Summary table below and select the Apply button.
  10. The Component Summary table updates according to the parameters specified in the Select Fragments section.
  11. On the top right side of the page, select the MS2 Spectra tab.
  12. MS/MS spectrum containing fragment information for a selected component
    Figure MS/MS spectrum containing fragment information for a selected component
  13. The MS/MS spectrum appears for the component selected in the Results table, with the selected fragment types labeled.
  14. At the top of the MS2 Spectra pane, the Activation list provides the available fragmentation types and the Resolution list provides the available resolution types for the MS/MS spectrum.
  15. Edit the Select Fragments section as necessary to view the Component Summary results and fragment-labeled MS/MS spectra for the selected component.