You can use the Peptide Match ID Details pane to interpret the disulfide bonds in the protein.

Prerequisites

  1. You have loaded the experiment results and are viewing the Peptide Match ID Details pane (tabbed together with the Chromatogram pane) on the Process and Review page.

Procedure

  1. On the Process and Review page, in the Results table, filter the ID Type column to "MS2" to display the components with an associated MS/MS spectrum.
  2. Filter the results to display components with a disulfide bond (denoted 1ss) in the Identification or Modification columns.
  3. Select a resulting component in the Results table.

  4. NOTE

    For an experiment with multiple raw data files, expand (+/− icon) a component row in the Results table and select the row for a single raw data file.

  5. On the top right side of the page, select the MS2 Spectra tab.
  6. The MS/MS spectrum appears for the selected component.
  7. View the disulfide bond information as follows:
  8. The Peptide Match ID pane displays the sequence containing the disulfide bond.
  9. The MS2 Spectra pane displays the DD Bond drop-down list which lists the peptide sequences involved in the disulfide bond.
  10. The Fragment Coverage Map now show the sequence with the selected disulfide bond.
Figure Peptide Match ID Details, Fragment Coverage Map, and MS2 Spectra panes showing the selected disulfide bond
Peptide Match ID Details, Fragment Coverage Map, and MS2 Spectra panes showing the selected disulfide bond