The Peptide Sequence Coverage pane on the Process and Review page displays the Fragment Coverage Map which contains color-coded peptide fragment information. The Fragment Coverage Map is only available for identified components with associated MS/MS data.

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 Fragment Coverage Map.
  4. On the left side of the Process and Review page, select the Peptide Sequence Coverage tab.
  5. Do one of the following:
  6. Select the row of an identified component with an MS/MS spectrum in the Results table.
  7. The Fragment Coverage Map in the Peptide Sequence Coverage pane shows the fragment coverage information stored in the reference raw data file.
  8. By default, the application considers the first raw data file in an experiment as the reference raw data file.
  9. 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.
  10. The Fragment Coverage Map in the Peptide Sequence Coverage pane shows the fragment coverage information predicted from the MS/MS data in the selected raw data file.
  11. image/svg+xml
    Figure Fragment coverage map
  12. The Fragment Coverage Map color-codes the ions according to ion intensity and provides the color key below the graphic.
  13. For components without significant b/y or c/z fragment ions, the color key for each color displays "ND" (not detectable).

The Fragment Coverage Map in the Peptide Sequence Coverage pane displays the following:

  • Peptide sequence with its corresponding modifications and charge state.
  • Sometimes an amino acid letter code in the peptide sequence changes to a different letter, based on a specific modification at that site.
  • Average structural resolution (in number of residues) with a value of 1.0 indicating the highest resolution.
  • Peptide sequence showing the numbered amino acid sequence and the identified fragments.
  • The map labels the fragment ions with b and c ions on top and y and z ions on bottom.
  • The first position on the map is the N-terminal and the last position is the C-terminal of the peptide.
  • Sequence graphic showing the identified fragment ions using a color code for ion intensity (red, yellow, green, cyan, and blue), with red as most intense and blue as the least intense.
  • The sequence graphic displays the peptide sequence and lists the identified fragment ions.
  • Each fragment ion displays the ion type assignment and, in some cases, its modifications and/or mass-to-charge ratio; for example: y5−2H2O(626.9).

NOTE

If your protein is very large, the standard copy and paste functions in the Peptide Sequence Coverage pane may not capture the Fragment Coverage Map appropriately.

Instead, use a screen capture application to capture the Fragment Coverage Map and paste the screen capture into a third-party application.