For this sample:

  • Peptides containing only a single lysine show roughly a 1:2:4 ratio for the light:medium:heavy intensities
  • Peptides containing a single arginine show a 4:2:1 ratio for the light:medium:heavy peptide intensities

In this step, list only the lysine containing peptides and verify the ratios.


  1. Select the Peptide Groups tab.
  2. Select the Display Filter to open the Display Filter pane.
  3. The Display Filter pane opens.
  4. Select the Add property box, and select Sequence, select does not contain, and enter K in the text box.
  5. This is the first filter.
  6. Select the Add property box and select Abundances, select is greater than, enter 0 in the text box, and then select in every sample.
  7. This is the second filter.
  8. Select Apply.
  9. None of the peptide sequences contain lysine, and the bottom of the window shows that 226/1576 peptide groups are showing.
  10. The SILAC quantification values are assigned to one of the up to three peptide groups, one each for light, medium, and heavy, for a given arginine-containing peptide. The other two groups are marked as redundant, and the filter hides them. The visible peptide group lists the quantification values for all three quantification channels.
  11. Select Filter or the close icon (X) in the upper right corner of the Display Filter pane.
  12. Select the Show Quan Channel Values icon in the toolbar and select the top row in the Peptide Groups table.
  13. TIP

    You can also display the Quan Channel Values chart from the menu bar by selecting View > Quan Channel Values.

  14. NOTE

    The expected ratio is 4:2:1 for arginine-containing peptides, but the actual ratio of these peptides is 3:2:1.

  15. Select the Show Chromatogram Traces View icon in the toolbar.
  16. By default, the Chromatogram Traces View appears above the Quan Channel Values chart.
  17. The Chromatogram Traces View shows three traces, one each for the light, medium, and heavy form of the peptide.
  18. Select and hold the title bar of the Chromatogram Traces View, and drag the pane on top of the Quan Channel Values chart.
  19. Hold the cursor over the view arranger tool.
  20. The tool indicates that this view will be moved to the right of the Quan Channel Values chart.
  21. Release the mouse button to place the Chromatogram Traces View to the right of the Quan Channel Values chart.
  22. You can dock and stack most application views, and then you can save the layouts for reuse. Refer to the section on Interpreting Search Results with the Results File in the Proteome Discoverer Help.
  23. Select the header Annotated Sequence, and scroll (or filter) for [K].RLTPFDR.[A].
  24. The Quan Channel Values chart and the Chromatogram Traces View update to those values associated with that peptide.