This section shows how to use the heat map to distinguish between lysine- and arginine- terminated peptides.


  1. On the Peptide Groups page, select the Display Filter and do the following:
  2. In the Display Filter pane, remove the two filters set previously, and then select Apply.
  3. Close the Display Filter pane by selecting the close icon (X) in the upper right corner of the Display Filer pane.
  4. Select the Data Distribution icon, and select the Heat Map tab.
  5. For Data Source, select Peptide Groups : Abundances (Grouped).
  6. For Scale Values, select None.
  7. Select Refresh.
  8. Hold the cursor over the red section in the upper left corner of the heat map.
  9. The peptide group sequence corresponding to that row will be highlighted.
  10. Each sequence in that section includes a lysine with no arginines. Because the lysine labels are expected to show a 1:2:4 light:medium:heavy ratio, this is the expected result. Holding the cursor over the green region in the lower left shows only arginine-containing peptides, which also matches the 4:2:1 pattern expected for arginines.
  11. The dendrogram on the left side of the heat map shows the peptides that cluster closely together by expression profile; the dendrogram on the top of the heat map shows those quan channels that cluster most closely together.
  12. Move the cursor to the branch of the dendrogram on the left side of the window in the middle of the heat map to highlight those specific rows in green.
  13. Double-click without moving the cursor.
  14. The dendrogram zooms in to the selected rows.
  15. Right-click the heat map, and select Check All Visible Points.
  16. On the Peptide Groups page, select the Checked column header to move the checked peptides to the top of the list.
  17. Many of these peptides include both a lysine and an arginine. For these peptides, the 4:2:1 ratio for lysine are mixed with the 1:2:4 ratio for the arginine peptides, leading to roughly the same abundance for all three channels.
  18. Close the Report Item Distribution pane.