This section shows how to use the heat map to distinguish between lysine- and arginine- terminated peptides.
Procedure
- On the Peptide Groups page, select the Display Filter
and do the following: - In the Display Filter pane, remove the two filters set previously, and then select Apply.
- Close the Display Filter pane by selecting the close icon (X) in the upper right corner of the Display Filer pane.
- Select the Data Distribution icon, and select the Heat Map tab.
- For Data Source, select Peptide Groups : Abundances (Grouped).
- For Scale Values, select None.
- Select Refresh.
- Hold the cursor over the red section in the upper left corner of the heat map.
- The peptide group sequence corresponding to that row will be highlighted.
- 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.
- 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.
- 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.
- Double-click without moving the cursor.
- The dendrogram zooms in to the selected rows.
- Right-click the heat map, and select Check All Visible Points.
- On the Peptide Groups page, select the Checked column header to move the checked peptides to the top of the list.
- 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.
- Close the Report Item Distribution pane.