Display different fragment ions in the Fragment Matches pane and the Fragment Spectrum pane - Proteome Discoverer Software - Display different fragment ions in the Fragment Matches pane and the Fragment Spectrum pane - Proteome Discoverer Software - Proteome Discoverer Software

Procedure

1. Clear the Use Search Settings checkbox.
2. Select or clear the checkboxes for the appropriate ions in the Fragments area of the Options pane.
3. Select the Ion Series tab in the ion table.
4. If you select fragment ions in the Fragments area of the Options pane but do not see them displayed in the Fragment Spectrum pane, you might need to take one of the following steps to make them visible:
1. If there is not enough room in the Fragment Spectrum pane to display the label text of the fragment ions, zoom in on the spectrum by dragging the cursor over the area that you want to enlarge.
2. If the application does not label peaks with a height that is less than 5 percent of the base peak in the Fragment Spectrum pane, set the Annotation Threshold option in the Options pane to 0 percent of the Base Peak to see whether the ion labels become visible.