The generated fragments can be used in many ways, for example, with bar code spectra, for fragment comparison of different structures, or for export to Microsoft Excel. The automated generator can predict a large number of theoretically possible fragments, so you might need to extract only selected fragments for use in the mentioned methods. To do so you can mark fragments (m/z values) that should be either considered or ignored during further processing.

Three types of mark can be used in the Fragments & Mechanisms module:

1. Set (Only fragments with a given m/z value will be considered)

2. Exclude (All fragments with a given m/z value will be ignored)

3. Default (No m/z value marked)

The Set mark has the highest priority. If you mark one or more m/z values - “Set” only these will be considered. If you mark one or more fragments - “Exclude” then these fragments will not be considered. If no fragments are marked (by default) then all the fragments will be considered.

The fragment marks apply to Bar Code spectra, Fragments Comparator window and copying to Excel.

To mark an m/z value:

• Select the m/z value and click the Set or Exclude buttons, or

• Click the appropriate check box for an m/z value in the m/z list (on the right side of the window). The check box can have one of three states: Set , Exclude , or Default

To delete a mark:

• Select the marked m/z value and then click one of the mark buttons

• Or, click the check box of the m/z value once or twice until the check box is in the default state

• Or, if you want to delete all marks, click the Default button in the bottom right corner of the window.