Assigning Fragments to Spectral Peaks

Use the Mass Frontier application for the automated prediction of fragments from a structure. If you start the generation of fragments from Database Manager window and the active record contains a structure (an MS1 structure for Spectral Tree), the application automatically links the generated fragments with peaks in the spectra according to their m/z values. For additional information, see Linking Generated Fragments with a Spectrum.

v	To predict fragments from a structure

1.	Choose Tools > Fragments and Mechanisms from the Mass Frontier main menu.


Note The selected record must contain an MS1 structure in the spectral tree.

2.	Specify your criteria and click OK.

3.	To display the mechanisms leading to an explained peak, click Mechanisms in the Fragments & Mechanisms window and then do one of the following:

a.	On the Spectrum page of the Database Manager window, hold your cursor over a highlighted peak.

b.	Click the peak.

v	To automatically assign generated fragments to peaks

1.	Choose Tools > Fragments and Mechanisms from the Mass Frontier main menu.

2.	Specify your criteria and click OK.

3.	In the Database Manager window, click the Spectrum tab.

4.	Right-click the Spectrum page and choose Auto Annotation > Generated Fragments from the shortcut menu.


Note This command is not available unless the Fragments & Mechanisms window remains open.

5.	Specify your criteria and click OK.

v	To manually assign a fragment structure to a peak

1.	Click the Assign Structure to m/z Value button, , in the Database Manager toolbar.


Note Do not confuse this button with its generic equivalent in the Mass Frontier toolbar, which opens a Structure Editor that does not automatically connect the fragment to its spectral peak.

2.	Draw a fragment or open a structure.

3.	When you finish the fragment, click OK.

Based on the fragment m/z value, the application automatically connects your structure to its spectral peak in the Spectrum pane.

4.	To connect the fragment to a different peak, drag the connecting circle at the baseline to any other peak.

5.	To resize the drawn fragment, click the fragment and drag the handles.


Note You cannot search structures assigned to spectral peaks.