Because fragmentation libraries largely contain ionic structures that can undergo resonance
reactions, the Mass Frontier application can perform a resonance substructure search. This search feature ensures the correct retrieval of all resonance structures, even when the query structure is in a different resonance form than the library structure. This feature is fully automatic, so you need not worry about the particular resonance state of the ionic structures. However, be aware of this functionality when reviewing search results, as the query and library structures in positive search results might appear different if the resonance reactions are possible. In this case, do not consider this difference as an error, but rather be aware that there might be complex resonance variations. For additional information about resonance reactions, see Resonance Page
You can ignore charges and radicals in (sub)structure searches if their location is ambiguous.
When searching structures with an unspecified charge location or substituents, review the applicable search rules. For descriptions of these search rules, see (Sub)Structure Search Rules
Depending on the merge option you select, the search results appear in the Work library
pane of the Database Manager window or in a new Database Manager window. The search results display the query substructure in red in the library structure.