Use the Fragments Comparator module to process and compare fragments generated in the
Fragments & Mechanisms window. The fragments can originate from different structures. This module supports fragments generated using any ionization method. Using fragment marks in the Fragments & Mechanisms window, you can export a selected set of fragments into the Fragments Comparator module. The fragments are organized in columns. Each column represents a set of fragments provided by an associated Fragments & Mechanisms window. The Fragments Comparator module can hold a large number of fragment sets, limited only by system resources. For detailed instructions for marking fragments, see Marking Fragments
The Fragments Comparator was designed as an integral part of the Fragments & Mechanisms
module. When you double-click any fragment in the Fragments Comparator module, the associated mechanisms appear in the Fragments & Mechanisms window. The Fragments Comparator can recall only mechanisms that are present in an open Fragments & Mechanisms window. When you close the associated Fragments & Mechanisms window, the link is lost.
The comparison feature is especially useful when analyzing the fragmentation products of
structurally related compounds. Common fragments point toward a common substructure in terms of fragmentation. Fragment differences can indicate fragments along with corresponding peaks in a spectrum that are characterized by distinct structural details. Predicted m/z
values of fragments that are different for structurally related compounds are displayed on the Compare Spectra page in the Database Manager window. For a detailed description of the Compare Spectra page, see Using the Compare Spectra Page
The Fragments Comparator window consists of Table and Structures pages. The Table page
lists the numerical m/z
values of fragments, and the Structures page displays structural drawings of possible fragments. Because the Fragments & Mechanisms module can generate several isobaric isomers for a single m/z
value, the Structures page imports only the first fragment for each generated m/z
value. The Mass Frontier application simultaneously imports fragments into these two pages but manages the information independently. Moving or deleting a column on one page does not affect the other page.
The Fragments Comparator window can display structures of fragments only as long as the
associated Fragments & Mechanisms window is open. When you close the associated Fragments & Mechanisms window, the corresponding column of fragments on the Structures page is removed.
Both the Table and Structures pages in the Fragments Comparator window are divided into
two parts. The left side displays columns of imported fragments for each Fragments & Mechanisms window. The right side displays three columns that show three types of comparison results. The first result column shows all available fragments (logical OR), the second column shows all common fragments (logical AND), and the third column shows different fragments (logical NAND).