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*   Comparing Fragments
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.
Fragments Comparator Window
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.
On the Table page, you can select a column or a part of a column and copy the data. You can then paste the m/z values into an Excel spreadsheet or a similar application.
You can resize the cell on the Structure page with the Cell Size track bar, move columns in both pages, and delete the columns for imported fragments (the leftmost columns).
Table page in the Fragments Comparator window
Structures page in the Fragments Comparator window
Comparison Results
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).
Note  The Mass Frontier application compares all fragments by their m/z values using Resolution Settings (see Accuracy). The fragments are usually predicted in several isomeric forms, making a structural comparison unreasonable. Because the application compares the fragments by m/z values, the calculated precision as defined in the Resolution Settings significantly influences the comparison results.

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Related Topics:
  Drawing Fragmentation Reactions
  Editing a Fragmentation Scheme
  Working with Records
  Extracting Mechanisms
  Using Library Reactions in Fragmentation Prediction
  Searching for Fragmentation Criteria
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