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The Fragments Comparator module allows you to process and compare fragments generated in Fragments & Mechanisms windows. The fragments can originate from different structures. This module support fragments generated using any ionization method. Using fragment marks in the Fragments & Mechanism window, it is possible to export only 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 an almost unlimited number of fragment sets, limited only by system resources. The Fragments Comparator was designed as an integral part of the Fragments & Mechanisms module. If you double-click any fragment in the Fragments Comparator module, the associated mechanisms will appear in the Fragments & Mechanisms window. Note: | The Fragments Comparator is only able to recall mechanisms that are present in an open Fragments & Mechanisms window. If you close the associated Fragments & Mechanisms window, the link will be 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. The most interesting are however the fragment differences. They can indicate fragments along with corresponding peaks in a spectrum that are characteristic for the distinction of structural details. Predicted m/z values of fragments that are different for structurally related compounds should attract your attention when examining spectral differences in Database Manager in the Compare Tab. |
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Fragments Comparator Window |
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The Fragments Comparator window consists of Table and Structures views. Table view lists the numerical m/z values of fragments and Structures view displays structural drawings of possible fragments. Because the Fragments & Mechanisms module can generate several isobaric isomers for a single m/z value, the Structures view imports only the first fragment for each generated m/z value. Fragments are imported into these two views simultaneously but the information is managed independently. If a column in one view is moved or deleted, this action does not affect the other view. In table view it is possible to select a column, or a part of a column, and copy the data. The m/z values can then be pasted into Excel or any spreadsheet program. In Structure view the cell can be resized with the Cell Size track bar. Columns can be moved, in both views. The columns for imported fragments (left part) can be deleted. Note: | The Fragments Comparator can only display structures of fragments if the associated Fragments & Mechanisms window is still open. If you close the associated Fragments & Mechanisms window, the corresponding column of fragments in the Structures tab will be removed. |
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Both Table and Structures views in Fragments Comparator window are divided into two parts. The left part contains columns of imported fragments for each Fragments & Mechanisms window. The right part contains 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 (AND), and third column shows different fragments (NAND). Note: | All fragments are compared by m/z values using Resolution Settings. The fragments are usually predicted in several isomeric forms, therefore a structural comparison would not be reasonable. Because the fragments are compared by m/z values the calculated precision, defined in the Resolution Settings, has a significant influence on the comparison results. |
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