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*   Adding Structures to a Record
The Database Manager module uses chemical structures at every stage, and you can add these chemical structures to a corresponding record. You can create user libraries with structures including isotopes, ions, radicals, and optically active compounds. You can use structures in the Database Manager window in connection with the Fragments & Mechanism window to check the consistency of a mass spectrum and chemical structure. You can use the Database Manager features to perform structural elucidation by modifying the input structure and regenerating product fragments.
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To add a structure to a record that contains a tree
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When dealing with spectral trees, structures are associated with nodes and not with an entire tree.
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This is useful for elucidation and database maintenance of collision-induced dissociation (CID) spectra.
The top level node, MS1, holds structural information about the neutral compound. A structure displayed in the Database Manager window is associated with a selected node. You can add a structure not only to a spectrum or tree node but also to any peak.
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To add a structure to a peak
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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 window that does not automatically connect the fragment to its spectral peak.
The Structure Editor – Database Manager dialog box opens.
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For detailed instructions about using the Structure Editor, see Structure Editor Module.
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Based on the fragment's m/z value, the application automatically connects your structure to its spectral peak in the Spectrum pane.
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To paste a structure to a record
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You can copy a structure into the Database Manager window from anywhere in the Mass Frontier application.
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Choose Edit > Paste > Structure from the Mass Frontier main menu.
When you add a structure to a record or replace an existing structure, the word “Updated” appears at the bottom of the structure pane. When you change anything in the record, including the structure, a small circle is displayed in the ID Number column in the spreadsheet. After you have added or changed a structure, the application automatically calculates and updates the molecular formula and molecular mass.
When you add a structure to a tree node or replace an existing structure, the Restore Precursor m/z button, , at the bottom of the structure pane becomes active, if the molecular mass of the structure differs from the existing precursor m/z value. Using this button, you can set the precursor m/z value of the active product spectrum according to the molecular mass of the drawn structure.
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To import structures into records
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Choose File > Open > Structure from the Mass Frontier main menu.
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Select a .mol, .mcs, or .tml file and click Open.
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To assign a structure to a peak
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The Data page lists all peaks in the spectrum.
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Click the Structure Editor button, , in the Fragment column.
The Structure Editor opens.
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The structure is added to the peak.
For details about using the Structure Editor, see Structure Editor Module.
Note  You cannot search structures assigned to spectral peaks. Structures are assigned to the m/z value so the annotation does not require a peak to be present in a spectrum.
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To add formatted text to a peak
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The Data page lists all peaks in the spectrum.
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Click the Spectrum tab.
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Click the Assign Text to m/z Value button, .
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The cursor changes to a special text cursor.
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The Annotation dialog box opens.
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The application places the text on the Spectrum page.
Note  Text is assigned to the m/z value, so the annotation does not require that a peak be present in a spectrum.
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To add an annotation to a peak
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The Data page lists all peaks in the spectrum.
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Click the Annotation button, , in the Annotation column.
The Annotation dialog box opens.
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The Spectrum page displays the annotated text with the optional connecting line.


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Related Topics:
  Managing Spectral Records
  Exporting Data to an Excel Spreadsheet
  Importing Spectra from an Excel Spreadsheet
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