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*   Bar Code Spectra
The Mass Frontier application can automatically predict possible fragments from a chemical structure using general rules and fragmentation libraries, along with initial determination of the structural plausibility of generated ions. Predicting mass spectra is hindered by the difficulty of predicting thermochemical data, thermodynamic stability of product ions, and reaction rates. However, you can use generated fragments and their m/z values for creating bar code spectra. A bar code spectrum contains peaks at predicted m/z values with identical (maximal) intensity.
For additional information, see Previewing Unimolecular Reactions or Using Library Reactions in Fragmentation Prediction.
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To create a bar code spectrum
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Click the Bar Code Spectrum button, , in the Fragments & Mechanisms window.
The Select Target dialog box opens.
2.
Select one of the open Database Manager windows, or click New Database Manager to open a new window.
The created bar code spectrum is displayed in the selected Database Manager window.
Bar code spectra are automatically linked with their original Fragments & Mechanisms windows. When you select any bar code peak in the Database Manager window, the Fragments & Mechanisms window displays the corresponding fragments and their formation mechanisms. This link remains in place as long as the corresponding Fragments & Mechanisms window is open. For additional information, see Linking Generated Fragments with a Spectrum.
You can use bar code spectra in several strategies for investigating spectra-structure relationships. The primary purpose of generating bar code spectra is that they make identifying spectral differences possible in structurally similar compound classes for which mass spectra are not available. To study fragmentation dissimilarities between structurally-related compounds, comparing multiple bar codes in the Database Manager window is easier than manually comparing fragments and their m/z ratios between multiple Fragments & Mechanisms windows. For additional information, see Using the Compare Spectra Page.
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To compare multiple bar codes
In the following example, you are interpreting an unknown spectrum and you have established two structural proposals. To find out which structure belongs to the unknown spectrum, do the following:
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In the Difference Spectrum pane, you should see the specific peaks that this pair of spectra do not have in common.
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When a specific peak is present in the unknown spectrum and the mechanism of formation seems to be simple and plausible, you can select the most likely structure. This approach, using bar codes, is far superior to simply comparing explained peaks, because you can simultaneously apply it to a large number of structural proposals.
In the following example, the abundance is proportional to the number of generated m/z values that fit into a single integer m/z value.
Comparing multiple bar codes


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Related Topics:
  Linking Generated Fragments with a Spectrum
  Eliminating Generated Fragments Not Present in a Spectrum
  Simulating Fragmentation Processes in MS/MS Experiments
  Unexplained Peaks
  Marking Fragments
  Specifying Precision and Isobaric Differentiation
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