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*   Application Limitations
Although the Mass Frontier application is fully featured, there are application limitations.
The application deals primarily with small organic structures rather than peptides and other biologically-related molecules. The Structure Editor and other modules dealing with structures have a limit of 199 non-hydrogen atoms per structure. When you exceed this number, a message appears, which reminds you of this limitation.
The application is designed for pure substances only. It does not accept mixtures. The system considers a mixture to be two or more structures, depicted in the same window, which are not connected by a bond (represented as a line). If you try to generate fragments and mechanisms from a mixture, a message alerts you that this action is not permitted. The Check Structures option will also detect mixtures as an error. For additional information, see Structure Editor Module.
However, library utilities support mixtures to ensure backward compatibility with commercial libraries. You may add mixtures to a user library, but the Fragmentation Library does not support mixtures.
New aspects of the Mass Frontier system have greatly extended the automated generation of fragments and mechanisms, but some restrictions still remain. For additional information, see Previewing Unimolecular Reactions. The Mass Frontier application offers the ability to select reagent gases for chemical ionization. However, it cannot modify the relative ionization potentials of reagent gases. Negative ionization (deprotonation) is only supported using the Fragmentation Library. For additional information, see Fragmentation Library. There are no general rules for negative ionization. Because “soft” ionization techniques are mainly low energetic experiments, which often yield complex skeletal and “random” rearrangements, the predictability of these fragmentation and rearrangement processes is not as high as what can be attained by electron impact ionization. You can improve the degree of predictability by using compound specific fragmentation mechanisms in the Fragmentation Library module.
The Mass Frontier application is primarily designed for neutral and single charged molecules. As a consequence you can attach the charge symbol (+ or –) to only one atom. If the charge multiplicity is described, in general you can use the unspecified charge location option in the Structure Editor window. None of the modules support biradicals.
This application supports high resolution mass spectra with an m/z range of 1–3000 mass units. Classification modules allow only 800 peaks per spectrum. If a spectrum contains more than 800 peaks, the classification procedure selects the 800 most prominent peaks. For additional information, see Spectra Classifier Module.
All spectral modules support spectral trees except Spectra Classifier, which uses total composite spectra generated from spectral trees. For additional information, see Spectral Tree Module.

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  New Features in Mass Frontier 7.0
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