Mass Frontier™ offers a number of advanced features. However, there are some limitations you should be aware of:

1. Mass Frontier 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. If you try to exceed this number a message box will appear, which reminds you of this limitation.
   
   
2. Mass Frontier is designed for pure substances only. Mixtures are not accepted. The program 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 the message box will alert you that this action is not permitted. The Check Structures option will also detect mixtures as an error. However, library utilities support "mixtures", to assure backward compatibility with commercial libraries. Mixtures may also be added to a user library. Fragmentation Library does not support mixtures.
   
   
3. The automated generation of fragments and mechanisms has been greatly extended by numerous new aspects, but some restrictions still remain. Mass Frontier offers the ability to select reagent gases for Chemical Ionization (CI). However, the relative ionization potentials of reagent gases cannot be modified. Negative ionization (deprotonation) is only supported using the Fragmentation Library™. There are no general rules for negative ionization. Since ”soft” ionization techniques are mainly low energetic experiments, which often yield complex skeletal and ”random” rearrangements, the predictability of these fragmentation and rearrangements processes is not as high as attained by electron impact ionization. The degree of predictability can be improved by using compound specific fragmentation mechanisms in the Fragmentation Library module.
   
   
4. Mass Frontier 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 should be described in general you can use unspecified charge location option in Structure Editor. Biradicals are not supported by any module.
   
   
5. Mass Frontier supports high resolution mass spectra with a m/z range of 1-3000 mass units. Mass spectra containing peaks with a mass-to-charge ratio higher then 3000 are not displayed. Classification modules allows only 800 peaks per spectrum. If a spectrum contains more than 800 peaks, the classification procedure will select the 800 most prominent peaks.
   
   
6. Classification methods supports low resolution spectra only. If you try to classify high resolution spectra the program automatically converts them into low resolution spectra. Spectral trees are supported by all the spectral modules except Spectra Classifier, which uses total composite spectra generated from spectral trees.

Mass Frontier™, Fragmentation Library™ and Spectral Tree™ are trademarks of HighChem, Ltd., Slovak Republic.