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*   Ionization and Cleavage Page
Use the Ionization & Cleavage page to specify the ionization method.
When comparing generated fragments and mechanisms with a mass spectrum, carefully choose the correct ionization method. The application warns you if the reaction restrictions are set for protonation techniques or chemical ionization and you are attempting to compare generated fragments with a spectrum from the NIST library, which contains only EI spectra. However, if the spectrum is from a file, the application does not check mass spectrum type and ionization techniques for consistency. For additional information, see Importing the NIST/EPA/NIH Mass Spectral Database.
Ionization & Cleavage page of the Reaction Restrictions dialog box
Positive ionization [M+H]+. The protonation mode represents “soft ionization” techniques such as Electrospray Ionization (ESI), Atmospheric Pressure Chemical Ionization (APCI), Fast Atom Bombardment (FAB), and other techniques.
Negative ionization [M–H]. The deprotonation mode represents “soft ionization” techniques such as Electrospray Ionization (ESI), Atmospheric Pressure Chemical Ionization (APCI), Fast Atom Bombardment (FAB), and other techniques.
The deprotonation option does not support General Fragmentation Rules in the knowledge base. For additional information, see Base Page.
You can only use deprotonation in connection with the Fragmentation Library. For additional information, see Fragmentation Library.
[M+NH4]+ or [M+H3O]+
[M+Li]+, [M+Na]+, [M+K]+
The chemical ionization option offers three basic ionization reactions: protonation, hydride abstraction (see Reaction Formalism), and adduct formation.
In addition, you can select one of six most common reaction gases: methane (CH4), hydrogen (H2), isobutane (i–C4H10), ammonia (NH3), water (H2O), and nitrogen monoxide (NO).
Performs ionization on Pi bonds. Available only when Electron Impact or Protonation ionization methods are selected.
Performs ionization on Sigma bonds. Available only when Electron Impact ionization method is selected.
Use alpha cleavage when generating fragments and mechanisms. Available only when Electron Impact ionization method is selected.
Display This Window Every Time Generation of Fragments & Mechanisms Is Started
Opens the Reaction Restrictions dialog box each time you start fragment generation. Clear this check box if you want to use the same parameter settings for subsequent fragment generations and do not want to see this dialog box each time.
If you clear this option and want to return to displaying the Reaction Restrictions dialog box each time you start fragment generation, follow the instructions To restore the Reaction Restrictions dialog box each time you start fragment generation.
Restores all default values in the Reaction Restrictions dialog box. These values take effect after the regeneration of fragments and mechanisms and affect all subsequent generations. The current Fragments & Mechanisms windows are not affected.


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Related Topics:
  Base Page
  H-Rearrangements Page
  Resonance Page
  Additional Page
  Sizes Page
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