In the Ionization & Cleavage tab in the Reaction Restrictions window you can choose between the ionization mode Electron Impact (EI) that produces M+ . ions, the protonation mode that produces [M+H]+ ions, deprotonation - negative ionization [M-H]-, cluster ion formation [M+NH4]+, [M+H3O]+, alkali metal adducts [M+Li]+, [M+Na]+, [M+K]+ and Chemical Ionizatio (CI) . The protonation and deprotonation mode represents “soft ionization” techniques such as Electrospray Ionization (ESI) , Atmospheric Pressure Chemical Ionization (APCI), Fast Atom Bombardment (FAB) and other techniques. The chemical ionization option offers three basic ionization reactions: protonation, hydride abstraction 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).

When comparing generated fragments and mechanisms with a mass spectrum, you should always choose the correct ionization method. The program will show a warning message 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 EI spectra only. However, if the spectrum is from a file, the mass spectrum type and ionization techniques are not checked for consistency. So be sure to use the correct settings.

The second tab in the Reaction Restriction window is H-Rearrangement. This contains controls for setting four basic hydrogen rearrangements:

The hydrogen rearrangements that involve radical (odd electron ions) rHA are set by default for hydrogen transfer from a steric optimal atom, usually from an g-atom (McLafferty rearrangement). Hydrogen shift to adjacent position (rH1,2) is activated by default and cannot be deactivated.

There can be two possible reasons for changing the default setup of rearrangements. Firstly, if you are missing an important peak and you suspect an unusual rearrangement, you can compel hydrogen transfer from an a, b, g or d atom. Secondly, you may want to simplify a mechanism by deactivating rearrangements that cause redundant reaction steps.

Mass Frontier generates fragmentation and rearrangement mechanisms along with electron shift reactions (resonance reactions). Since these reactions may, even for relatively small structures, cause a huge number of by-products, by default the resonance reactions are not depicted. To keep the reaction network clear and simple, the program performs a reduction of reaction complexity, by not displaying resonance reactions. Thus, elementary reaction steps that include resonance reactions are merged into a single step. An inexperienced mass spectrometrist might have problems in understanding such reduced mechanisms because several reaction steps are merged. If such a problem with unclear elementary reaction steps should arise, you can compel the system to display all resonance reactions by clicking the Yes radio button in the Display Resonance Reactions group box in the Resonance tab in the Reaction Restrictions dialog window.

By default, cleavage on an aromatic ring is not activated. However, when you dealing with small aromatic compounds, you should activate bond cleavage on aromatic rings by clicking the Cleavage check box in the Allowed on Aromatic Systems pane in the Additional tab in the Reaction Restrictions dialog window. For example, when you generate fragments and mechanisms of phenol, the important fragment corresponding to the peak m/z 66 can be generated only if cleavage on aromatic systems has been activated.

Cleavage on aromatic systems is deactivated by default (Due to the fact that huge numbers of fragments can be generated from large aromatic compounds and the aromatic bond is a very strong bond.)