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.