The default settings provided in QCxMS are a good starting point for the calculations. The default setting is performing an EI calculation.

To change the behavior of the program, keywords have to be put into a qcxms.in file. The file can be created manually, or is created automatically by first running the program, using the default settings. If other run modes are required (e.g. CID or DEA), example inputs are given below. The keywords provided are points of orientation and there are more settings that can be used to tune the calculations which are described in detail in section Running QCxMS.


The default values are not always giving the best results, but are set to cover the majority of systems. Molecules have different characteristics that can significantely influence the outcome. Changing the input settings can improve upon the final result, e.g. decreasing the molecular ion peak abundance or producing more low m/z fragments.

EI - positive Ion Electron Ionization

ntraj *<integer>*
tmax  *<integer>*
eimp0 *<real>*

The EI run mode is automatically used with the [default] settings described by the keywords, leading to a run using xtb2, so actually there is no keyword required in the qcxms.in file. To provide some guidance, the setting showed above can be used and the <integer> and <real> placeholders switched to actual values.

DEA - negative Ion Electron Ionization

charge -1
upper 15
lower 0

For EA calculations, the ma-def2-SVP/ma-def2-TZVP basis sets are recommended. Production runs are recommended to be conducted at DFT level, however, these are computationally very expensive and GFN-xTB can be used for a quantitative overview. The most cost-effordable DFT settings are <functional> = PBE | <basis> = ma-def2-svp

Less IEE energy is required for DEA fragmentation, so it is recommended to reduce the IEE distribution limits by using the upper and lower keywords (the old keywords dea and scan are obsolete).

CID - positive Ion Collision Induced Dissociation

charge 1
elab 40
lchamb 0.25

The general activation method is automatically used, but can also be expicitely switched on using the fullauto keyword.

For the forced activation run-type, use collauto. The number of collisions are set by using collno <integer> to set number of collisions (including fragment-gas collisions (fgc)). For setting ONLY ion–gas collisions, use maxcoll <integer>.

The thermal activation method is switched on with temprun and scales the internal energy to a value given by the keyword esi <real>. This is the fastest method, but requires a good initial guess for the internal energy value.

For more details, see section Running QCxMS.