Comet parameter: max_fragment_charge

  • This parameter sets the maximum fragment charge state that will be considered in the analysis.
  • Typically, the fragment charge state range that is analyzed is from 1+ to one charge less than the precursor charge state.
  • For high precursor charge states (i.e. 6+), the default behavior would analyze fragment ions with 1+ through 5+ charges on them. This parameter is a mechanism to limit the fragment charge range that is analyzed.
  • For example, if max_fragment_charge is set to 3 then the maximum fragment charge state that will be analyzed is 3+. However, the default rule will still limit 1+ and 2+ precursor ions to only have 1+ fragments considered. And similarly 3+ precursors will still only have 1+ and 2+ fragments considered.
  • Valid values are any non-zero integer.
  • The default value is "3" if this parameter is missing. A maximum allowed value of "5" is enforced for this parameter.

max_fragment_charge = 3