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.

Example:

max_fragment_charge = 3