Comet parameter: precursor_charge

• This parameter specifies a precursor charge range.
• This parameter expects two integer values as input.
• If the first input value is 0 then this parameter is ignored, as is “override_charge”. A spectrum with a precursor charge is searched at that charge state. A spectrum with no precursor charge is searched as 1+ if more than 95% of the spectrum’s total peak intensity is below the precursor m/z (or the spectrum has no peaks), or as both 2+ and 3+ otherwise.
• If the first input value is not 0, then with the default “override_charge = 0”:
  • A spectrum with a precursor charge is searched at that charge state; this parameter does not override it.
  • A spectrum with no precursor charge is searched at all charge states between (and inclusive of) the first and second input values.
• See “override_charge” for how the range is applied with other settings.
• Any charge state above max_precursor_charge is not searched.
• The default value is “0 0” if this parameter is missing.

Example:

precursor_charge = 0 0
precursor_charge = 0 2 (parameter is ignored because the first entry is 0)
precursor_charge = 2 6
precursor_charge = 3 3