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”.
• This charge range is only applied when “override_charge” is set to 1, 2, or 3. See that parameter for how the range is used with each setting.
• With “override_charge = 0” (the default), this parameter has no effect:
  • 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.
• To keep any precursor charge present in the input file and use this charge range (instead of 2+/3+) for spectra with no precursor charge, set “override_charge = 3”. The 1+ rule above still applies with that setting.
• 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