Comet parameter: override_charge

• This parameter controls whether and how the charge range specified by the “precursor_charge” parameter is applied.
• This parameter has no effect if the first “precursor_charge” value is 0.
• Valid values are 0, 1, 2, and 3:
  • 0 = do not use the “precursor_charge” range. Search spectra with a known precursor charge 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.
  • 1 = ignore known precursor charge state values in the input files and instead search all spectra at all charge states in the “precursor_charge” range.
  • 2 = search spectra with a known precursor charge only if that charge state is within the “precursor_charge” range; spectra with a precursor charge outside that range are not searched. Bug: spectra with no precursor charge are not searched at all with this setting. If no spectra in the input file have a precursor charge, nothing is searched and Comet reports “Warning - no spectra searched.” Releases prior to 2024.01 searched these spectra at all charge states in the “precursor_charge” range.
  • 3 = search spectra with a known precursor charge at that charge state, even if it is outside the “precursor_charge” range. 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); otherwise it is searched at all charge states in the “precursor_charge” range.
• The default value is “0” if this parameter is missing.

Example:

override_charge = 0
override_charge = 1
override_charge = 2
override_charge = 3