Comet parameter: precursor_tolerance_type

• This parameter controls how the “peptide_mass_tolerance” parameter is applied. That tolerance can be applied to the singly charged peptide mass or it can be applied to the precursor m/z.
• Note that this parameter is applied only when amu or mmu tolerances are specified. It is ignored when ppm tolerances are specified.
• Valid values are 0 or 1.
• Set this parameter to 0 to specify that the mass tolerance is applied to the singly charged peptide mass.
• Set this parameter to 1 to specify that the mass tolerance is applied to the precursor m/z.
• The default value is “0” if this parameter is missing.

Example:

precursor_tolerance_type = 0
precursor_tolerance_type = 1

For example, assume a 1.0 Da peptide_mass_tolerance was specified. If “precursor_tolerance_type = 0” then a peptide with MH+ mass of 1250.4 will be queried against peptide sequences with MH+ masses between 1249.4 to 1251.4. If “precursor_tolerance_type = 1” then say the 2+ m/z is 625.7 so the search mass range would be 624.7 m/z to 626.7 m/z which corresponds to MH+ masses between 1248.4 and 1252.4, effectively scaling the mass tolerance by the charge state.