Comet parameter: precursor_tolerance_type

08/22/2014 NOTE: always set this parameter to 0!
There is a bug in it's implementation and it turns out that this parameter is not needed at all.
This parameter will be deprecated in the next release.

  • 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.
  • 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 2.1 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 1248.3 to 1252.5.

If "precursor_tolerance_type = 1" for a 10 ppm peptide_mass_tolerance, then the 10 ppm tolerance is applied at the precursor m/z level. Assuming the precursor charge is 3+ for the 1320.8 MH+ mass, this means the precursor m/z is 440.93855. +/- 10 ppm on 440.93855 gives the range 440.9341 to 440.94296. This range corresponds to peptides with MH+ masses between 1320.7868 and 1320.8132.