Comet parameter: peptide_mass_tolerance_lower

• This parameter controls the lower bound of the precursor mass tolerance value.
• The units of the mass tolerance is controlled by the parameter “peptide_mass_units”.
• Usually you want to specify a negative number for this lower bound tolerance.
• The default value is “-3.0” if this parameter is missing.
• The mass error is defined as (experimental - theoretical). So if the lower tolerance is set to “-3.0”, this means that identified peptides can be up to “3.0” units larger than the experimental mass.
• For a wide window, open mod search, you would want to set peptide_mass_tolerance_upper to something large, e.g. “200.0” Da, and peptide_mass_tolerance_lower to something smaller, e.g. “-10.0” Da.
• This parameter was implemented in version 2024.01.0.

Example:

peptide_mass_tolerance_lower = -3.0
peptide_mass_tolerance_lower = -20.0