Comet parameter: scale_fragmentNL

• The fragment neutral loss field is the 8th entry in the variable_mod0X parameter.
• If this parameter is set to 0, any fragment ion that contains the modified residue will also have the neutral loss mass subtracted from the fragment ion and analyzed. This is irrespective of the number of modified residues contained in the fragment ion.
• If this parameter is set to 1, any fragment ion that contains the modified the modified residue will have N times the neutral loss mass subtracted from the fragment ion and analyzed where N is the number of modified residues contained in the fragment. So this parameter controls whether or not to scale/multiply the neutral loss mass by the nubmer of modified residues.
• Valid values are 0 and 1.
• The default value is “0” if this parameter is missing.
• This parameter was added in Comet release 2023.01.0.

Example:

scale_fragmentNL = 0
scale_fragmentNL = 1