Comet parameter: show_fragment_ions

Note: this parameter, together with .out file output, was removed in release 2025.03.0.

• This parameter affects .out files only e.g. when output_outfiles is set to 1. This parameter controls whether or not the theoretical fragment ion masses for the top peptide hit are calculated and displayed at the end of an .out file.
• Valid values are 0 and 1.
• The default value is “0” if this parameter is missing.

Example:

show_fragment_ions = 0
show_fragment_ions = 1