Comet parameter: theoretical_fragment_ions

• This parameter specifies how theoretical fragment ion peaks are represented.
• Even though Comet does not generate/store a theoretical spectrum, it does calculate fragment ion masses and this parameter controls how the acquired spectrum intensities at these theoretical mass locations contribute to the correlation score.
• A value of 0 indicates that the fast correlation score will be a sum of the intensities at each theortical fragment mass bin and half the intensity of each flanking bin.
• A value of 1 indicates that the fast correlation score will be the sum of the intensities at each theoretical fragment mass bin.
• For extremely coarse fragment_bin_tol values such as the historical ~1 Da bins, a theoretical_fragment_ions value of 1 is optimal.
• But for narrower bins, such as ~0.3 for ion trap data or ~0.02 for high-res MS/MS spectra, a value of 0 is optimal to incorporate intensities from the flanking bins.
• Allowed values are 0 or 1.
• The default value is “1” if this parameter is missing.

Example:

theoretical_fragment_ions = 0
theoretical_fragment_ions = 1