Comet parameter: fragment_bin_offset

  • This parameter controls how each fragment bin of size fragment_bin_tol is defined in terms of where each bin starts.
  • For example, assume a fragment_bin_tol of 1.0. Most intuitively, the fragment bins would be 0.0 to 1.0, 1.0 to 2.0, 2.0 to 3.0, etc. This set of bins corresponds to a fragment_bin_offset of 0.0. However, consider if we set fragment_bin_offset to 0.5; this would cause the bins to be 0.5 to 1.5, 1.5 to 2.5, 2.5 to 3.5, etc.
  • So this fragment_bin_offset gives one a mechanism to define where each bin starts and is centered.
  • For ion trap data with a fragment_bin_tol of 1.0005, it is recommended to set fragment_bin_offset to 0.4.
  • For high-res MS/MS data, one might use a fragment_bin_tol of 0.02 and a corresponding fragment_bin_offset of 0.0.
  • Allowed values are between 0.0 and 1.0. The actual offset value is scaled by the fragment_bin_tol value.
  • I know this is esoteric and any normal user should not give this parameter any thought beyond using the recommended settings.
  • The default value is "0.4" if this parameter is missing.

fragment_bin_offset = 0.4
fragment_bin_offset = 0.0