Comet parameter: fragment_bin_tol

  • This parameter controls the bin size associated with fragment ions.
  • The bin size defines the mass width associated with a single MS/MS peak as it is stored internally in an array element.
  • Although it's not explicitly a fragment ion tolerance, it's probably easiest to think of it as such.
  • Note, there is a direct correlation between the value selected for the fragment_bin_tol and the memory used in a search. The lower the fragment_bin_tol setting, the more memory a search will use. A test of 4,515 query spectra used ~700MB RAM with a 0.4 fragment_bin_tol value, ~1.5GB RAM with a 0.10 value, and ~9GB RAM with a 0.01 value. For small fragment_bin_tol values where computer memory becomes an issue, either set use_sparse_matrix to true and/or make use of the spectrum_batch_size parameter
  • The minimum allowed value is 0.01.
  • The default value is "1.0005" if the parameter is missing.

fragment_bin_tol = 1.0005
fragment_bin_tol = 0.4
fragment_bin_tol = 0.02