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 loading ~40K query spectra used roughly 8GB RAM with a 1.0005 fragment_bin_tol value, 12GB RAM with a 0.02 value, and 14 GB RAM with a 0.01 value. For small fragment_bin_tol values where computer memory becomes an issue, set a non-zero value in the spectrum_batch_size parameter.
• The minimum allowed value is 0.01.
• The default value is “1.0005” if the parameter is missing.

Example:

fragment_bin_tol = 1.0005
fragment_bin_tol = 0.02