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
- 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