Comet parameter: equal_I_and_L

• This parameter controls whether the Comet treats isoleucine (I) and leucine (L) as the same/equivalent with respect to a peptide identification.
• For low-energy fragmentation, there’s no way to distinguish between an I and L in a spectrum. Because of this, it doesn’t make sense to assign a spectrum to peptide DIGSTK but not DLGSTK. With “equal_I_and_L = 1”, Comet will treat these peptides as the same identification and map proteins from either peptide to the output protein list.
• A user can change this behavior and treat a I residue as being different than an L residue by setting “equal_I_and_L = 0”.
• Valid values are 0, 1:
  • 0 treats I and L as different
  • 1 treats I and L as the same
• The default value is “1” if this parameter is missing.

Example:

equal_I_and_L = 0