Comet parameter: fragindex_max_fragmentmass

• This parameter defines the maximum fragment ion mass to include in the fragment ion index.
• The mass is the singly charged fragment mass.
• A smaller value will use less memory and generate the fragment ion index faster as less fragment ions will be added to the index.
• Specifying too small a value may remove fragment ions from consideration that would otherwise aid in peptides passing the fragment ion index filter.
• If this value is not specified, the default value is 2000.0.
• Valid values are a positive decimal number.

Example:

fragindex_max_fragmentmass = 1500.0
fragindex_max_fragmentmass = 2000.0