Comet parameter: fragindex_min_ions_score

• This parameter sets the minimum number fragment ions a peptide must match against the fragment ion index in order to proceed to xcorr scoring.
• This parameter could be different (typically same or larger) than the fragindex_min_ions_report parameter.
• This parameter is intended to allow more candidate peptides to be scored, thus filling out the xcorr score histogram for a better E-value calculation. However, only peptides that pass the fragindex_min_ions_report filter will be reported in the output list.
• Valid values are a positive integer, 1 or larger.

Example:

fragindex_min_ions_score = 3