Parameter: top_count


This parameter specifies the number of top scoring peptides to store in the first pass of the Kojak analysis. A second pass follows pairing cross-linked peptides to these top sequences to produce the final cross-linked peptide score. Setting this number too low will cause cross-linked sequences to be missed. Setting this number too high will degrade performance of the algorithm. Optimal settings will depend on database size and the number of modifications in the search. Recommended values are between 5 and 50 (20 is probably a good start).

SPECIAL NOTE For Kojak releases prior to version 1.6.0, this parameter had different context. For those earlier versions, use a top_count between 300 and 500.




1.0 - present


top_count = 25