DEPRECATED This parameter has been deprecated and is ignored in the current release of Kojak.
Increases speed of Kojak by reducing cross-link search space for each spectrum to only the peptides that have a corresponding partner within the presumed precursor mass tolerances. This changes the profile of top scoring singlet peptides (set with top_count) and thus will alter the results in two ways:
- Some low scoring cross-links may be have new results based on the new singlet profiles.
- Delta scores may change for some cross-link results.
These differences tend to be few and far between for most datasets and are not necessarily better or worse. Statistical validation (with Percolator, for example) should ultimately be used to determine error rates and thresholds.
The increase in speed is affected by database size, number and complexity of cross-linker moieties, and differential modification frequency. It is mathematically possible (although rare) to achieve no benefit with this parameter enabled with a very large database and many modifications. In these cases, use of the parameter only adds overhead to the analysis and should be turned off. However, most cases will see a search speed increase of 25%-90%.
- 0 = Disabled
- 1 = Enabled
1.5.0 - 1.6.1 DEPRECATED
turbo_button = 1