Next Alpha Release

August 25, 2021

For those following Kojak development via the GitHub source tree, you probably noticed iterative changes every few months that haven’t been reflected on this site. To put everything back in synchrony, I’m posting the latest alpha release (number 8) here. Unfortunately, it did not make the cutoff in time for the new TPP 6.0.0 release, but hopefully that will be corrected soon. If you do use the TPP, please download Kojak from this site and overwrite the outdated version of Kojak in your TPP/bin folder.

New Tutorial Posted

January 6, 2021

Happy New Year! The long overdue TPP tutorial has been posted. The tutorial visuals show the upcoming TPP 6.0 release - available as release candidates for those willing to work ahead of its official release. The updates to PeptideProphet in TPP 6.0 include optimizations for Kojak and a more streamlined interface for both the pipeline and viewing the results. PeptideProphet is the recommended tool for validating cross-linked peptide spectrum matches from Kojak at this time, with additional recommendations with other tools forthcoming. The tutorial can be found in the Documentation->Instructions.

Also, I think I’m way overdue for updating the release candidates. Internally, I’m several versions ahead of the website. I hope to rectify this lag soon.