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.
The Next Alpha Release
December 20 2019
This update adds a major new feature: decoy database generation. Previously, it was up to the user to supply decoys of their choice - and this is still possible. However, many other users just want to supply target protein sequences and let the algorithm worry about decoys. There are some advantages to this approach, such as complete control by Kojak over those decoys. The strategy Kojak uses for decoy generation is to reverse the amino acids between enzymatic cleavage points. The result is a set of peptides identical in number, length, and mass as the target set of peptides, but with a unique fragment pattern. There are peculiarities: short peptides are more likely to be palendromic and therefore appear in both the target and decoy sets; also, the leading methionine remains fixed, which can create an edge case in peptide counts. Importantly, though, is that each target protein has an equivalent decoy protein with the same number of peptides of equal mass. This has huge implications for downstream validation of inter- and intra-protein error estimation. This new decoy database feature requires updating the decoy_filter parameter to support the new format. Also, if you are using Kojak to generate your decoy sequences, a new FASTA file is generated in your output that contains the exact decoy (and target) sequences used in the analysis for further evaluation in any downstream tools.
November 27 2019
I’m releasing Kojak 2.0.0 for Windows and Linux (64-bit). This is an alpha release, indicating that this version is in active development, but I think it is worth using. There are many new features, such as improving scoring (e-values), a better troubleshooting interface, and performance improvements. More files are now supported, such as mzIdentML to conform with the Proteomics Standards Initiative (PSI). However, as the new features are being developed, some bugs may exist. I suspect many of them are specifically related to mzIdentML, so if you don’t use that format, you’ll probably appreciate this new version. If you use the PeptideProphet/iProphet validation of the Trans-Proteomic Pipeline, you might notice a much needed boost in performance. I have several more additions planned before this release is finalized, so check back soon. Also, as these are going to be rapid release, I’m not distributing the MSI installer for windows or with KojakViewer included. Please simply use the ZIP files provided on the Download page.
Site Refresh and More To Come
November 7 2019
There are major upcoming changes to Kojak and the website. You might have noticed that the usual release schedule had slowed down. This was to make time for the next major release of Kojak. As I’m in the process of putting it all together, it isn’t ready today, but I hope to have it ready soon. Part of the changes meant refreshing this site, as it had become a bit stale. This is also an ongoing process. So far I’ve updated the site structure and style, and I’m currently updating the tutorials and instructions. Stay tuned, there’s a lot more to come.
Update for TPP Users
December 1 2017
This update fixes an issue with validating PSMs that use 15N with PeptideProphet in TPP when using the browser front end. Thanks much for the user reports that found this edge case. Essentially, 15N-labeled proteins were being grouped with the 14N counterparts, rather than being treated as independent proteins. The solution was a quick fix to the Kojak pepXML output in version 1.6.1 AND when using TPP add ‘-nR’ to the “Enter additional options to pass directly to the command-line (expert use only!)” field of the PeptideProphet options on the Analyze Peptides page. That ‘-nR’ parameter instructs the TPP to also resist the urge to group 15N and 14N proteins into the same group based on sequence homology. Future versions of TPP will be able to figure this out on its own, but TPP is on a different release schedule.
To put this latest version of Kojak in the TPP, backup your existing Kojak.exe file in the C:\TPP\bin folder by renaming it. Then copy the new Kojak into that folder. It will then work natively in the TPP environment.
Next update to the page will include a series of new demos for using Kojak in the TPP.