Kojak is a command-line application for obtaining peptide spectrum matches (PSMs) for MS/MS spectra. These results must be visualized using a spectrum viewer with a graphical user interface. Most existing viewers cannot display results from cross-linked peptides. Similarly, spectrum viewers designed for any particular cross-link search algorithm will not work with results from a different algorithm.
To provide a better solution, the Kojak Spectrum Viewer was created. It is open source and cross-platform. It accepts search results in the widely-used pepXML format. It can display both cross-linked and typical PSMs. The viewer operates independently of Kojak. Thus, it can be used to visualize Kojak results, or any other database search results in the pepXML format, whether from a cross-link algorithm or a standard search algorithm.
The Kojak Spectrum Viewer comes packaged with Kojak (as of version 1.4.3). It can be found in the main folder after installation. If you do not need Kojak, but wish to use the viewer, it can be downloaded as a separate binary. Also, if you want the most recent viewer builds, I suggest downloading the separate binaries, as they are updated more frequently than the Kojak package at this time. Source code can be obtained by following the links in the menu on the right. Documenation is sparse at this time, but will be completed on a rolling basis. Thank you for your patience and support.
If you use the Kojak Spectrum Viewer in your research or publication figures, please cite:
Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, and Moritz RL. “An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results” J Am Soc Mass Spectrom 2016 July 28 (web) Link