Formal documentation is forthcoming. Until then, here are a few quick tips:
The viewer only reads pepXML files. If the path in the pepXML file doesn’t point to your corresponding data file (mzML or mzXML),
then make sure this data file is in the same folder as the pepXML you are loading.
The spectrum, table, and feature panes are resizeable. Click and drag on the separator between the panes.
The sort/filter button lets you customize your table of results. Filtering is case sensitive.
Click and drag on the spectrum pane to zoom in. Right-click to zoom out.
Use the settings (gear icon) to change your mass tolerance.
Linux Users - MUST READ!
The Kojak Spectrum Viewer is, naturally, only usable from a Linux with a desktop. If you operate from commandline through a terminal,
the window will not display.
The viewer also requires the SDL2 (Simple Direct Media Layer 2.0) and associated SDL2-TTF (True Type Font) libraries to be installed
on the system. With Debian/Ubuntu distros, this can be done with the following commands:
Finally, if the application does not launch from the desktop icon, the permissions may need to be updated: