The original command line version could finish processing a Q Exactive file in about the amount of time it took me to push the enter button. As features have piled up on MSFragger to make it more useful, it has slowed down, but it is still a program that is darned fast for a desktop CPU program.
So....it says something....I'm not sure what....something, for sure....when a 2 hours TIMMYTOF run with PASEF takes 70 minutes, on average, to process with MSFragger and that is massively outstripping the competition.
Good news -- there is another tool to process PASEF-TOF data with!
Bad news -- you still have to be patient. This data is dense!
You can check all this out here.