Getting a good snapshot of this great tool was tough (and file name dedacted just in case it matters to my collaborator).
TIMSTOF files can be gigantic and digging through them for peptides that you know are there can take a really long time. Apparently some people at Max Plank noticed this fact and decided to take a swing at fixing that part with!
Have you done enough reading for this lifetime? You can just download AlphaTIMS at this Github.
Lots of folders?
There is a "One Click GUI" and the software is pretty straight forward. You can filter your data by scan number, retention time, quadrupole settings, 1/k0 value, ion intensity, etc.,
What you'll find is that it's really easy and extremely fast to hunt down specific ions in your data. I'm still a little unclear the differences between the m/z index isolation and quad isolation functions. Wait. Nope. I just needed to type this (and maybe espresso to do espresso things) for it to click in my head. The quad filter is for the literal quadrupole. The m/z index is just my m/z view window. That's why the former doesn't do anything if I don't have fragment ions selected.
You can also use this to kick out data as HDF, CSV or MGF.
My understanding is that this is just the beginning of a whole bunch of new tools for this system that are in various levels of development, but I'm using this one constantly now and just looking forward to seeing what is next.