Also, I know that in DIA-NN there is a "threads" parameter that can be set, for the i9 that should be at least at 24 (and the OS hopefully schedules that to be each on separate cores). Maybe that helps :)

Haha pretty sure they'd be happy to hear about it though. As a dev I can confirm that it's hard to keep track of all the changes in the hardware world ;)

Might be because the software maybe isn't adapted to properly use all the cores in the new Intel CPUs yet? E.g. no more hyper threading on Intel CPUs and if it only uses performance cores there will be a huge performance loss compared to Ryzen CPUs. Probably worth asking the devs.

PS: If you haven't read our paper on the initial release of MS Annika 3.0 which supports proteome-wide non-cleavable crosslink identification yet, check it out here 😉
www.nature.com/articles/s42...