What is THE biggest problem with DIA-NN? By far? My vote would be that all I get is this sheet and I have to believe Neurotic Network things that it is real. I can't check my peak quality or my fragments because all I have is a bunch of text files.
What if you erase that limitation by using another 100% free -to - you incredibly well supported, validated, respected and ultra powerful software - like Skyline???
Dr. Brett Phinney, Director of the world renowned UC Davis proteomics facility to the rescue. Check this ridiculously great video out here!
On that topic, all of the videos from the UC Davis proteomics course are also online. You can find these here.