You could do on-bead digestion to exclude the SDS. For bioID I used to do on-bead digestion and then 1st “elution” with AmBic and 2nd with 4:1 ACN:TFA. As for removal of SDS, I would be worried to go for anything less than SP3. Still weird that it’s only a particular treatment though!

Thank you, yes I was reading this paper just few days back. Our experience with FAIMS/DDA is already quite different than theirs (no boost in protein IDs but more unique peptides with FAIMS in my hands), so I assume FAIMS/DIA might also end up being different...

Thank you, this is what I was thinking too. Definitely will try library-free as well and stick with what works better.