One of the last remaining arguments for the dDa crowd like me is PTMs! When that domino falls (if possible), we'll see a full paradigm shift.
A lot of time when people talk about PTMs in proteomics they just mean "phosphoproteomics" and a lot of tools let try to look for them.
How do they stack up? You don't have to do it yourself, this team tried them all out!
Worth noting, after 3 months of waiting for my university to issue a PO, I just downloaded SpectroNaut 17 and this paper used 16.