19,000 phosphopeptides by microflow DIA! Is the PTM tipping point finally here?

 

When you think about why to not do DIA you've got maybe 2 reasons right now. Limited multiplexing capabilities - and PTMs.

Obviously the PTM data is there, right? We need the informatics and maybe the methods to grow up. 

Is this great new study signaling the tipping point is already upon us for one annoying PTM? 

There is a LOT of good work in this paper. Not limited to - wow - that's a lot of IDs for microflow - as well as the use of multiple search tools to get to these data (comparisons of library generation!). That last part is cool because all the spectra used for these deep learning tools for peptides are from Orbitraps. The spectra of other mass analyzers may look a little different. There is a lot to read into this if you're on a SCIEX TOF platform. In any case, a really nice study for multiple reasons including way way way more phosphopeptides than we've ever seen in our lab out of DIA. Maybe it's time to try lookin at some old files again.