This is great! Does anyone have one of these for ADP-ribosylations? I have yet to see one in our data, and we can't tell if the TIMS is too rough on the mod (in-source decay?) or if they move funny in ion mobility space.
They did this by creating project specific phosphoproteomics data with DDA processed through MSFragger (!!!) and then they used this program (pyDIAid) to create their method (!!!)