The reason to be excited about this great new paper In Press at MCP is the subtitle on the top of each page:
The biologists have been super excited about these things for a long time -- and probably more than a little disappointed in what proteomics has done to help them understand this ultra important class of PTMs.
Does this fix it? I don't know how many sites people will want/need or how many exist, but this sure looks like a ton of data.
For us mass spec nerds, maybe the most interesting part is the surprisingly complementary results generated by ETD and EThcD. In my head I kind of consider the two about the same thing. ETD makes mostly charge reduced species, but if you look close enough you'll find c and z ions. EThcD makes less charge reduced stuff, that -- in theory -- is replaced with a blend of c,z,b and y fragments -- but my experience is that Sequest can't make any sense out of it.
All this data processing was done in MaxQuant and allowed a dizzying number of dynamic mods:
This results in some beautiful data -- tons of sites identified and localized and data that ought to make the biologists a whole lot happier than anything I've seen before!
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