I'll be honest. I don't fully understand this cool new study. What I do understand is that when I fragment an intact protein I get fragment ions from the N and C terminus(es) and only in the very best cases do those fragments extend to the middle.
What they've worked on here is alleviating this by optimizing parameters and considering that the fragment ions might not be working all the way from each terminus. They use a special Mascot version (TD?) but explain how you can process this data in a similar way using other tools with a link to an older study (direct link to that study here).
It makes a lot of sense to me, we're hitting these intact proteins with a lot of energy and why wouldn't we get internal fragments? Thinking we're exclusively seeing b and y ions is convenient, but we see secondary fragmentation in some large peptides and definitely in peptides with PTMs, so why not proteins? All the work is performed with a Bruker FTICR so they use some pretty amazing mass tolerances to demonstrate that they can actually observe fragment matches.