I swear, I'm not changing this into a blog for intacts and top down. This just happens to be the only thing I've been doing lately.
This is really cool, and brazenly stolen from some ProsightPC training material.
Same protein, different amount of time that they get to react with the ETD anion. The end MS/MS spectra are completely different! I guess the 2 ms and 4 ms spectra have a lot of "incomplete" fragmentation points? But looking at it from that perspective it sounds like 2 ms not only ends dropping your cycle time but gives you more and better coverage. The 50 ms is what I'm more used to seeing, both in method setup and in sequence coverage, nice fragments from the C- and N- termini.
Worth keeping in mind, at the very least. In terms of ETD, more may not necessarily be better (or multiple MS/MS events with different ETD reaction times may be a great way to get a shit ton of data!)
Shoutout to David Horn for providing me with this (and a slew of other) slide(s).