Holy cow. How did I miss this great and super smart paper!?!??
Bogdan's team found a smart solution to reducing the amount of space their carrier channel takes up in each spectrum -- they just don't read it.
By putting the carrier/boost channel as 126 and then fixing the MS/MS spectra at 126.5 each spectrum is scaled up in relative intensity, which allows the job of the search tool to be a little easier.
On the HF-X that they used, I think that this doesn't actually have an effect on the number of ions within the instrument at any phase. There isn't, that I know of, an additional isolation after fragmentation. I'm also very sleepy. Long night.
However, on those fancy pants things that do perform additional isolation steps prior to reading out the reporter ions, I think this opens up some interesting ideas for how to circumvent the dreaded carrier channel effects on those instruments.
Besides that neat trick, this study is a gold mine of good ideas for applying SCP to drug discovery! I'm sad to say there are a bunch of formulas and math things in it as well, but you can do what I did and just skip that page - and it's still a really good paper.
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