If you're using a carrier or boost channel ala SCoPE-MS, IOregano, or whatever you call it, you generally start with this beautiful pool of all your conditions for the carrier channel.
When using that approach you're basically only BOOSTing the most abundant peptides from your pool. And...maybe those aren't the peptides you're actually the most interested in!
This group reports that frog egg yolk (which...if that doesn't put a gross image in your head, you're a weirdo...) makes up 90% of their peptide signal and they've already analyzed every gross egg yolk protein and would like to see something else.
I'm not clear on how they depleted the yolk proteins, but there is something called a "yolk depletion buffer" with 3 references that I'm too lazy to read (if I haven't whined about this on every post this week, RSV sucks, avoid it if you can). But their coverage goes through the roof on these FACs sorted frog cells. 15-fold more peptides than running it without?
This lab has a bunch of nice instruments, and in this specific case they used an Orbitrap Fusion II using an MS3 based quan. The fact they used 15,000 resolution for the MS3 threw me for a loop, but in the supplemental (excel sheet) you'll find they used unit resolution TMT tags. Side note, some of the nicest plots are in the supplemental PDF because they didn't have to condense some really nice data visualizations to fit into PDF panels. Worth taking a look at for sure. Even if frog biology isn't your thing, this study certainly suggests that this method would have other uses! Who couldn't find an immediate use for ACDC-FAC(ACtin Depleted Carrier For Any Cell)? I could think of 12 right now.
Anyway, solid study all around and I didn't know there were "Editor Choice" stickers for JPR papers and this one has one and deserves whatever that means!