Worse yet, there are tons and tons of polymer type things in there. Long polysaccharides all over the place (sometimes with amino acid attachments), but definitely stuff that retains well on C-18.
In this paper from Pier Righetti and Egisto Boschetti, they show the power of a couple of solutions to this problem. While the paper focuses a lot on something called CPLL (ligand binding something or other), I didn't read that part. Why lie to you?
What I found was interesting (is interesting) is that this is another place where spectral libraries show a ton of power. I've got some local friends who are kinda famous for spectral libraries and the more I visit them the more I've come to terms with: 1) Spectral libraries are way more powerful than I ever thought and 2) Ridiculously under-utilized.
Maybe I've mentioned this before? The fact that I saw a human tumor searched against a multi-GB spectral library and that the decoy spectral match was something in the range of 1e-3? Can't give details cause they're gonna publish this (soon, I hope!!!). Honestly, I've actually given talks (with some people from this lab in the audience....cringe...about spectral libraries being cool, but not really useful, cause I honestly thought they were dumb. And you know what? I was wrong. It happens a lot. Maybe someday someone will prove to me that SWATH isn't dumb...or flight tube ion mobility... I've got an open mind, fo' real, yo!
In this study they take a look at their problem. Not that they research plants, but the reasons why plants are hard to do proteomics on. Domination of high abundance proteins and polysaccharides all over the place. Generate some high quality spectral libraries and you can see through some of that noise. Just another paper on the stack of recent evidence that spectral libraries can boost our ID #s and make our lives easier.
Back to dancing time!!