It took a little while to wrap my head around this method, but in the end what you have is a really simple way to quantitatively study endogenous peptides. While this was used to study salt stress in plants, I don't see why it couldn't be applied to just about anything.
Salt stress in plants is a critical area of study right now with the climate changing and water availability becoming increasingly questionable just about everywhere. So definitely pay attention to that.
What I'm selfishly interested in is how this team extracted proteins (froze and ground the plant tissues with a mortar/pestle, then TCA precipitated to clean up to amino acid containing things. Once they resolubilized the proteins they used that to normalize their abundances (x mg of protein per sample). To get the endogenous peptides they simply used a 10kDa filter.
That's it. Then they cleaned them up, TMT labeled and ran everything the normal way. The TMT on the terminus helps add some mass and a partial charge to the peptides so they both fragment better and fit within our normal proteomics type methods if they're small.
My first thoughts were things like "what about small proteins or proteins that are degraded by the sampler harvest, lysis, extraction". And I'm sure you absolutely see those things as well, but if you control the conditions right, those are probably all 1:1s. What they find under salt stress is a population of peptides that are differentially regulated and they backtrack them to make a nice story.
If you often think "man, this peptidomics workflow seems way way too complicated" maybe it is and maybe it is worth thinking about this one?