Marshall Bern (wait, I know him!) et al., show in this new study that they can ditch the first LC part. Just run the digested reduced peptidoglycan out on a single dimensional LC gradient and use ETD and HCD and BOOM! you're done. (That sentence is too long).
By simplifying it they get to see some new, low-abundance muropeptides (glycopeptides) in C. difficile that they haven't seen before.
The paper points out that the traditional method is slooow. You use a phosphate buffer system to really get very clean separation of your compounds and fraction collect them. The phosphate buffer system is flushed out and then the remainder is analyzed with reverse phase. Yeah. Its slow. But this is the reason they've been doing it this way:
From a Dave Popham paper. They all look like this.)
Using the phosphate buffer system you can quantify it like its a NIST standard. Can you get a 4% CV? Heck yeah, you can.
Just shooting muropeptides on reverse phase alone as they did in this study?
Great for finding new muropeptides! Ummm....maybe not so great for quantifying them and ultimately elucidating the peptidoglycan 3D structure? Hmmm....if only there was a quantification technique that didn't care about peak shape...then you'd have the whole package.
But for straight-up discovery of new muropeptides? Single shot 1D ETD/HCD with Byonic processing looks like the solution!