Friday, April 6, 2018

Time to level up glycomics -- with your old ion trap!

It should come as no surprise to you that glycans are super important in all sorts of diseases. What we normally do, however, is say -- "hey! this site used to be glycosylated" and put it on the list (because we got rid of the glycans). Totally valid. Great science comes from this and will continue to. While we're seeing more studies with glycan oxonium ion triggered ETD that can work out peptides with glycosylations and what those chains are there are some limitations. First off -- 2 fragmentations slow your instrument down and second off (?) there is a finite limit to the length of the glycan chain you can study and third off (? I should restructure this sentence?) many of the stupid sugars have exactly the same stupid mass -- so you can't tell them apart.

As the body of work continues to build that the actual sugars within the glycan chain is of paramount importance -- here...and here.... --- is it fair to ask the question -- are we focusing our powers on the right side of the molecule?

Of course whether the glycosylation occurs or not is important.
Of course it would be great to know whether you get a di -- or branched-penta peptide at this site. But -- what if you treated a cell and the biggest and most profound difference in that cell was something like this --

-- umm -- I give up. I can't figure out how to rotate this. You're going to have to turn your head. What if your drug functions by completely eliminating an important class of glycosylations -- or two -- that have the same mass as one that it doesn't eliminate? Maybe you could find it, but it sure would be great to have a pipeline specifically find stuff like this (P.S. those papers up there aren't weird -- cancer people are talking about glycans all the time and coming up with crazy ideas for how to study them like making them stick to glass arrays and using lasers and stuff -- dedicated glycan analysis workflows could be VERY popular for your lab) --but how would you ever set one up?!?!  I sure don't want to think about it....WAIT....CHECK THIS OUT! 

What if this team was already setting up a revolutionary new kind of glycan analysis pipeline? What if you already have everything in your lab that you need to set it up? HPLC? Check. Ion trap? Check! Skyline?!?!?  YEAH!! 

In negative ion mode diagnostic fragment ions can be produced that can tell between the sugar isomers. This team works this out and shows you how to set up high throughput workflows to figure out what these sugars are. And -- it's Skyline -- you know we can quantify them. Time to break out the Accela (...or...umm...something else....) and put that Ion Trap back to work full-time!

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