Tuesday, November 24, 2020

Optimal Fragmentation of N- and O- Glycopeptides!

If you're like me and were just kinda hoping you could go the rest of your career without actually knowing the difference between an N-glycan and an O-glycan, I've got some very bad news for you

You're going to have to go to Wikipedia and get them straightened out in your head before you set up that instrument, particularly if you're thinking of using fancy fragmentation methods to get them straight in your head.

The good news is that these authors pretty much fine tuned this all out for you in this great paper. 
The one thing that I would mention is that there are differences from one instrument to the next in terms of the fragmentation energies required. (That's why things like PROCAL exist (<-- blog post for paper). Blog post with exact masses and link to JPT who sells it now. )  

The instrument specific fragmentation energies are somewhat easy to forget about when you're running peptides. They handily fragment well right at the peptide bond, but these authors show what appears to be a huge difference in N-glycopeptide identification with an HCD change from 30 to 35 (!yikes!). You might want to verify that your instrument(s) are really doing what they say they're doing if you're thinking about intact glycopeptide work! 

If you have multiple instruments, it's always good to know what settings match up. It would suck to optimize on your Fusion 1 and then move that to another instrument and waste all those glycopeptide runs! 

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