Monday, August 14, 2017

What can we learn from intentional protein carbamylation?

Carbamylation is one of the primary reasons that I always use the free Protein Metrics Preview node on my RAW files before queuing up a big run. It is generally an unintentional artifact caused by your proteins spending too much time in urea -- or in urea that is too hot.  However --

--these authors carbamylated some stuff on purpose!

This team intentionally carbamylates proteins and looks at changes in the MS1 profile of several different proteins.

This causes massive shifts in the number of charges the proteins can accept! As you might expect from some of the names on the study, the next thing they do is look at how these proteins fragment. The carbamylated proteins provide much worse HCD fragmentation spectra and (surprisingly to me) big shifts in the elution times.

However, UVPD fragmentation of these proteins remains mostly unchanged -- carbamylated or not. While the authors may have used this study as a way to learn more about how UVPD fragments intact proteins and conclude it does not follow the mobile proton model, I'm wondering if this could have other applications.

When looking at intact proteins, there are some big advantages to having proteins accepting fewer charges. This makes the protein isotopic envelope easier to deconvolute and helps reveal co-eluting species (often proteoforms). Obviously, there would be some disadvantages to carbamylating all your proteins -- like now you have another PTM to worry about -- and less charges means your proteins are in a higher m/z range, but I can't help but think this might come in handy later!

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