Sunday, February 13, 2022

12-Plex derivatization for accurate multiplexed quantification of citrullination!


Does that look hideously complex? It does to me, but the payout might be worth it because -- 

Protein or peptide citrullination is a really important thing to some people and it's something that, in general, LCMS based proteomics is not very good at accurately identifying. 

A citrulline is essentially an arginine plus 1.something very small (it's a Saturday and I don't remember it off the top of my head and I ain't looking it up). Even on an amazing Orbitrap running at 140,000 resolution once you get up to a peptide m/z of 800 or so it's tough for most search engines to determine what's a peptide that ends in a citrulline and what's the naturally occuing M+1 isotope.

You do get some hints in the fact that most trypsins won't cut a citrulline very well, but that's controversial as some of the super trypsins have been shown to do okay. You can also use the beautiful diagnostic fragment ion that the ProteomeTools project characterized. Since you can directly utilize that diagnostic ion in MaxQuant (or MSFragger) they're better tools to use.

What if you didn't have to guess and you could just multiplex citrullinated? Maybe that's worth derivatizing and...SCX...

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