Thursday, September 24, 2015

NeuCode labeling nematodes!

As depicted in the clip above, nematodes are hungry little guys. In this brand new paper in press at MCP from Rhoads and Prasad et al., we see a new way of taking advantage of this trait.

These Badgers fed nematodes NeuCode labeled E.coli and, voila!, NeuCode labeled nematodes!

Now, I know I've rambled on about NeuCode in this blog a bunch, but if you are unfamiliar there is a good description in this GenomeWeb article here.  In a nutshell, its very much like SILAC except by NEUtron endCODE(ing) the mass discrepancies between the various channels are very very small. You are limited by the number of channels you can use by the maximum resolution of your instrument. More resolution = more NeuCode channels.

(I stole the figure above from this open access paper here.)  P.S., the technology has been progressing significantly since the original study. I saw a slide a while back that suggested 40-plex is theoretically possible.

In this study, the nematodes are studied with an Orbitrap Elite that is running 480,000 resolution at the MS1 and 30k resolution at the MS/MS (which they refer to as "medium" resolution! man, I love this field!!!)

Now, you might think 480,000 resolution? That's so slow, they'll never identify anything that way!  What did they see? The top 50 most abundant proteins? Well, they did a little better than that. This might be the single most extensive proteome of the nemotode out there. Along the way they did phosphoproteomics and also worked out some of the key regulators or stress response in this important model organism.

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