Tuesday, June 13, 2017

More tools to find alternative splice variants in humans!

This is a bit of a continuation from yesterday's pre-coffee paper. These weird alternative splice variants -- or genes from over here and genes from other there forming transcripts and/or proteins that we might not be thinking to look for.

The paper I'm looking at is this new ASAP one at JPR.

I'm going to admit up front I don't 100% understand how they did this. The mass spectrometry is straight-forward, and the data has been deposited at PRIDE (PXD006026). The introduction  is eye opening (even if you were watching the Finals on the East Coast) and was enough for me to bumble through this...check this out!

I was thinking these weird alternative events were going to be very rare. Apparently I was thinking very incorrectly...

This is where I'm a little fuzzy on the details of this paper. What I do get: they generate databases that contain only tryptic peptides for alternative splice variants. I'm not 100% clear on how the databases were generated and filtured other than they employed a tool called SpliceVista that references two alternative splice variant databases called EcGene and EVBD. Perhaps the output from SpliceVista is just FASTA and that is all there is to it.

Once they had their databases the proteomics gets very interesting. They identify splice variants in their MS/MS data, just as Dr. Lazar found on her instrument in the paper I mentioned yesterday. Where this paper goes one step further is that they did phosphopeptide enrichment on their samples as well...and find phosphorylated splice variants!
..And they don't find a few variants. They finds a bunch of them -- enough to sit back and think -- wow...this HAS to have serious biological implications! How much more can we refine out of the hundreds (thousands?) of great historical phosphoproteomics datasets using the databases they generated here?

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