Okay -- so TMT is great if you're comparing 11 things, right? But -- WOW -- does it ever get less fun to use when you've got 12 samples. Or 34.
There are many ways to tackle this, and these different ways have varying degrees of success. When in a pinch, I go to my dumb method, but it's VERY clear to me that this is crude and I'd love to have a better way.
THIS.IS.A.BETTER.WAY
24 (TWENTY-FOUR?!?!?) TMT 10-plex batches.
Coisolation explored.
Label isotope contamination explored.
Did y'all know that there is an entire chromosome(!??!) that roughly 50% of the human population has that the other half does not?!??
They use this evidence to determine the biological FDR. Cause...cells from humans that lack that chromosome don't have genes to make those proteins. If they show up in cells that don't have the genes, your FDR is probably askew....
The data is processed in MaxQuant. The post MaxQuant analysis was done with a bunch of R things, but the basic workflow is explained very well in nice figures and I feel like I can follow this logic to improve the next multi-batch set I try to combine.
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