This new paper from Dean Hammond et al., is an absolutely elegant approach to exploring amino acid integration and protein turnover.
What'd they do? They took a bunch of voles (had to look up what there were, knew it was a rodent...)
and fed them food that contained stable isotope lysine! Then they studied the proteins from various organs of the cohort over time. How much time? 40 days!!
From these samples they did single dimension LC separation with 15cm EasySprays on <100 min gradients on a Q Exactive running a nice standard top10 method. The resulting RAW data was ran through Mascot and quantification was done with Progenesis.
To really assess the big question here -- protein turnover, they had to work up their own math and processing methods in-house, but the RAW data was put on PRIDE (PXD002054) and the calculations and logic laid out in great detail so anyone who wanted to look at these dynamics could check their methods (seriously...a well written paper!).
So what did we get out of this one? It seems like this is a starting point for this group. Here is a protein integration/turnover model system and now that they (and we!) have this system in place, they can start to look at more complex perturbations of this system. They specifically mention that they will be further applying this system to body mass altered systems. What we get is a really good dataset describing in a mammal, how reliable our turnover models (based largely on unicellular organisms!) are on a global level scale.
One challenge they had here was that the Vole doesn't have the best genome. But you know, someone somewhere out there is probably working on it, so this is a good dataset that will only get better with time!
I'd just like to throw out this thought: In the liver, they were able to calculate the turnover rates of over 1,000 proteins. >1,000!!! They did this with an incomplete genome, a 15cm EasySpray column and a Q Exactive classic and some really good biology! I am so psyched about where we are these days!
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