Tuesday, July 18, 2017
Amazing quantitative coverage of the RBC proteome!
I gotta run, but I want to leave this great paper ASAP at JPR here.
This is the second paper I've posted this year on the RBC proteome. The first paper (post here) suggested that we have been taking our knowledge of this "simple" cell for granted and there is more to discover. This new paper definitely supports this assertion!
They start with RBCs from 4 individuals and digest them with a modified med-FASP (multiple enzyme) methodology. They do something really cool here, lysing part of the RBC population forming "white ghost" cells (which appear to just be empty membranes) and digesting them /running them separately. This approach reveals a more comprehensive RBC proteome than we've seen before as well as some new information.
They show clear evidence of some membrane transporters that have not previously been seen in RBCs and show that RBCs contain over 2,500 distinct proteins. I expected this study to use the proteomics ruler but the reference for the math leads me to this paper on the Total Protein Approach (which looks awesome! but I have to go do work rather than spend time on it). Using this they can get a really clear number of the # proteins per cell. About 1,800 of the ones they identify are present in the RBCs at >100 copies per cell -- meaning that there are bunch here at less than 100 copies per cell -- and they have the sensitivity to identify and quantify them. Not the focus of the paper, but something I'm still amazed to see.
Some of their global observations don't jive with our historical understanding of protein abundance in RBCs -- so they order stable isotope labeled peptides and show that they are right. Global proteomics "relative quan", FTW!
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I'd suggest you have a look at the data files. the samples are so overloaded and saturated, I have a hard time to see how they can have good label-free analysis.