It seems to me that cell-free protein synthesis is not very used when it comes to protein expression, though its usage should avoid many problems, like the presence of inclusion bodies.
I was wondering if that's because this technique has huge disadvantages that limit its application.
By "cell-free protein sythesis" I mean protein expression via cell lysate.
By "traditional protein sythesis" I mean protein expression via viable cells.
I was taught that the main issue limiting application of cell free protein synthesis is its low yield.
The low yield of cell-free protein synthesis has been overcome. I think the main problem is that it is very expensive compared with growing cells, especially bacteria or yeast. It is especially useful when the protein being made would be toxic to the cells and when many different proteins are needed in small quantities.
Here is one vendor's literature on cell-free translation:
https://www.promega.com/-/media/files/resources/product-guides/proteomics/cell-free-protein-expression-systems.pdf?la=en
There would be a lot of reason why you would like to use a traditional approach :
Yield is still a problem, depending on the chosen cell lysate : ex. reticulocyte lysate still provides pretty low yields.
The cost is still a problem, it is pretty expensive compared to other traditional methods (bacteria, yeast)
Sometimes you may have premature transcription ending, so for big proteins it can be challenging.
You can find more limitations while searching online, but these are some of them.
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