Why analyse transcriptome instead of proteome?
Q: Why not just extract the proteins…


A: It’s not just a question of extracting the proteins, you would need to separate them and then isolate each of them. There is currently no practical way to do this for say, 10,000 proteins, which in any case may have multiple forms. The beauty of the RNAseq method is that it does not require physical separation or isolation of transcripts.

An approach more likely to be useful is to identify and quantify the proteins in situ, but this is still some way off having the comprehensiveness and sensitivity required.


  Q: …sequence them…


A: Protein sequencing is slow and difficult. It cannot be applied on a mass scale, unlike sequencing of DNA copies of RNA transcripts. Other methods of identification based on physical behaviour (migration or elution position) are more promising, and the direction that is likely to be followed.


  Q: …quantify them…


A: Even that is difficult, when you are eluting proteins from gels, for example. In contast, RNAseq methodology just counts transcripts. (But the likely direction this will go is quantitation by peak height, without separation or isolation, as with metabolomics, or by the intensity of some signal from the protein immobilized in the gel, staining of something more sophisticated.)

So, in general, you do protein analysis on particular individual proteins of interest to you, whereas you can do RNAseq analysis on all the transcripts in a biological sample, and then go fishing (among the results, and afterwards on the lake if that’s your thing).