Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (functional analyses, GO etc) to infer biological cellular consequences. RNAs are really only the middle-man. Presence of an mRNA doesn't necessarily mean that it will become a protein. It could be degraded by microRNAs etc. before translation. It is eventually the protein that are actually causal to a biological change.
So, my question is why not just go directly to the proteins. Why not just extract the proteins and sequence them, quantify them, analyse and draw conclusions? What are the compelling arguments to study the transcriptome to understand biological processes?