A hypothetical question. I have two closely related plants. One is suspected to lack a certain protein present in the other. How difficult is it to discover this difference in the following situations:

A.) I know the exact amino acid sequence of the protein that should be lacking 

B.) I have no idea which protein is lacking, I do not know its sequence

The task needs to be completed without the use of transcriptome or DNA analysis, only by the means of proteomics (Mass spectometry, Protein Electrophoresis, Western blot e.t.c) 

Which methods should I use? How reliable are they? How long will it take? 

In what case will this task be the most difficult to accomplish? 

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