I am getting 1.5 fold upregulation for a given protein through TMT labelled proteomics analysis but when I checked its transcript expression using qRT PCR it is showing almost 5 fold downregulation. What could be the possible justification for this kind of inverse correlation in protein and mRNA expression.
mRNA and protein levels are not necessarily proportional. One of the factors behind this phenomenon is different turnover times. Usually, the in-vivo half-lives of proteins are longer than mRNAs because of their post-translational modification and some other factors. The opposite scenario can also happen where proteins degrade faster than mRNAs. Then there are noises too that can cause measurement errors. Here is a nice article explaining these issues: Article Greenbaum D, Colangelo C, Williams K, Gerstein M. Comparing ...
The half-life of mRNA is shorter than protein. Thus, the expression level of protein and mRNA is not usually proportional.
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