For example, we were doing experiment to assess the micoglia activation and the effect of inflammatory response on tau pathology in Alzheimer's disease. One of the markers that we were interested in is CD11C (itgax) we ran qPCR to quantify its expression. I want to know which is more informative to quantify the transcripts or the protein itself?
It is essential to understand the discrepancy between mRNA level (transcriptional activity) and protein level (translational and ubiquitin-proteasome-dependent degradation level). Depending on the protein of interest and the tissue expressing that protein, the half-life period reflecting the protein stability is different. To elucidate how much mRNA and protein levels are different each other, you have to perform WB experiments with CHX (to stop the protein synthesis) and MG132 (to inhibit the protein degradation), respectively.
Analysing the regulation on mRNA leven gives you a good first hint. However, what eventually counts is the regulation on the level of active protein. This may not directly correlate to the mRNA regulation - there are several levels of post-transcriptional regulation like stabilization, degradation, phosphorylation, cleavage, localisation, the presence of required co-factors, and so on. That's very different for each protein, cell-type and cell-state. If it is not known, such things would need to be investigated.
In addition there may be cell subcompartment trafficking which may be missed especially if the protein measurement only samples soluble protein. This may be particularly relevant for an integrin which ultimately is secreted and may be not easily solubilised.
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