Which is more reliable to:
1) identify the target site of a drug? (maybe metabolomic approach is more consistent here)
2) study physiological responses of biological systems upon drug toxicity?
Both provide complementary information. A combination of both yields the best results.
What does the drug do? If it affects gene transcription, then transcription is easier and qrtPCR generally more reliable for gene expression. If it affects metabolic enzymes then metabolomics can be useful and very quantitative if you use stable isotopic techniques. If the drug is affecting protein-protein interactions and cell signalling, then you are stuck with proteomics methods and even there the issue comes down to what are you trying to measure.
If available, both should be explored. Often times, differential expression of proteins can be observed. Proteomics is being utilized a lot today due to MS advancement. Still a long way to go to maximize protein ID in order to rule out differential expression not a result of loss of protein during sample preparation.
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