I am interested in looking at protein profile after the treatment on the breast cancer cells, using Proteomics. However, I am not quite sure about the time point at which it will be the best to do Proteomics?
How do researchers usually decide the time point following treatment, at which protein expression profile should be assessed?
Depends on a number of factors and it is hard to point out them without knowing the proteins you are interested in. Best would be do to go for a time course. In any case, should be before you observe any cell death. Also for proteomics, it is useful to block cell death for instance by using caspase inhibitors if apoptosis is involved.
Hi Lakshya,
You should consider the nature of changes you expect to see. This will define the time scale of your experiment. For instance, production of new proteins in human cells occurs within hours and time scales of 6-12 h post-treatment may be reasonable to spot them. If what you are expecting to see is rather protein modification (phosphorylation, glycosylation etc), the response may be even more rapid. On the contrary, protein degradation occurs with very different rates and may take up to several days for certain proteins. If I expected to see some proteins disappear as a consequence of their expression shutdown, I would choose a 2-3 day time point to perform proteomics.
Keep in mind one more thing: the more distant is the time point from the beginning of treatment the higher is the number of indirect, downstream events you will see. One the one hand, it is good to have a complete picture of changes induced by the treatment. On the other hand, once it comes to the molecular mechanism, it becomes progressively difficult to interpret them.
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