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Immunoprecipitation and western blotting are both used to locate a specific protein within a sample and to isolate it. In immunoprecipitation, a specific antibody and agarose beads ( or other insoluble beads) are used to precipitate the protein. In western blotting, SDS-PAGE is carried out and primary and secondary antibodies are used to locate and isolate the proteins on the nylon membrane.

My question is: which technique should be used when? what is the difference between the two? is one of them "better" / does one of them have advantages over the other?

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The two techniques serve different purposes:

IP: purifies a protein

WB: visualizes or quantifies a protein

Most often when I have done IPs (in the hazy past) I have turned around and run the protein out on a WB, so one will frequently combine both techniques. Sometimes a protein is very low abundance so you will not see it in a small volume of crude cell lysate on a WB, and you have to IP it from a large number of cells to get enough protein to visualize on a WB.

Note that IPs will also co-purify associated proteins, so a good way to know whether two proteins stick together is to IP one of them and probe for the other on a WB. This "co-IP" analysis is a very common use case for both techniques.

Hope that helps.

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