If two proteins run in sds page with different molecular weights(having difference of 60 KDa),if both shows bands with same intensity,does it mean they have same concentration?
Hello Jijumon. Unfortunately you can't assume that two different sized proteins with the same intensity have the same concentration. This is due to the fact that specific antibodies (both primary and secondary) are used to bind to each of the proteins of interest. The intensity observed will depend on several characteristics of the antibody, i.e. monoclonal/polyclonal, quality, concentration, manufacturer, blocking buffer, dilution buffer, etc..
Coomassie blue will bind to all proteins regardless of size which makes it a good way of measuring the total amount of protein in a sample. However, because of this it is not possible to say that an observed band contains only your protein of interest. For example, if your protein is ~60kD it is possible that the band you are seeing around 60kD is not only the protein you are interested in but also other proteins in your sample which could be of similar size (i.e. 59/60/61 kD). Assuming you loaded samples containing several different proteins it means that you can't say for certain that the intensity/concentrations of the proteins are equivalent.
However, if you did load a sample that only had your two proteins of interest and there were two bands of equal intensity you could theoretically say they have equal concentration. But in practice coomassie dye will detect some proteins better than other due to their biochemistry, and some differences in intensity may not be detected because of the sensitivity of the dye. So even then I would say that you can't for certain say the concentrations are the same.
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