Not my forte but you may want a standard similar to the compound of interest. So for ethanol n-propanol is common. But beware of post mortem because n propanol or some other compounds could be formed.

My answer is a GC answer. Don't know if it works on electrophoresis

Hi Mainak, could you please specify your question? Why do you need an internal Standard for 2D? If you need it for quantification (for normalization of each gel) then you should think about using DIGE (difference gel electrophoresis). An internal standard should have the same characteristics like the sample you want to analyze. In case of 2D it is impossible to find one internal standard with the same characteristics like the hundreds to thousends of protein spots which were separated with 2D electrophoresis. The only exception is, by using the same material (or a mixture of your samples which should be compared) as an internal standard, and thats only possible with DIGE.

Hello Murat

Thanks for the answer. It appears that 2D gel electrophoresis cannot be used for quantitative analysis. Actually we don't have facilities for DIGE. Do you have any other technique in mind which can be used for quantitative analysis after identification of protein by 2D gel electrophoresis? I guess western blot can be used. Please suggest.

It is possible to use 2D gel electrophoresis for quantitative analysis also without dige (i.e. look at our publications conceirning 2D methodological improvements). There are lots of parameters that must be considered when doing quantitative 2D. Major issue for quantitative comparison of 2D Gels are the variances of each step of this methodology. If you are able to decrease the CV of your 2D experiments then it should be possible to use the 2D electrophoresis as a semiquantitative method (i.e. comparing two groups of samples like disease and control).

here is a software called Melanie. It calculates the concentration in the spot even from the gel-doc image without DIGE...I did with that..It is freely available as trial version but u can get the full version too.Its completely worth.

As you have mentioned there is the possibility of western blot if you can obtain an antibody for the protein you have identified. Otherwise, as Murat mentioned above there is the possibility to compare the protein levels from the 2D gels if you have two different groups. Keep in mind that in order to justify any difference in the protein levels you will have to repeat the experiment some times, so as to be sure about the results obtained. Good luck!