Honestly dind't understand the question...

Do you know what protein you're looking for (its molecular weight and pI) or that is precisely what you're trying to figure out?

Have you successfully spotted it in some gel/immunoblot at least once?

Develop some more: what protein, what immunolabel, what sample, ...?

Ok. sorry i didn't explain enough. the protein is unknown.  i am using total protein extract from bacteria to detect argpyrimidine residues using argpyrimidine specific Ab. i found protein. and i want to isolate it to send it for fingerprinting. but i can not isolate it from membrane as it must be isolated from gel. but the problem is that i can not localize same protein on silver stained gel of the same sample due to the error of determining same spot observed on 2D WB. 

Sometimes you can't find your protein of interest in the gels with silver or Coomassie blue staining as their sensitivity is quite low when compared to the WB antibody signal, thus the spot you identify with your antibody can be very faint in the gel.

You could try running new gels with a higher protein loading, 2 - 3 x more, that might help to increase the protein concentration for each spot, and maybe it will give you a better signal after the silver staining.