It would be helpful if you please show the picture of your western blotting and describe the procedure how you did it (which protease inhibitor cocktail, reduced or non-reduced conditions, the source of the original protein preparation, when exactly you used protein inhibitors, and so on).

Without that info it would be hard to make any recommendations.

Thanks 

The N  stands for nucleoplasmic fraction samples, C is cytoplasmic fraction samples. I used protease inhibitor cocktails consists of group of serine inhibitors. It is non-reducing conditions, added the protease cocktail integrated with lysis bubffer first I finished the fractionation of the cells. 

Sorry, the western blotting carried out in reducing conditions!

• I did sonication for these samples, to shear genomic DNA, does this affect integrity of the proteins I am detecting?

Based on the info you provided above, it looks like you might use not the full range of protease inhibitors (depending on the source of the initial protein prep) or it's just some kind of another splicing variant of your protein. When you need very specific recommendations for your answers you need to provide very specific descriptions of your experiments.

 Thank you for the suggestions .. I do think the first suggestion you come up with is more sensible