Under conditions you described, you will see a lot of proteins that just didn't enter the stacking gel and a very strong and long smear from the loading pocket to the end of the gel. You won't be able to see individual proteins under conditions your described because of the influence of DNA, RNA, polysaccharides, membrane proteins, and many other influencing factors. If you want to see some proteins in the inclusion bodies I would recommend first to isolate the fraction of the inclusion bodies by ultracentrifugation. If your protein is expressed at very high level in the inclusion bodies you might be able to see one dominating band matching the MW of your protein under reduced conditions.

You should expect to see inclusion body protein as well as soluble proteins and membrane proteins, since you did not do any centrifugation, and since inclusion body protein will dissolve when heated in SDS-PAGE sample buffer. To distinguish between soluble and insoluble protein, a centrifugation step is used prior to adding sample buffer.

Under conditions you described, you will see a lot of proteins that just didn't enter the stacking gel and a very strong and long smear from the loading pocket to the end of the gel. You won't be able to see individual proteins under conditions your described because of the influence of DNA, RNA, polysaccharides, membrane proteins, and many other influencing factors. If you want to see some proteins in the inclusion bodies I would recommend first to isolate the fraction of the inclusion bodies by ultracentrifugation. If your protein is expressed at very high level in the inclusion bodies you might be able to see one dominating band matching the MW of your protein under reduced conditions.

The description may not be quite clear enough but It seems there is insoluble E coli expression and you are trying to assay whole cells and total cell homogenate by SDS-PAGE to see if there are any differences between the two samples, right?  If the expression is relatively high enough (refractility under phase contrast microscopy, 1 or more inclusions per cell, tenths of a micron in diameter), you wash the cell pellet before Laemmli buffer treatment, and you use a tiny load,  then you might see the target protein in a background of host proteins that are close and distant to the target band; this assumes you are running a lane of uninduced cells next to the induced cells.  You could also detect the band of interest without too much concern for background by using a Western blot assuming there's specific antibody.  When preparing whole cells with Laemmli buffer it is best to shear the DNA after all the material becomes solubilized.  This will lower the viscosity so as not to have a "stringy sample during loading.  There's a device which spins a thin PTFE rod in microfuge tubes to accomplish the shearing:   https://www.fishersci.com/shop/products/fisherbrand-pellet-pestle-cordless-motor/12141361

Thank you for your awesome answers. I just did the centrifugation to separate pellet and supernatant (15000x g, 30 min, 4 C). My proteins are in pellet fraction, so does it necessarily mean that they are in inclusion bodies? The problem is that I am having positive control (catalyses certain reaction by homologous enzymes) and the proteins of my positive control are in pellet too. So It means my positive control works and still the proteins are in pellet fraction (they are supposed to be cytosolic proteins). Or is there any other explanation why are nicely functioning cytosolic proteins in pellet fraction? 

Thank you for your answers in advance

It is possible that a portion of the expressed protein was soluble and therefore in the supernatant, whereas the majority of it was insoluble, not necessarily as inclusion bodies, and therefore in the pellet. This is a common occurrence. You may be able to increase the proportion in the supernatant by adjusting the expression conditions, such as by inducing expression at a lower temperature, using a different expression strain, or reducing the inducer concentration.