Bromophenol Blue is just a dye, runs with the ion front on SDS-PAGE gels using the Laemmli buffer system (separation of proteins ≥1 kDa). This includes gels of a single percentage or gradient gels. The molecular weight (MW) of bromophenol blue on these gels is negligible and is considered to be zero in the calculation of the MW of a protein.

Comassie Blue binds the proteins and these interactions have been characterised (please check the paper attached). 

I hope this helps you.

Hi Aswin CBB250 is usually used to stain proteins, while bromophenol blue (BPB) is used as a tracking dye on SDS PAGE, because it does not bind proteins.

Having both dyes in a gel is a bad idea. CBB250 binds proteins and changes their mobility in SDS PAGE.

The reason why the bromophenol blue dye front is smeared is usually due to high salt in the sample (greater than 0.1M) The BPB dye front should be straight as an arrow if the gel is run properly.

In tricine SDS-PAGE, both the sample buffer (tracking) and staining solution contain Coomassie Brilliant Blue G250

https://www.nature.com/nprot/journal/v1/n1/full/nprot.2006.4.html

Hi Aswin, are you running tricine PAGE  which according to the ref of Mangal does not interfere with the proteins, or are you running a regular PAGE?

thank you Domenico_Sanfelice for your valuable answer and the pdf shared...I will soon update you after reading through the PDF

thank you Steingrimur_Stefansson for your answer...I don't think my sample has more salt content I will check it out once and the method I followed is TRIS TRICINE based SDS PAGE which employs CBB-G250 in both 4X non-reducing sample buffer and staining solution as Mangal Singh stated.

Thank you Mangal Singh for sharing that paper on Tricine SDS-PAGE...I will go through it...