Can you please share some details like the amount of SDS, staining time, other chemicals you added, or are you going for chromatography?
Normally, you need to get rid of extra SDS and other chemicals. In addition, treating the sample with deglycoslase before resolving the sample onto the SDS-PAGE will help you to make the protein band sharper. you can use the in-gel tryptic digestion kit.
I don't know what stain you use since you provided no info about that. But, if not considered, I suggest you to use colloidal stain or even MS compatible silver stain. Both are senesitive to detect prorein in a minute quantities.