Its very complex problem. Optimization of final chromatography conditions is possible by optimization one, few or all steps below:
- method of extraction (SPE, LLC, mixed methods etc) try use most selective method for your analyte
- detection method (try to use best detector to your purpose, generaly MS/MS is really very useful in most cases, but some times FL or amperometric detectors give nice results)
- chromatography (try to use best chromatographic conditions - column and gradient, flow temperature etc etc)
There are numerous publications describing different procedures so please try check some from Journal chromatography A, Biomedical Chromatography etc.
If after method pre validation still some plasma peaks are problematic that mean some elements of the method needs to be optimized again. First try new gradient conditions, next try modify gradient solvents, if not works, change column, if not works check subsequent extraction steps.
Please remember sometimes using different columns you can change dramatically your chromatogram:
Article Application of ultra-performance columns in high-performance...
I am agree with Dr. Grabowski. You should focus on sample extraction methods (unfortunately, it is hit and trial process), if you have satisfactory chromatogram of your drug.
If you want to use only HPLC and do not want to use was suggested (sample preparation) you can develop a method such as the peaks of interest elute in a region that can be diverted to the drain, or you can use prep HPLC and collect only the fractions of interest and reinject them again. Well equipped labs have 2DLC capabilities that use SEC in the first dimension and RPLC in the second dimension.