Protein-Oligo molecule is new class of biomolecules containing Protein-Oligo conjugation. The molecule contains two different modalities: protein and Oligonucleotide. At neutral pH, protein may be positively or negatively charged whereas Oligonucleotide is negatively charged. The net charge of molecule is affected by pI of surrounding environment. Microchip based CZE coupled to a MS can be used to identify the major impurities as well as the variants of the final product CZE can resolve. Traditional capillary based CZE can be used to separate and characterize all these species with the more user friendly and robust UV based detection. The unique challenges of the new conjugate require the development of new methods to perform product characterization.