The application of Bottom-Up strategy is limited by incomplete or ambiguous characterization of alternative splice forms, diverse modifications and endogenous protein cleavages. As an alternative, the Top-Down strategy has been utilized more with the advancement of analytical instruments. Except for FT-ICR mass spectrometer, invention and innovation of orbitrap mass spectrometer has promote the development of top-down proteomics.

Because there is no digestion of proteins before analysis, the information which is lost when shotgun method is used, for example, the quaternary structure with disulfide bonds, can be maintained and detected when the Top-Down strategy is applied, which show unique advantage in protein-level characterization of disulfide bonds. This make it get more and more application in QC analysis of protein therapeutics, such as insulin, to make the recombinant protein are correctly expressed, folded and assembled.