Biosimilars are significant in the current medical treatment arena because they represent lower-priced “generic” options for patients who otherwise might be faced with cost-prohibitive single-source therapeutics. These molecules require extensive characterization to prove that they are highly similar in structure and function when compared to the approved reference (‘innovator’) molecules they mimic. In addition to demonstrating safety and therapeutic efficacy, structural similarity to the innovator is critical for market and patient adoption and regulatory approval. As is true with all biologics, biosimilars must adhere to strict critical quality attributes (CQA) and maintain reproducibility and structural integrity at all levels of manufacturing. The novel AQS³pro utilizes a quantum cascade laser (QCL) and microfluidic flow cell to provide the critical quality attribute of secondary structural characterization of the biosimilar and its innovator via Microfluidic Modulation Spectroscopy (MMS). This unique approach to IR spectroscopy provides confidence in the ‘similarity’ of the two therapeutic entities by comparing their intrinsic IR spectra. The improved sensitivity provided by the QCL and the real time buffer background subtraction powered by the MMS technology enable the ultrasensitive detection of the smallest differences between the biosimilar and reference that may serve to protect the intellectual property (IP) on the innovator or confirm similarity of the ‘biosimilar’.